Atlas of Genetics and Cytogenetics in Oncology and Haematologyatlasgeneticsoncology.org/Journal/Arch1998Vol2Num1.pdf · 2008. 12. 10. · Atlas of Genetics and Cytogenetics in Oncology

Atlas of Genetics and Cytogenetics in Oncology and Haematology

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TABLE OF CONTENTS Volume 2, Number 1, Jan-Mar 1998 Previous Issue / Next Issue

Genes PICALM (phosphatidylinositol binding clathrin assembly protein) (11q14-21) . Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 1-5. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/CALM.html

NUP214 (nucleoporin 214kDa) (9q34.3). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 6-10. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/CAN.html

DDX10 (11q22). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1):11-14. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/DDX10.html

DEK (6p23). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 15-19. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/DEK_23.html

HOXA9 (7p15). Jean-loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 20-24. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/HOXA9.html

NUP98 (nucleoporin 98 kDa) (11p15). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 25-33. [Full Text] [PDF]

Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1) I

URL : http://AtlasGeneticsOncology.org/Genes/NUP98.html

TCTA (T-cell leukemia translocation-associated gene) (3p21). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 34-37. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/TCTA.html

BLM (Bloom) (15q26.1). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 38-48. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/BLM109.html

TRIP11 (thyroid hormone receptor interactor 11) (14q32). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 49-52. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/CEV14.html

FACC (Fanconi anaemia complementation group C) (9q22.3). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 53-58. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/FACC101.html

FGFR3 (Fibroblast Growth Factor Receptor 3) (4p16.3). Jacky Bonaventure. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 59-64. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/FGFR99.html

JAK2 (janus kinase 2) (9p24). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 65-76. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/JAK98.html

RHOH (Ras homolog gene family, member H) (4p13). Sylvie Galiègue-Zouitina. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 77-81. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/RHOH93.html

Leukaemias Agnogenic myeloid metaplasia; Idiopathic myelofibrosis - updated. Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 82-84. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Anomalies/MM.html

Multiple myeloma. Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 85-89. [Full Text] [PDF]

Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1) II

URL : http://AtlasGeneticsOncology.org/Anomalies/MMULID2038.html

1p32 rearrangements; t(1;14)(p32;q11); t(1;7)(p32;q34). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 90-92. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Anomalies/t0114.html

t(1;22)(p13;q13) - updated. Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 93-96. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Anomalies/t0122.html

t(3;13)(q27;q14). Jean-Loup Huret, Jean-Luc Laï. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 97-98. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Anomalies/t0313.html

t(3;21)(q26;q22) - updated. Jean-Loup Huret, François Desangles. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 99-101. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Anomalies/t0321.html

t(4;12)(q11-q21;p13) . Jean-Loup Huret, Marina Lafage-Pochitaloff. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 102-104. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Anomalies/t0412.html

t(5;12)(q33;p13). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 105-107. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Anomalies/t0512.html

t(6;9)(p23;q34). Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 108-111. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Anomalies/t0609.html

t(10;11)(p13;q21) . Jean-Loup Huret. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 112-114. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Anomalies/t1011bis.html

t(11;14)(q13;q32) in multiple myeloma. Jean-Loup Huret and Jean-Luc Laï. Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1): 115-116. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Anomalies/t1114MM.html

Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1) III

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Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1) IV


PICALM (phosphatidylinositol binding clathrin assembly protein)

IdentityHugo PICALM Location 11q14-21

CALM (11q14-21) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics.

Laboratories willing to validate the probes are welcome : contact [email protected]

DNA/RNATranscription major mRNA: 4 kb; other: 3 and 9 kb

Protein

Description 652 amino acids Expression wide Function role in the integration of signals from different pathways (clathrin,

phosphoinositols, receptor-mediated endocytosis) Homology with ap-3, a clathrin assembly protein (mouse)

Implicated inEntity t(10;11)(p13;q14-21) -->CALM-AF10 and/or AF10-CALM Disease yet to be well delineated; T-cell ALL Prognosis uncertain (median survival 2 yrs?) Cytogenetics may well be confused with the t(10;11)(p12;q23), where MLL on 11q23 is

involved, instead of CALM Hybrid/Mutated Gene 5' CALM - 3' AF10 and 5' AF10 - 3' CALM

Atlas Genet Cytogenet Oncol Haematol 1998; 2 (1) - 1 -

Abnormal Protein both CALM-AF10 and the reciprocal AF10-CALM are expressed

Breakpoints

External links Nomenclature

Hugo PICALM GDB PICALM Entrez_Gene PICALM 8301 phosphatidylinositol binding clathrin assembly protein

Cards Atlas CALM GeneCards PICALM Ensembl PICALM CancerGene CALM Genatlas PICALM GeneLynx PICALM eGenome PICALM euGene 8301

Genomic and cartography GoldenPath PICALM - chr11:85346134-85457756 - 11q14.2 (hg17-May_2004) Ensembl PICALM - 11q14.2 [CytoView] NCBI Genes Cyto Gene Seq [Map View - NCBI] OMIM Disease map [OMIM] HomoloGene PICALM

Gene and transcription


Genbank AF060939 [ SRS ] AF060939 [ ENTREZ ] Genbank AF060940 [ SRS ] AF060940 [ ENTREZ ] Genbank AK128786 [ SRS ] AK128786 [ ENTREZ ] Genbank AY326466 [ SRS ] AY326466 [ ENTREZ ] Genbank BC048259 [ SRS ] BC048259 [ ENTREZ ] RefSeq NM_001008660 [ SRS ] NM_001008660 [ ENTREZ ] RefSeq NM_007166 [ SRS ] NM_007166 [ ENTREZ ] RefSeq NT_086784 [ SRS ] NT_086784 [ ENTREZ ] AceView PICALM AceView - NCBI TRASER PICALM Traser - Stanford Unigene Hs.163893 [ SRS ] Hs.163893 [ NCBI ] HS163893 [ spliceNest ]

Protein : pattern, domain, 3D structure SwissProt Q13492 [ SRS] Q13492 [ EXPASY ] Q13492 [ INTERPRO ] Prosite PS50942 ENTH [ SRS ] PS50942 ENTH [ Expasy ] Interpro IPR008943 PI_bind_N [ SRS ] IPR008943 PI_bind_N [ EBI ] CluSTr Q13492 Pfam PF01417 ENTH [ SRS ] PF01417 ENTH [ Sanger ] pfam01417 [ NCBI-CDD ] Blocks Q13492

Polymorphism : SNP, mutations, diseases OMIM 603025 [ map ] GENECLINICS 603025 SNP PICALM [dbSNP-NCBI] SNP NM_001008660 [SNP-NCI] SNP NM_007166 [SNP-NCI] SNP PICALM [GeneSNPs - Utah] PICALM [SNP - CSHL] PICALM] [HGBASE - SRS]

General knowledge Family Browser PICALM [UCSC Family Browser] SOURCE NM_001008660 SOURCE NM_007166 SMD Hs.163893 SAGE Hs.163893 Amigo component|Golgi apparatus Amigo function|clathrin binding Amigo component|coated pit Amigo function|phosphatidylinositol binding


Amigo function|phospholipid binding Amigo process|protein complex assembly Amigo process|receptor mediated endocytosis BIOCARTA Endocytotic role of NDK, Phosphins and Dynamin PubGene PICALM

Other databases Probes

Probe Cancer Cytogenetics (Bari) Probe PICALM Related clones (RZPD - Berlin)

PubMed PubMed 6 Pubmed reference(s) in LocusLink

BibliographyThe t(10;11)(p13;q14) in the U937 cell line results in the fusion of the AF10 gene and CALM, encoding a new member of the AP-3 clathrin assembly protein family.Dreyling MH, Martinez-Climent JA, Zheng M, Mao J, Rowley JD, Bohlander SK Proc Natl Acad Sci U S A 1996 May 14;93(10):4804-9 Medline 96209813 Hematologic malignancies with the t(10;11) (p13;q21) have the same molecular event and a variety of morphologic or immunologic phenotypes.Kobayashi H, Hosoda F, Maseki N, Sakurai M, Imashuku S, Ohki M, Kaneko Y Genes Chromosomes Cancer 1997 Nov;20(3):253-9 Medline 98032536 REVIEW articles automatic search in PubMed Last year publications automatic search in PubMed

BiblioGene - INIST

Contributor(s)Written 01-1998 Jean-Loup Huret

CitationThis paper should be referenced as such : Huret JL . PICALM (phosphatidylinositol binding clathrin assembly protein). Atlas Genet Cytogenet Oncol Haematol. January 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/CALM.html



CAN

NUP214 (nucleoporin 214kDa)

IdentityOther names CAIN NUP214 (nuclear pore complex protein 241 kDa) Nucleoporin Hugo NUP214 Location 9q34.3 more telomeric than ABL1; less than TAN1.

CAN (9q34.3) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics. Laboratories

willing to validate the probes are welcome : contact [email protected]

DNA/RNADescription spans on a 130 kb and more genomic segment Transcription 7.5 kb mRNA

Protein

Description 2090 amino acids; 214 kDa; dimerization domains (2 leucine zippers) and a repeated motif; forms homodimers

Expression thymus, bone marrow, spleen, kidney, testis, brain; apparently not in other tissues Localisation nuclear membrane localisation


Function nucleoporin: associated with the nuclear pore complex; role in nucleocytoplasmic transport processes and cell cycle progression

Homology C-term part of CAN has homologies with proteins of the nucleoporin family

Implicated inEntity t(6;9)(p23;q34)/ANLL or MDS -->DEK - CAN Disease M2, M4 ANLL or MDS Prognosis remission difficult to obtain Cytogenetics this chromosome anomaly may be over loocked Hybrid/Mutated Gene 5' DEK - 3' CAN; chromosome 6 breakpoint clusters in a single intron

Abnormal Protein

head to tail DEK/CAN fusion protein (the alternative SET/CAN is exceptional); almost the entire DEK protein fused to the C-terminal two-thirds of the CAN protein; nuclear localization

Entity t(6;9)(p23;q34)/AUL --> SET-CAN (exceptional)

Breakpoints


Hugo NUP214 GDB NUP214 Entrez_Gene NUP214 8021 nucleoporin 214kDa


Cards Atlas CAN GeneCards NUP214 Ensembl NUP214 CancerGene NUP214 Genatlas NUP214 GeneLynx NUP214 eGenome NUP214 euGene 8021

Genomic and cartography

GoldenPath NUP214 - 9q34.3 chr9:131030535-131138644 + 9q34.13 (hg17-May_2004) Ensembl NUP214 - 9q34.13 [CytoView] NCBI Genes Cyto Gene Seq [Map View - NCBI] OMIM Disease map [OMIM] HomoloGene NUP214

Gene and transcription Genbank AB159230 [ SRS ] AB159230 [ ENTREZ ] Genbank AJ420413 [ SRS ] AJ420413 [ ENTREZ ] Genbank AL832609 [ SRS ] AL832609 [ ENTREZ ] Genbank BC012500 [ SRS ] BC012500 [ ENTREZ ] Genbank BC045620 [ SRS ] BC045620 [ ENTREZ ] RefSeq NM_005085 [ SRS ] NM_005085 [ ENTREZ ] RefSeq NT_086756 [ SRS ] NT_086756 [ ENTREZ ] AceView NUP214 AceView - NCBI TRASER NUP214 Traser - Stanford Unigene Hs.461860 [ SRS ] Hs.461860 [ NCBI ] HS461860 [ spliceNest ]

Protein : pattern, domain, 3D structure SwissProt P35658 [ SRS] P35658 [ EXPASY ] P35658 [ INTERPRO ] Interpro IPR001680 WD40 [ SRS ] IPR001680 WD40 [ EBI ] Interpro IPR011046 WD40_like [ SRS ] IPR011046 WD40_like [ EBI ] CluSTr P35658

Pfam PF03093 Nucleoporin_FG [ SRS ] PF03093 Nucleoporin_FG [ Sanger ] pfam03093 [ NCBI-CDD ]

Smart SM00320 WD40 [EMBL] Blocks P35658


Polymorphism : SNP, mutations, diseases OMIM 114350 [ map ] GENECLINICS 114350 SNP NUP214 [dbSNP-NCBI] SNP NM_005085 [SNP-NCI] SNP NUP214 [GeneSNPs - Utah] NUP214 [SNP - CSHL] NUP214] [HGBASE - SRS]

General knowledge Family Browser NUP214 [UCSC Family Browser] SOURCE NM_005085 SMD Hs.461860 SAGE Hs.461860 Amigo component|integral to membrane Amigo component|nuclear pore Amigo component|nuclear pore Amigo component|nucleus Amigo component|outer membrane Amigo function|porin activity Amigo process|protein-nucleus import, docking Amigo process|transport Amigo function|transporter activity PubGene NUP214


Probe Cancer Cytogenetics (Bari) Probe NUP214 Related clones (RZPD - Berlin)


BibliographyThe translocation (6;9), associated with a specific subtype of acute myeloid leukemia, results in the fusion of two genes, dek and can, and the expression of a chimeric, leukemia-specific dek-can mRNA.von Lindern M, Fornerod M, van Baal S, Jaegle M, de Wit T, Buijs A, Grosveld G Mol Cell Biol 1992 Apr;12(4):1687-97 Medline 92195315


Relocation of the carboxyterminal part of CAN from the nuclear envelope to the nucleus as a result of leukemia-specific chromosome rearrangements.Fornerod M, Boer J, van Baal S, Jaegle M, von Lindern M, Murti KG, Davis D, Bonten J, Buijs A, Grosveld G Oncogene 1995 May 4;10(9):1739-48 Medline 95273090 Interaction of cellular proteins with the leukemia specific fusion proteins DEK-CAN and SET-CAN and their normal counterpart, the nucleoporin CAN.Fornerod M, Boer J, van Baal S, Morreau H, Grosveld G Oncogene 1996 Oct 17;13(8):1801-8 Medline 97050788 REVIEW articles automatic search in PubMed Last year publications automatic search in PubMed

BiblioGene - INIST


CitationThis paper should be referenced as such : Huret JL . CAN; NUP214 (nucleoporin 214kDa). Atlas Genet Cytogenet Oncol Haematol. January 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/CAN.html © Atlas of Genetics and Cytogenetics in Oncology and Haematology



DDX10

IdentityOther names HRH-J8 Hugo DDX10 Location 11q22 telomeric to ATM.

DDX10 (11q22) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics. Laboratories


DNA/RNADescription at least 12 exons; spans more than a 200-kb region Transcription alternative splicing; 3.2 and 5.0 kb mRNA

Protein

Description contains 2 nuclear localization signals (NLS), a DEAD box (DEAD for: ASP-GLU_ALA-ASP)

Expression wide Localisation nucleolus (probable) Function putative ATP-dependent DEAD box RNA helicase; possible role in ribosome


assembly through rRNA processing Homology SPB4 and DRS1 (yeast)

Implicated inEntity inv (11)(p15q22)/MDS or ANLL --> NUP98-DDX10 Disease therapy related MDS and ANLL; de novo ANLL Hybrid/Mutated Gene 5' NUP98 - 3' DDX10

Abnormal Protein

fuses the GLFG repeat domains of NUP98 to the charged amino acids domain of DDX11


Hugo DDX10 GDB DDX10 Entrez_Gene DDX10 1662 DEAD (Asp-Glu-Ala-Asp) box polypeptide 10

Cards Atlas DDX10 GeneCards DDX10 Ensembl DDX10 CancerGene DDX10 Genatlas DDX10 GeneLynx DDX10 eGenome DDX10 euGene 1662

Genomic and cartography

GoldenPath DDX10 - 11q22 chr11:108041026-108316856 + 11q22.3 (hg17-May_2004) Ensembl DDX10 - 11q22.3 [CytoView] NCBI Genes Cyto Gene Seq [Map View - NCBI] OMIM Disease map [OMIM] HomoloGene DDX10

Gene and transcription Genbank AB040537 [ SRS ] AB040537 [ ENTREZ ] Genbank BC049217 [ SRS ] BC049217 [ ENTREZ ]


Genbank BC064921 [ SRS ] BC064921 [ ENTREZ ] Genbank U28042 [ SRS ] U28042 [ ENTREZ ] RefSeq NM_004398 [ SRS ] NM_004398 [ ENTREZ ] RefSeq NT_086787 [ SRS ] NT_086787 [ ENTREZ ] AceView DDX10 AceView - NCBI TRASER DDX10 Traser - Stanford Unigene Hs.525115 [ SRS ] Hs.525115 [ NCBI ] HS525115 [ spliceNest ]

Protein : pattern, domain, 3D structure SwissProt Q13206 [ SRS] Q13206 [ EXPASY ] Q13206 [ INTERPRO ]

Prosite PS00039 DEAD_ATP_HELICASE [ SRS ] PS00039 DEAD_ATP_HELICASE [ Expasy ]

Interpro IPR001410 DEAD [ SRS ] IPR001410 DEAD [ EBI ] Interpro IPR000629 DEAD_box [ SRS ] IPR000629 DEAD_box [ EBI ] Interpro IPR001650 Helicase_C [ SRS ] IPR001650 Helicase_C [ EBI ] CluSTr Q13206 Pfam PF00270 DEAD [ SRS ] PF00270 DEAD [ Sanger ] pfam00270 [ NCBI-CDD ]

Pfam PF00271 Helicase_C [ SRS ] PF00271 Helicase_C [ Sanger ] pfam00271 [ NCBI-CDD ]

Smart SM00487 DEXDc [EMBL] Smart SM00490 HELICc [EMBL] Blocks Q13206

Polymorphism : SNP, mutations, diseases OMIM 601235 [ map ] GENECLINICS 601235 SNP DDX10 [dbSNP-NCBI] SNP NM_004398 [SNP-NCI] SNP DDX10 [GeneSNPs - Utah] DDX10 [SNP - CSHL] DDX10] [HGBASE - SRS]

General knowledge Family Browser DDX10 [UCSC Family Browser] SOURCE NM_004398 SMD Hs.525115 SAGE Hs.525115 Amigo function|ATP binding Amigo function|ATP-dependent helicase activity Amigo function|RNA binding Amigo function|RNA helicase activity


PubGene DDX10 Other databases Probes

Probe Cancer Cytogenetics (Bari) Probe DDX10 Related clones (RZPD - Berlin)


BibliographyA human gene (DDX10) encoding a putative DEAD-box RNA helicase at 11q22-q23.Savitsky K, Ziv Y, Bar-Shira A, Gilad S, Tagle DA, Smith S, Uziel T, Sfez S, Nahmias J, Sartiel A, Eddy RL, Shows TB, Collins FS, Shiloh Y, Rotman G Genomics 1996 Apr 15;33(2):199-206 Medline 96301396 The inv(11)(p15q22) chromosome translocation of de novo and therapy-related myeloid malignancies results in fusion of the nucleoporin gene, NUP98, with the putative RNA helicase gene, DDX10.Arai Y, Hosoda F, Kobayashi H, Arai K, Hayashi Y, Kamada N, Kaneko Y, Ohki M Blood 1997 Jun 1;89(11):3936-44 Medline 97309415 REVIEW articles automatic search in PubMed Last year publications automatic search in PubMed

BiblioGene - INIST


CitationThis paper should be referenced as such : Huret JL . DDX10. Atlas Genet Cytogenet Oncol Haematol. January 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/DDX10.html




DEK

IdentityHugo DEK Location 6p23

DEK (6p23) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics. Laboratories


DNA/RNADescription spans on a 40 kb genomic segment Transcription 2.7 kb mRNA; coding sequence: 1.1 kb

Protein

Description 375 amino acids; 43 kDa; contains numerous acidic domains (Asp/Glu rich) and a nuclear localisation signal

Expression wide Localisation potentially nuclear Function site specific DNA binding protein involved in transcriptional regulation and signal

transduction

Implicated inEntity t(6;9)(p23;q34)/ANLL or MDS -->DEK-CAN Disease M2, M4 ANLL or MDS Prognosis remission difficult to obtain Cytogenetics this chromosome anomaly may be over loocked


Hybrid/Mutated Gene 5' DEK - 3' CAN; chromosome 6 breakpoint clusters in a single intron

Abnormal Protein

head to tail DEK/CAN fusion protein (the alternative SET/CAN is exceptional); almost the entire DEK protein fused to the C-terminal two-thirds of the CAN protein; nuclear localization


Hugo DEK GDB DEK Entrez_Gene DEK 7913 DEK oncogene (DNA binding)

Cards Atlas DEK_23 GeneCards DEK Ensembl DEK CancerGene DEK Genatlas DEK GeneLynx DEK eGenome DEK euGene 7913

Genomic and cartography GoldenPath DEK - 6p23 chr6:18332392-18372750 - 6p22.3 (hg17-May_2004) Ensembl DEK - 6p22.3 [CytoView] NCBI Genes Cyto Gene Seq [Map View - NCBI] OMIM Disease map [OMIM] HomoloGene DEK

Gene and transcription Genbank AL031774 [ SRS ] AL031774 [ ENTREZ ] Genbank BC012442 [ SRS ] BC012442 [ ENTREZ ] Genbank BC035259 [ SRS ] BC035259 [ ENTREZ ] Genbank BX641063 [ SRS ] BX641063 [ ENTREZ ] Genbank X64229 [ SRS ] X64229 [ ENTREZ ] RefSeq NM_003472 [ SRS ] NM_003472 [ ENTREZ ] RefSeq NT_086686 [ SRS ] NT_086686 [ ENTREZ ] AceView DEK AceView - NCBI TRASER DEK Traser - Stanford


Unigene Hs.484813 [ SRS ] Hs.484813 [ NCBI ] HS484813 [ spliceNest ] Protein : pattern, domain, 3D structure

SwissProt P35659 [ SRS] P35659 [ EXPASY ] P35659 [ INTERPRO ] Interpro IPR003034 SAP [ SRS ] IPR003034 SAP [ EBI ] Interpro IPR000897 SRP54 [ SRS ] IPR000897 SRP54 [ EBI ] CluSTr P35659 Pfam PF02037 SAP [ SRS ] PF02037 SAP [ Sanger ] pfam02037 [ NCBI-CDD ] Blocks P35659

Polymorphism : SNP, mutations, diseases OMIM 125264 [ map ] GENECLINICS 125264 SNP DEK [dbSNP-NCBI] SNP NM_003472 [SNP-NCI] SNP DEK [GeneSNPs - Utah] DEK [SNP - CSHL] DEK] [HGBASE - SRS]

General knowledge Family Browser DEK [UCSC Family Browser] SOURCE NM_003472 SMD Hs.484813 SAGE Hs.484813 Amigo function|DNA binding Amigo function|GTP binding Amigo function|RNA binding Amigo process|SRP-dependent cotranslational protein-membrane targeting Amigo function|histone binding Amigo component|nucleus Amigo process|regulation of transcription from Pol II promoter Amigo component|signal recognition particle (sensu Eukaryota) Amigo process|signal transduction Amigo function|specific RNA polymerase II transcription factor activity Amigo process|viral genome replication PubGene DEK


Probe Cancer Cytogenetics (Bari) Probe DEK Related clones (RZPD - Berlin)



BibliographyThe translocation (6;9), associated with a specific subtype of acute myeloid leukemia, results in the fusion of two genes, dek and can, and the expression of a chimeric, leukemia-specific dek-can mRNA.von Lindern M, Fornerod M, van Baal S, Jaegle M, de Wit T, Buijs A, Grosveld G Mol Cell Biol 1992 Apr;12(4):1687-97 Medline 92195315 Relocation of the carboxyterminal part of CAN from the nuclear envelope to the nucleus as a result of leukemia-specific chromosome rearrangements.Fornerod M, Boer J, van Baal S, Jaegle M, von Lindern M, Murti KG, Davis D, Bonten J, Buijs A, Grosveld G Oncogene 1995 May 4;10(9):1739-48 Medline 95273090 Interaction of cellular proteins with the leukemia specific fusion proteins DEK-CAN and SET-CAN and their normal counterpart, the nucleoporin CAN.Fornerod M, Boer J, van Baal S, Morreau H, Grosveld G Oncogene 1996 Oct 17;13(8):1801-8 Medline 97050788 DEK, an autoantigen involved in a chromosomal translocation in acute myelogenous leukemia, binds to the HIV-2 enhancer.Fu GK, Grosveld G, Markovitz DM Proc Natl Acad Sci U S A 1997 Mar 4;94(5):1811-5 Medline 97203143 REVIEW articles automatic search in PubMed Last year publications automatic search in PubMed

BiblioGene - INIST


CitationThis paper should be referenced as such : Huret JL . DEK. Atlas Genet Cytogenet Oncol Haematol. January 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/DEK_23.html



HOXA9

IdentityOther names HOX1G (homeobox-1G); Hugo HOXA9 Location 7p15

Protein

Description 129 amino acids; DNA binding domain (homeobox) in C-term Localisation nuclear Function sequence specific transcription factor; role during embryonic development

(patterning); HOX genes are also expressed in adult tissues, including blood cells; probable role in blood cell differenciation

Homology with class 1 homeodomain proteins

Implicated inEntity t(7;11)(p15;p15)/ANLL --> NUP98-HOXA9 Disease M2-M4 ANLL mostly; occasionally: CML-like cases Prognosis mean survival: 15 mths Cytogenetics sole anomaly most often Hybrid/Mutated Gene 5' NUP98 - 3' HOXA9

Abnormal Protein fuses the GLFG repeat domains of NUP98 to the HOXA9 homeobox

Breakpoints



Hugo HOXA9 GDB HOXA9 Entrez_Gene HOXA9 3205 homeo box A9

Cards Atlas HOXA9 GeneCards HOXA9 Ensembl HOXA9 CancerGene HOXA9 Genatlas HOXA9 GeneLynx HOXA9 eGenome HOXA9 euGene 3205

Genomic and cartography GoldenPath HOXA9 - 7p15 chr7:26975298-26978389 - 7p15.2 (hg17-May_2004) Ensembl HOXA9 - 7p15.2 [CytoView] NCBI Genes Cyto Gene Seq [Map View - NCBI] OMIM Disease map [OMIM] HomoloGene HOXA9

Gene and transcription Genbank AF010258 [ SRS ] AF010258 [ ENTREZ ] Genbank U81511 [ SRS ] U81511 [ ENTREZ ] Genbank BC006537 [ SRS ] BC006537 [ ENTREZ ] Genbank BC010023 [ SRS ] BC010023 [ ENTREZ ]


Genbank BG258601 [ SRS ] BG258601 [ ENTREZ ] RefSeq NM_002142 [ SRS ] NM_002142 [ ENTREZ ] RefSeq NM_152739 [ SRS ] NM_152739 [ ENTREZ ] RefSeq NT_086703 [ SRS ] NT_086703 [ ENTREZ ] AceView HOXA9 AceView - NCBI TRASER HOXA9 Traser - Stanford Unigene Hs.127428 [ SRS ] Hs.127428 [ NCBI ] HS127428 [ spliceNest ]

Protein : pattern, domain, 3D structure SwissProt P31269 [ SRS] P31269 [ EXPASY ] P31269 [ INTERPRO ] Prosite PS00027 HOMEOBOX_1 [ SRS ] PS00027 HOMEOBOX_1 [ Expasy ] Prosite PS50071 HOMEOBOX_2 [ SRS ] PS50071 HOMEOBOX_2 [ Expasy ] Interpro IPR001356 Homeobox [ SRS ] IPR001356 Homeobox [ EBI ] Interpro IPR009057 Homeodomain_like [ SRS ] IPR009057 Homeodomain_like [ EBI ] Interpro IPR006711 Hox9_act [ SRS ] IPR006711 Hox9_act [ EBI ] Interpro IPR000047 HTH_lambrepressr [ SRS ] IPR000047 HTH_lambrepressr [ EBI ] CluSTr P31269 Pfam PF00046 Homeobox [ SRS ] PF00046 Homeobox [ Sanger ] pfam00046 [ NCBI-CDD ]Pfam PF04617 Hox9_act [ SRS ] PF04617 Hox9_act [ Sanger ] pfam04617 [ NCBI-CDD ] Smart SM00389 HOX [EMBL] Prodom PD000010 Homeobox[INRA-Toulouse]

Prodom P31269 HXA9_HUMAN [ Domain structure ] P31269 HXA9_HUMAN [ sequences sharing at least 1 domain ]

Blocks P31269 Polymorphism : SNP, mutations, diseases

OMIM 142956 [ map ] GENECLINICS 142956 SNP HOXA9 [dbSNP-NCBI] SNP NM_002142 [SNP-NCI] SNP NM_152739 [SNP-NCI] SNP HOXA9 [GeneSNPs - Utah] HOXA9 [SNP - CSHL] HOXA9] [HGBASE - SRS]

General knowledge Family Browser HOXA9 [UCSC Family Browser] SOURCE NM_002142 SOURCE NM_152739 SMD Hs.127428 SAGE Hs.127428


Amigo process|development Amigo component|nucleus Amigo component|nucleus Amigo process|regulation of transcription, DNA-dependent Amigo process|transcription Amigo function|transcription factor activity Amigo function|transcriptional activator activity PubGene HOXA9


Probe HOXA9 Related clones (RZPD - Berlin) PubMed

PubMed 21 Pubmed reference(s) in LocusLink

BibliographyFusion of the nucleoporin gene NUP98 to HOXA9 by the chromosome translocation t(7;11)(p15;p15) in human myeloid leukaemia.Nakamura T, Largaespada DA, Lee MP, Johnson LA, Ohyashiki K, Toyama K, Chen SJ, Willman CL, Chen IM, Feinberg AP, Jenkins NA, Copeland NG, Shaughnessy JD Jr Nat Genet 1996 Feb;12(2):154-8 Medline 96154187 The t(7;11)(p15;p15) translocation in acute myeloid leukaemia fuses the genes for nucleoporin NUP98 and class I homeoprotein HOXA9.Borrow J, Shearman AM, Stanton VP Jr, Becher R, Collins T, Williams AJ, Dube I, Katz F, Kwong YL, Morris C, Ohyashiki K, Toyama K, Rowley J, Housman DE Nat Genet 1996 Feb;12(2):159-67 Medline 96154188 Mice bearing a targeted interruption of the homeobox gene HOXA9 have defects in myeloid, erythroid, and lymphoid hematopoiesis.Lawrence HJ, Helgason CD, Sauvageau G, Fong S, Izon DJ, Humphries RK, Largman C Blood 1997 Mar 15;89(6):1922-30 Medline 97211745 REVIEW articles automatic search in PubMed Last year publications automatic search in PubMed

BiblioGene - INIST


Contributor(s)Written 01-1998 Jean-loup Huret

CitationThis paper should be referenced as such : Huret JL . HOXA9. Atlas Genet Cytogenet Oncol Haematol. January 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/HOXA9.html © Atlas of Genetics and Cytogenetics in Oncology and Haematology



NUP98 (nucleoporin 98 kDa) (updated: old version not available)

IdentityHugo NUP98 Location 11p15

DNA/RNATranscription 3.6, 6.5 , 7.0 kb mRNA

Protein

NUP98 protein - Lyndal Kearney

Description 920 amino acids; 97 kDa; contains repeated motifs (GLFG and FG) in N-term and a RNA binding motif in C-term

Expression wide Localisation nuclear membrane localisation Function nucleoporin: associated with the nuclear pore complex; role in nucleocytoplasmic

transport processes Homology member of the GLFG nucleoporins

Implicated inEntity inv (11)(p15q22)/ myelodysplasic syndrome (MDS) or acute non lymphocytic

leukemia (ANLL) --> NUP98-DDX10 Disease therapy related MDS (t-MDS) and ANLL; de novo ANLL Hybrid/Mutated Gene 5' NUP98 - 3' DDX10

Abnormal Protein fuses the GLFG repeat domains of NUP98 to the acidic domain of DDX10

Entity t(1;11)(q23;p15.5) / t-MDS orANLL --> NUP98-PMX1


Disease One case of t-ANLL Hybrid/Mutated Gene 5' NUP98 - 3' PMX1

Abnormal Protein fuses the GLFG repeat domains of NUP98 to the homeodomain of PMX1

Entity t(2;11)(q31;p15)/treatment related leukaemia --> NUP98-HOXD13 Disease so far, only 1 case of treatment related myelodysplasia evolving towards M6

acute non lymphocytic leukaemia Hybrid/Mutated Gene 5' NUP98 - 3' HOXD13

Abnormal Protein fuses the GLFG repeat domains of NUP98 to the HOXD13 homeodomain

Entity t(4;11)(q21;p15.5)/ T- acute lymphoblastic leukemia (ALL) --> NUP98-

RAP1GDS1 Disease 3 cases of adult T-ALL Hybrid/Mutated Gene 5' NUP98 - 3' RAP1GDS1

Abnormal Protein

fuses the GLFG repeat domains of NUP98 to the entire coding region of RAP1GDS1. The product, rap1gds, has guanine nucleotide exchange factor activity.

Entity t(5;11)(q35;p15.5)/ ANLL--> NUP98-NSD1 Disease ANLL. 5 cases reported to date. All were children or young adults (age range 3-

18 years). Note that the t(5;11)(q35;p15.5) is not detectable by G-banding. Three cases were reported as cryptic t(5;11) associated with del(5q); a further two cases were identified in apparently normal karyotypes.

Hybrid/Mutated Gene 5' NUP98 - 3' NSD1

Abnormal Protein

fuses the GLFG repeat domains of NUP98 to the conserved SET, SAC and PHD finger domains of the NSD1 gene.

Entity t(7;11)(p15;p15) /ANLL --> NUP98-HOXA9 Disease M2-M4 ANLL mostly; occasionally: CML-like cases Prognosis mean survival: 15 mths Cytogenetics sole anomaly most often Hybrid/Mutated Gene 5' NUP98 - 3' HOXA9


Abnormal Protein fuses the GLFG repeat domains of NUP98 to the HOXA9 homeobox

Entity t(9;11)(p22;p15.5)/ANLL--> NUP98-LEDGF Disease One case of de novo ANLL Hybrid/Mutated Gene 5' NUP98 - 3' LEDGF

Abnormal Protein

fuses the GLFG repeat domains of NUP98 to the COOH terminal of the LEDGF gene (encoding transcriptional activators p52 and p75)

Entity t(11;12)(p15;q13)/treatment related leukemia (t-ANLL/MDS) Disease 1patient with t-MDS/ANLL Hybrid/Mutated Gene 5'; NUP98 - 3'; unknown

Entity t(11;17)(p15.5;q21) t-MDS/ANLL Disease 1 patient with t-MDS/ANLL Hybrid/Mutated Gene 5' NUP98 - 3' unknown

Entity t(11;20)(p15.5;q11)/ANLL, t-MDS/ANLL--> NUP98-TOP1 Disease ANLL, t-MDS/ANLL Hybrid/Mutated Gene 5' NUP98 - 3' TOP1

Abnormal Protein fuses the GLFG repeat domains of NUP98 to the catalytic domain of TOP1

Breakpoints



Hugo NUP98 GDB NUP98 Entrez_Gene NUP98 4928 nucleoporin 98kDa

Cards Atlas NUP98 GeneCards NUP98 Ensembl NUP98 CancerGene NUP98 Genatlas NUP98 GeneLynx NUP98 eGenome NUP98 euGene 4928

Genomic and cartography GoldenPath NUP98 - 11p15 chr11:3689635-3775468 - 11p15.4 (hg17-May_2004) Ensembl NUP98 - 11p15.4 [CytoView] NCBI Genes Cyto Gene Seq [Map View - NCBI] OMIM Disease map [OMIM] HomoloGene NUP98


Gene and transcription Genbank AB038344 [ SRS ] AB038344 [ ENTREZ ] Genbank AB040538 [ SRS ] AB040538 [ ENTREZ ] Genbank AF071076 [ SRS ] AF071076 [ ENTREZ ] Genbank AF071077 [ SRS ] AF071077 [ ENTREZ ] Genbank AF116074 [ SRS ] AF116074 [ ENTREZ ] RefSeq NM_005387 [ SRS ] NM_005387 [ ENTREZ ] RefSeq NM_016320 [ SRS ] NM_016320 [ ENTREZ ] RefSeq NM_139131 [ SRS ] NM_139131 [ ENTREZ ] RefSeq NM_139132 [ SRS ] NM_139132 [ ENTREZ ] RefSeq NT_086779 [ SRS ] NT_086779 [ ENTREZ ] AceView NUP98 AceView - NCBI TRASER NUP98 Traser - Stanford Unigene Hs.524750 [ SRS ] Hs.524750 [ NCBI ] HS524750 [ spliceNest ]

Protein : pattern, domain, 3D structure SwissProt P52948 [ SRS] P52948 [ EXPASY ] P52948 [ INTERPRO ] CluSTr P52948 Blocks P52948

Polymorphism : SNP, mutations, diseases OMIM 601021 [ map ] GENECLINICS 601021 SNP NUP98 [dbSNP-NCBI] SNP NM_005387 [SNP-NCI] SNP NM_016320 [SNP-NCI] SNP NM_139131 [SNP-NCI] SNP NM_139132 [SNP-NCI] SNP NUP98 [GeneSNPs - Utah] NUP98 [SNP - CSHL] NUP98] [HGBASE - SRS]

General knowledge Family Browser NUP98 [UCSC Family Browser] SOURCE NM_005387 SOURCE NM_016320 SOURCE NM_139131 SOURCE NM_139132 SMD Hs.524750 SAGE Hs.524750


Amigo process|DNA replication Amigo component|nuclear pore Amigo process|nuclear pore organization and biogenesis Amigo process|nucleocytoplasmic transport Amigo component|nucleoplasm Amigo function|protein binding Amigo process|protein transport Amigo process|protein-nucleus import, docking Amigo function|structural constituent of nuclear pore Amigo function|transporter activity PubGene NUP98


Probe NUP98 Related clones (RZPD - Berlin) PubMed


BibliographyFusion of the nucleoporin gene NUP98 to HOXA9 by the chromosome translocation t(7;11)(p15;p15) in human myeloid leukaemia.Nakamura T, Largaespada DA, Lee MP, Johnson LA, Ohyashiki K, Toyama K, Chen SJ, Willman CL, Chen IM, Feinberg AP, Jenkins NA, Copeland NG, Shaughnessy JD Jr. Nat Genet 1996 Feb;12(2):154-158 Medline 96154187 The inv(11)(p15q22) chromosome translocation of de novo and therapy-related myeloid malignancies results in fusion of the nucleoporin gene, NUP98, with the putative RNA helicase gene, DDX10.Arai Y, Hosoda F, Kobayashi H, Arai K, Hayashi Y, Kamada N, Kaneko Y, Ohki M. Blood 1997 Jun 1;89(11):3936-44 Medline 97309415 The vertebrate GLFG nucleoporin, Nup98, is an essential component of multiple RNA export pathways.Powers MA, Forbes DJ, Dahlberg JE, Lund E J Cell Biol 1997 Jan 27;136(2):241-50 Medline 97167679 NUP98-HOXD13 gene fusion in therapy-related acute myelogenous leukemiaRaza-Egilmez SZ, Jani-Sait SN, Grossi M, Higgins MJ, Shows TB, Aplan PD


Cancer Res 1998; 58(19): 4269-4273 Medline 98438040 The t(11;20)(p15;q11) chromosomal translocation associated with therapy-related myelodysplastic syndrome results in an NUP98-TOP1 fusion.Ahuja HG, Felix CA, Aplan PD Blood 1999; 94(9): 3258-3261 Medline 10556215 The (4;11)(q21;p15) translocation fuses the NUP98 and RAP1GDS1 genes and is recurrent in T-cell acute lymphocytic leukemia.Hussey DJ, Nicola M, Moore S, Peters GB, Dobrovic A. Blood 1999; 94(6): 2072-2079. Medline 10477737 A new recurrent translocation, t(5;11)(q35;p15.5), associated with del(5q) in childhood acute myeloid leukemia.Jaju RJ, Haas OA, Neat M, Harbott J, Saha V, Boultwood J, Brown JM, Pirc-Danoewinata H, Krings BW, Muller U, Morris, SW, Wainscoat JS, Kearney L. Blood 1999; 94(2): 773-780. Medline 10397745 NUP98 gene rearrangements in leukemia detected by fluorescence in situ hybridization (FISH).Kobzev YN, Rowley JD. Blood 1999; 94 Suppl 1: Abst 2221. NUP98 is fused to PMX1 homeobox gene in human acute myelogenous leukemia with chromosome translocation t(1;11)(q23;p15).Nakamura T, Yamazaki Y, Hatano Y, Miura I. Blood 1999 ;94(2): 741-747 Medline 10397741 Potential role for DNA topoisomerase II poisons in the generation of t(11;20)(p15;q11) translocations.Ahuja HG, Felix CA, Aplan PD Genes Chromosomes Cancer 2000; 29(2): 96-105 Medline 10959088 t(9;11)(p22;p15) in acute myeloid leukemia results in a fusion between NUP98 and the gene encoding transcriptional coactivators p52 and p75-lens epithelium-derived growth factor (LEDGF).Ahuja HG, Hong J, Aplan PD, Tcheurekdjian L, Forman SJ, Slovak ML.


Cancer Res 2000; 60(22): 6227-6229 Medline 11103774 A novel gene, NSD1, is fused to NUP98 in the t(5;11)(q35;p15.5) in de novo childhood acute myeloid leukemia.Jaju RJ, Fidler C, Haas OA, Strickson AJ, Watkins F, Clark K, Cross NC, Cheng JF, Aplan PD, Kearney L, Boultwood J, Wainscoat JS. Blood 2001; 98(4): 1264-1247 Medline UI NUP98 gene fusions in hematologic malignancies.Lam DH, Aplan PD. Leukemia 2001; 15(11): 1689-1695 (REVIEW) Medline 11681408 A cryptic t(5;11)(q35;p15.5) in two AML children with apparently normal karyotypes, identified by a multiplex FISH telomere assayBrown M, Jawad M, Eils R, Twigg SFR, Saracoglu K, Sauerbrey A, Thomas AE, Harbott J, Kearney L. Blood (2002) (in press) REVIEW articles automatic search in PubMed Last year publications automatic search in PubMed

BiblioGene - INIST

Contributor(s)Written 01-1998 Jean-Loup Huret Updated 11-1998 Jean-Loup Huret Updated 02-2000 Jean-Loup Huret Updated 03-2002 Lyndal Kearney

CitationThis paper should be referenced as such : Huret JL . NUP98 (nucleoporin 98 kDa). Atlas Genet Cytogenet Oncol Haematol. January 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/NUP98.html Huret JL . NUP98 (nucleoporin 98 kDa). Atlas Genet Cytogenet Oncol Haematol. November 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/NUP98.html Huret JL . NUP98 (nucleoporin 98 kDa). Atlas Genet Cytogenet Oncol Haematol. February 2000 .


URL : http://www.infobiogen.fr/services/chromcancer/Genes/NUP98.html Kearney L . NUP98 (nucleoporin 98 kDa). Atlas Genet Cytogenet Oncol Haematol. March 2002 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/NUP98.html




TCTA (T-cell leukemia translocation-associated gene) (updated: old version not available)

IdentityHugo TCTA Location 3p21

DNA/RNA

DNA diagram Transcription 2.1 kb mRNA

Protein

Description 103 amino acids; 11 kDa; rich in hydrophobic amino acids (residues 41-61) Expression wide, especially in kidneys Localisation may be a membrane associated protein, as there is a hydrophobic domain Function unknown Homology none is known

Implicated inEntity t(1;3)(p32;p21)/T-cell ALL --> TAL1 - TCTA Disease T-cell ALL Hybrid/Mutated Gene head to head orientation of TAL1 and TCTA

Abnormal Protein no fusion protein, but possibly promoter exchange and gene disregulation

To be noted


on day 04 Feb 1998, nothing new has appeared since the above coted paper


Hugo TCTA GDB TCTA Entrez_Gene TCTA 6988 T-cell leukemia translocation altered gene

Cards Atlas TCTA GeneCards TCTA Ensembl TCTA CancerGene TCTA Genatlas TCTA GeneLynx TCTA eGenome TCTA euGene 6988

Genomic and cartography GoldenPath TCTA - 3p21 chr3:49424643-49428912 + 3p21.31 (hg17-May_2004) Ensembl TCTA - 3p21.31 [CytoView] NCBI Genes Cyto Gene Seq [Map View - NCBI] OMIM Disease map [OMIM] HomoloGene TCTA

Gene and transcription Genbank AK000824 [ SRS ] AK000824 [ ENTREZ ] Genbank BC005157 [ SRS ] BC005157 [ ENTREZ ] Genbank CR457411 [ SRS ] CR457411 [ ENTREZ ] Genbank L41143 [ SRS ] L41143 [ ENTREZ ] RefSeq NM_022171 [ SRS ] NM_022171 [ ENTREZ ] RefSeq NT_086638 [ SRS ] NT_086638 [ ENTREZ ] AceView TCTA AceView - NCBI TRASER TCTA Traser - Stanford Unigene Hs.517962 [ SRS ] Hs.517962 [ NCBI ] HS517962 [ spliceNest ]

Protein : pattern, domain, 3D structure SwissProt P57738 [ SRS] P57738 [ EXPASY ] P57738 [ INTERPRO ] CluSTr P57738 Blocks P57738


Polymorphism : SNP, mutations, diseases OMIM 600690 [ map ] GENECLINICS 600690 SNP TCTA [dbSNP-NCBI] SNP NM_022171 [SNP-NCI] SNP TCTA [GeneSNPs - Utah] TCTA [SNP - CSHL] TCTA] [HGBASE - SRS]

General knowledge Family Browser TCTA [UCSC Family Browser] SOURCE NM_022171 SMD Hs.517962 SAGE Hs.517962 PubGene TCTA


Probe TCTA Related clones (RZPD - Berlin) PubMed


BibliographyCloning and characterization of TCTA, a gene located at the site of a t(1;3) translocation.Aplan PD, Johnson BE, Russell E, Chervinsky DS, Kirsch IR Cancer Res 1995 May 1;55(9):1917-21 Medline 95246031 REVIEW articles automatic search in PubMed Last year publications automatic search in PubMed

BiblioGene - INIST

Contributor(s)Written 01-1998 Jean-Loup Huret Updated 03-1998 Jean-Loup Huret

CitationThis paper should be referenced as such : Huret JL . TCTA (T-cell leukemia translocation-associated gene). Atlas Genet Cytogenet Oncol Haematol. January 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/TCTA.html Huret JL . TCTA (T-cell leukemia translocation-associated gene). Atlas Genet Cytogenet Oncol


Haematol. March 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/TCTA.html




BLM (Bloom) (updated: old version not available)

IdentityHugo BLM Location 15q26.1

DNA/RNATranscription 4.4kb mRNA

Protein

Description 1417 amino acids; ATP binding in amino acid 689-696; DEAH box in 795-798; two putative nuclear localization signals in the C-term in 1334-1349

Expression accumulates to high levels in S phase of the cell cycle, persists in G2/M and sharply declines in G1. Hyperphoshorylated in mitosis

Localisation nuclear (PML nuclear bodies and nucleolus) Function • 3'-5'DNA helicase; probable role in DNA replication and double-strand break

repair • Preferred substrates : G-quadruplex DNA, D-loops structures and X-junctions. • Recombinant protein promotes ATP-dependent branch migration of Hollyday junctions, effects, with topoisomerase III?, the resolution of a recombination intermediate containing a double Holliday junction with no flanking sequence exchanges, and possess a strand pairing activity. • Recombinant BLM possess a strand pairing activity. • Participates in a supercomplex of BRCA1 -associated proteins named BASC (BRCA1-Associated genome Surveillance Complex) containing ATM (defective in ataxia telangiectasia), NBS1 (defective in Nijmegen syndrome) and MRE11 (defective in ataxia-telangiectasia-like disorder), MLH1, MSH2 and MSH6, which are involved in human non-polyposis colorectal cancer, RAD50 and DNA replication factor C. • Participates in a complex named BRAFT (BLM, RPA, FA, Topoisomerase III) containing five of the Fanconia Anemia (FA) complementation group proteins (FANCA, FANCG, FANCC, FANCE and FANCF). • Interacts physically and/or functionally with p53, 53BP1, WRN, MLH1, RAD51, TRF2, ATR, the largest subunit of CAF-1, ligase IV, FEN1, Mus81, the


monoubiquitinated FANCD2 isoform • Is Associated with telomeres and ribosomal DNA repeats. • Is phosphorylated in mitotic cells through the cdc2 pathway, and in response to DNA damaging agents or stalled replication forks.

Homology homologous to RecQ helicases, a subfamily of DExH box-containing helicases; in particular, similarity with the four known human members in the RecQ subfamily, human RecQL, human Wrn, the product of the Werner syndrome gene, and the human RecQL4, involved in the Rothmund-Thomson syndrome, and RecQL5 proteins

MutationsGerminal five BLM mutations introducing amino acid substitutions and four BLM

mutations introducing premature nonsense codons into the coding sequence have been described to date; one BLM mutation consisting in a 6 bp deletion accompanied by a 7 bp insertion at nucleic acid position 2281 is common in patients from Ashkenazi Jewish ancestry, leading to a truncated protein of 739 amino acids in length; two BLM mutations, 631delCAA and 1610insA were detected in japanese patients.

Implicated inEntity Bloom syndrome Disease Bloom syndrome is a chromosome instability syndrome/cancer prone disease (at

risk of numerous, early occurring cancers of various types) Prognosis 1/3 of patients are dead at mean age 24 yrs, and the mean age of the 2/3 remaining

alive patients is 22 yrs Cytogenetics chromatid/chromosome breaks; triradial and quadriradial figures, highly elevated

spontaneous sister chromatid exchange rate


Hugo BLM GDB BLM Entrez_Gene BLM 641 Bloom syndrome

Cards Atlas BLM109 GeneCards BLM Ensembl BLM CancerGene BLM


Genatlas BLM GeneLynx BLM eGenome BLM euGene 641

Genomic and cartography GoldenPath BLM - 15q26.1 chr15:89061606-89159601 + 15q26.1 (hg17-May_2004) Ensembl BLM - 15q26.1 [CytoView] NCBI Genes Cyto Gene Seq [Map View - NCBI] OMIM Disease map [OMIM] HomoloGene BLM

Gene and transcription Genbank BC034480 [ SRS ] BC034480 [ ENTREZ ] Genbank U39817 [ SRS ] U39817 [ ENTREZ ] RefSeq NM_000057 [ SRS ] NM_000057 [ ENTREZ ] RefSeq NT_086832 [ SRS ] NT_086832 [ ENTREZ ] AceView BLM AceView - NCBI TRASER BLM Traser - Stanford Unigene Hs.169348 [ SRS ] Hs.169348 [ NCBI ] HS169348 [ spliceNest ]

Protein : pattern, domain, 3D structure SwissProt P54132 [ SRS] P54132 [ EXPASY ] P54132 [ INTERPRO ]

Prosite PS00690 DEAH_ATP_HELICASE [ SRS ] PS00690 DEAH_ATP_HELICASE [ Expasy ]

Prosite PS50967 HRDC [ SRS ] PS50967 HRDC [ Expasy ] Interpro IPR001410 DEAD [ SRS ] IPR001410 DEAD [ EBI ] Interpro IPR002464 DEAH_box [ SRS ] IPR002464 DEAH_box [ EBI ] Interpro IPR001650 Helicase_C [ SRS ] IPR001650 Helicase_C [ EBI ] Interpro IPR002121 HRDC [ SRS ] IPR002121 HRDC [ EBI ] Interpro IPR004589 RecQ [ SRS ] IPR004589 RecQ [ EBI ] CluSTr P54132 Pfam PF00270 DEAD [ SRS ] PF00270 DEAD [ Sanger ] pfam00270 [ NCBI-CDD ]

Pfam PF00271 Helicase_C [ SRS ] PF00271 Helicase_C [ Sanger ] pfam00271 [ NCBI-CDD ]

Pfam PF00570 HRDC [ SRS ] PF00570 HRDC [ Sanger ] pfam00570 [ NCBI-CDD ] Blocks P54132

Polymorphism : SNP, mutations, diseases OMIM 604610 [ map ]


GENECLINICS 604610 SNP BLM [dbSNP-NCBI] SNP NM_000057 [SNP-NCI] SNP BLM [GeneSNPs - Utah] BLM [SNP - CSHL] BLM] [HGBASE - SRS]

General knowledge Family Browser BLM [UCSC Family Browser] SOURCE NM_000057 SMD Hs.169348 SAGE Hs.169348 Enzyme 3.6.1.- [ Enzyme-SRS ] 3.6.1.- [ Brenda-SRS ] 3.6.1.- [ KEGG ] 3.6.1.- [ WIT ] Amigo function|ATP binding Amigo function|ATP-dependent DNA helicase activity Amigo function|DNA binding Amigo process|DNA recombination Amigo process|DNA repair Amigo process|DNA replication Amigo process|antimicrobial humoral response (sensu Vertebrata) Amigo function|hydrolase activity Amigo component|nucleus PubGene BLM


Probe BLM Related clones (RZPD - Berlin) PubMed


BibliographyCloning and characterization of RECQL, a potential human homologue of the Escherichia coli DNA helicase RecQPuranam KL, and Blackshear PJ. J Biol Chem 1994; 269: 29838-29845. Medline 95050841 Molecular cloning of cDNA encoding human DNA helicase Q1 which has homology to Escherichia coli RecQ helicase and localization of the gene at chromosome 12p12.Seki M, Miyazawa H, Tada S, Yanagisawa J, Yamaoka T, Hoshino SI, Ozawa K, Eki T, Nogami M, Okumura K, Taguchi H, Hanaoka F, Enomoto T.


Nucl Acids Res 1994; 22: 4566-4573. Medline 95075633 The Bloom's syndrome gene product is homologous to RecQ helicases.Ellis NA, Groden J, Ye TZ, Straughen J, Lennon DJ, Ciocci S, Proytcheva M, German J. Cell 1995; 83: 655-666 Medline 96069866 Positional cloning of the Werner's syndrome gene.Yu CE, Oshima J, Fu YH, Wijsman EM, Hisama F, Alish R, Matthews S, Nakura J, Miki T, Ouais S, Martin GM, Mulligan J, Schellenberg GD. Science 1996; 272, 258-262. Medline 96181115 Molecular genetics of Bloom's syndrome.Ellis NA, German J Hum Mol Genet 1996; 5 Spec No:1457-1463. Medline 97029240 Characterization of a new BLM mutation associated with a topoisomerase II alpha defect in a patient with Bloom's syndromeFoucault F, Vaury C, Barakat A, Thibout D, Planchon P, Jaulin C, Praz F, Amor-Gueret M. Hum Mol Genet 1997 ; 6: 1427-1434. Medline 97449163 BLM (the causative gene of Bloom syndrome) protein translocation into the nucleus by a nuclear localization signal.Kaneko H, Orii KO, Matsui E, Shimozawa N, Fukao T, Matsumoto T, Shimamoto A, Furuichi Y, Hayakawa S, Kasahara K, Kondo N. Biochem Biophys Res Commun 1997; 240: 348-353. Medline 98049834 The Bloom's syndrome gene product is a 3'-5' DNA helicase.Karow JK, Chakraverty RK, Hickson ID. J Biol Chem 1997; 272 : 30611-30614. Medline 98049515 Cloning of two new human helicase genes of the RecQ family: Biological significance of multiple species in higher eukaryotes.Kitao S, Ohsugi I, Ichikawa K, Goto M, Furuichi Y, Shimamoto A. Genomics 1998 ; 54 : 443-452. Medline 99097344


The Bloom's syndrome helicase unwinds G4 DNA.Sun H, Karow JK, Hickson ID, Maizels N. J Biol Chem 1998; 273: 27587-27592. Medline 9765292 PML is critical for ND10 formation and recruits the PML-interacting protein daxx to this nuclear structure when modified by SUMO-1.Ishov AM, Sotnikov AG, Negorev D, Vladimirova OV, Neff N, Kamitani T, Yeh ET, Strauss JF 3rd, Maul GG. J Cell Biol 1999; 147 : 221-234. Medline 10525530 Nuclear structure in normal and Bloom syndrome cells.Yankiwski V, Marciniak RA, Guarente L, Neff NF. Proc Natl Acad Sci U S A. 2000; 97: 5214-5219. Medline 10779560 Rothmund-Thomson syndrome due to RECQ4 helicase mutations: report and clinical and molecular comparisons with Bloom syndrome and Werner syndrome.Lindor NM, Furuichi Y, Kitao S, Shimamoto A, Arndt C, Jalal S. Am J Med Genet; 2000; 90: 223-228. Medline 20142127 Cell cycle regulation of the endogenous wild type Bloom's syndrome DNA helicase.Dutertre S, Ababou M, Onclercq R, Delic J, Chatton B, Jaulin C, Amor-Gueret M. Oncogene 2000; 19: 2731-2738. Medline 20309931 Identification of a novel BLM missense mutation (2706T>C) in a moroccan patient with Bloom's syndrome.Barakat A, Ababou M, Onclercq R, Dutertre S, Chadli E, Hda N, Benslimane A, Amor-Gueret M. Hum Mutat 2000; 6: 584-585. Medline 20321320 Binding and melting of D-loops by the Bloom syndrome helicase.van Brabant AJ, Ye T, Sanz M, German III JL, Ellis NA, Holloman WK. Biochemistry 2000; 39: 14617-14625. Medline 11087418 ATM-dependent phosphorylation and accumulation of endogenous BLM protein in response to ionizing radiation.


Ababou M, Dutertre S, Lecluse Y, Onclercq R, Chatton B, Amor-Gueret M. Oncogene 2000; 19 : 5955-5963. Medline 11146546 The Bloom's syndrome gene product promotes branch migration of holliday junctions.Karow JK, Constantinou A, Li JL, West SC, Hickson ID. Proc Natl Acad Sci USA. 2000; 97: 6504-6508. Medline 20300930 BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures.Wang Y, Cortez D, Yazdi P, Neff N, Elledge SJ, Qin J. Genes Dev 2000; 14: 927-939. Medline 20245492 The Bloom's and Werner's syndrome proteins are DNA structure-specific helicases.Mohaghegh P, Karow JK, Brosh Jr RM Jr, Bohr VA, Hickson ID. Nucleic Acids Res 2001; 29: 2843-2849. Medline 11433031 The Bloom's syndrome protein (BLM) interacts with MLH1 but is not required for DNA mismatch repair.Langland G, Kordich J, Creaney J, Goss KH, Lillard-Wetherell K, Bebenek K, Kunkel TA, Groden J. J Biol Chem 2001; 276 : 30031-30035. Medline 11325959 Direct association of Bloom's syndrome gene product with the human mismatch repair protein MLH1.Pedrazzi G, Perrera C, Blaser H, Kuster P, Marra G, Davies SL, Ryu GH, Freire R, Hickson ID, Jiricny J, Stagljar I. Nucleic Acids Res 2001; 29 : 4378-4386. Medline 11691925 The Bloom syndrome protein interacts and cooperates with p53 in regulation of transcription and cell growth control.Garkavtsev IV, Kley N, Grigorian IA, Gudkov AV. Oncogene 2001; 20: 8276-8280. Medline 11781842 Functional interaction of p53 and BLM DNA helicase in apoptosis.Wang XW, Tseng A, Ellis NA, Spillare EA, Linke SP, Robles AI, Seker H, Yang Q, Hu P, Beresten S, Bemmels NA, Garfield S, Harris CC.


J Biol Chem 2001; 276: 32948-32955. Medline 11399766 Potential role for the BLM helicase in recombinational repair via a conserved interaction with RAD51.Wu L, Davies SL, Levitt NC, Hickson ID. J Biol Chem 2001; 276: 19375-19381. Medline 11278509 Regulation and localization of the Bloom syndrome protein in response to DNA damage.Bischof O, Kim SH, Irving J, Beresten S, Ellis NA, Campisi J. J Cell Biol 2001; 153: 367-380. Medline 11309417 The processing of Holliday junctions by BLM and WRN helicases is regulated by p53.Yang Q, Zhang R, Wang XW, Spillare EA, Linke SP, Subramanian D, Griffith JD, Li JL, Hickson ID, Shen JC, Loeb LA, Mazur SJ, Appella E, Brosh RM Jr, Karmakar P, Bohr VA, Harris CC. J Biol Chem 2002; 277: 31980-31987. Medline 12080066 Bloom's syndrome protein response to ultraviolet-C radiation and hydroxyurea-mediated DNA synthesis inhibition.Ababou M, Dumaire V, Lecluse Y, Amor-Gueret M. Oncogene 2002; 21: 2079-2088. Medline 11960380 Colocalization, physical, and functional interaction between Werner and Bloom syndrome proteins.von Kobbe C, Karmakar P, Dawut L, Opresko P, Zeng X, Brosh RM Jr, Hickson ID, Bohr VA. J Biol Chem 2002; 277: 22035-22044. Medline 11919194 The Bloom syndrome helicase BLM interacts with TRF2 in ALT cells and promotes telomeric DNA synthesis.Stavropoulos DJ, Bradshaw PS, Li X, Pasic I, Truong K, Ikura M, Ungrin M, Meyn MS. Hum Mol Genet 2002; 11: 3135-3144. Medline 12444098 Telomere-binding protein TRF2 binds to and stimulates the Werner and Bloom syndrome helicases.Opresko PL, von Kobbe C, Laine JP, Harrigan J, Hickson ID, Bohr VA. J Biol Chem 2002; 277: 41110-41119.


Medline 12181313 The BLM helicase is necessary for normal DNA double-strand break repair.Langland G, Elliott J, Li Y, Creaney J, Dixon K, Groden J. Cancer Res 2002; 62: 2766-2770. Medline 12019152 Increased error-prone non homologous DNA end-joining--a proposed mechanism of chromosomal instability in Bloom's syndrome.Gaymes TJ, North PS, Brady N, Hickson ID, Mufti GJ, Rassool FV. Oncogene 2002; 21: 2525-2533. Medline 11971187 Dephosphorylation and subcellular compartment change of the mitotic Bloom's syndrome DNA helicase in response to ionizing radiation.Dutertre S, Sekhri R, Tintignac LA, Onclercq-Delic R, Chatton B, Jaulin C, Amor-Gueret M. J Biol Chem 2002; 277 : 6280-6286. Medline 11741924 A multiprotein nuclear complex connects Fanconi anemia and Bloom syndrome.Meetei AR, Sechi S, Wallisch M, Yang D, Young MK, Joenje H, Hoatlin ME, Wang W. Mol Cell Biol 2003; 23: 3417-2346. Medline 12724401 BLM helicase-dependent transport of p53 to sites of stalled DNA replication forks modulates homologous recombination.Sengupta S, Linke SP, Pedeux R, Yang Q, Farnsworth J, Garfield SH, Valerie K, Shay JW, Ellis NA, Wasylyk B, Harris CC. EMBO J 2003; 22: 1210-1222. Medline 12606585 Possible anti-recombinogenic role of Bloom's syndrome helicase in double-strand break processing.Onclercq-Delic R, Calsou P, Delteil C, Salles B, Papadopoulo D, Amor-Gueret M. Nucleic Acids Res 2003; 31: 6272-6782. Medline 14576316 Telomere and ribosomal DNA repeats are chromosomal targets of the bloom syndrome DNA helicase.Schawalder J, Paric E, Neff NF. BMC Cell Biol 2003; 4:15. Medline 14577841


Relatively common mutations of the Bloom syndrome gene in the Japanese population.Kaneko H, Isogai K, Fukao T, Matsui E, Kasahara K, Yachie A, Seki H, Koizumi S, Arai M, Utunomiya J, Miki Y, Kondo N. Int J Mol Med 2004; 14: 439-442. Medline 15289897 Physical and functional interaction between the Bloom's syndrome gene product and the largest subunit of chromatin assembly factor 1.Jiao R, Bachrati CZ, Pedrazzi G, Kuster P, Petkovic M, Li JL, Egli D, Hickson ID, Stagljar I. Mol Cell Biol 2004; 24: 4710-4719. Medline 15143166 Functional interaction between BLM helicase and 53BP1 in a Chk1-mediated pathway during S-phase arrest.Sengupta S, Robles AI, Linke SP, Sinogeeva NI, Zhang R, Pedeux R, Ward IM, Celeste A, Nussenzweig A, Chen J, Halazonetis TD, Harris CC. J Cell Biol 2004; 166: 801-813. Medline 15364958 Human bloom protein stimulates flap endonuclease 1 activity by resolving DNA secondary structure.Wang W, Bambara RA. J Biol Chem 2004 Dec 4 (in press) Medline 15579905 Genetic interactions between BLM and DNA ligase IV in human cells.So S, Adachi N, Lieber MR, Koyama H. J Biol Chem 2004; 279: 55433-55442. Medline 15509577 A major role for mitotic CDC2 kinase inactivation in the establishment of the mitotic DNA damage checkpoint.Bayart E, Grigorieva O, Leibovitch S, Onclercq-Delic R, Amor-Gueret M. Cancer Res 2004; 64: 8954-8959. Medline 15604258 BLM helicase facilitates Mus81 endonuclease activity in human cells.Zhang R, Sengupta S, Yang Q, Linke SP, Yanaihara N, Bradsher J, Blais V, McGowan CH, Harris CC. Cancer Res 2005 ; 65: 2526-2531. Medline 15805243 RECQ family members combine strand pairing and unwinding activities to catalyze strand


exchange.Machwe A, Xiao L, Groden J, Matson SW, Orren DK. J Biol Chem 2005 (in press) REVIEW articles automatic search in PubMed Last year publications automatic search in PubMed

BiblioGene - INIST

Contributor(s)Written 02-1998 Jean-Loup Huret Updated 09-2000 Mounira Amor-Guéret Updated 05-2005 Mounira Amor-Guéret

CitationThis paper should be referenced as such : Huret JL . BLM (Bloom). Atlas Genet Cytogenet Oncol Haematol. February 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/BLM109.html Amor-Guéret M . BLM (Bloom). Atlas Genet Cytogenet Oncol Haematol. September 2000 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/BLM109.html Amor-Guéret M . BLM (Bloom). Atlas Genet Cytogenet Oncol Haematol. May 2005 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/BLM109.html




TRIP11 (thyroid hormone receptor interactor 11)

IdentityOther names CEV14 (clonal evolution related gene on chromosome 14) Hugo CEV14 Location 14q32

DNA/RNATranscription major transcripts: 7, 9 and 10.5 kb; coding sequence: 2.2 kb

Protein

Description 729 amino acids; contains a N-term leucine zipper and a C-term putative thyroid hormone receptor interacting domain

Expression is wide; high expression in heart, muscle, pancreas; found expressed in hematopoietic cell lines

Function may be a transcriptional factor

Implicated inEntity t(5;14)(q33;q32)/ANLL --> CEV14 - PDGFRb Disease poorly known: 1 case of ANLL Cytogenetics found as an additional anomaly Hybrid/Mutated Gene 5' CEV14 - 3' PDGFRb

Abnormal Protein

leucine zipper from CEV14 fused to the transmembrane domain and the Tyr kinase domain of PDGFRb


Hugo CEV14 GDB TRIP11 Entrez_Gene TRIP11 9321 thyroid hormone receptor interactor 11

Cards Atlas CEV14


GeneCards TRIP11 Ensembl TRIP11 CancerGene TRIP11 Genatlas TRIP11 GeneLynx TRIP11 eGenome TRIP11 euGene 9321

Genomic and cartography GoldenPath TRIP11 - 14q32 chr14:91505614-91576139 - 14q32.12 (hg17-May_2004) Ensembl TRIP11 - 14q32.12 [CytoView] NCBI Genes Cyto Gene Seq [Map View - NCBI] OMIM Disease map [OMIM] HomoloGene TRIP11

Gene and transcription Genbank AF007217 [ SRS ] AF007217 [ ENTREZ ] Genbank AF011368 [ SRS ] AF011368 [ ENTREZ ] Genbank BC002656 [ SRS ] BC002656 [ ENTREZ ] Genbank BX641024 [ SRS ] BX641024 [ ENTREZ ] Genbank L40380 [ SRS ] L40380 [ ENTREZ ] RefSeq NM_004239 [ SRS ] NM_004239 [ ENTREZ ] RefSeq NT_086807 [ SRS ] NT_086807 [ ENTREZ ] AceView TRIP11 AceView - NCBI TRASER TRIP11 Traser - Stanford Unigene Hs.546327 [ SRS ] Hs.546327 [ NCBI ] HS546327 [ spliceNest ]

Protein : pattern, domain, 3D structure SwissProt Q15643 [ SRS] Q15643 [ EXPASY ] Q15643 [ INTERPRO ] Prosite PS50913 GRIP [ SRS ] PS50913 GRIP [ Expasy ] Interpro IPR000237 GRIP [ SRS ] IPR000237 GRIP [ EBI ] CluSTr Q15643 Blocks Q15643

Polymorphism : SNP, mutations, diseases OMIM 604505 [ map ] GENECLINICS 604505 SNP TRIP11 [dbSNP-NCBI] SNP NM_004239 [SNP-NCI]


SNP TRIP11 [GeneSNPs - Utah] TRIP11 [SNP - CSHL] TRIP11] [HGBASE - SRS] General knowledge

Family Browser TRIP11 [UCSC Family Browser] SOURCE NM_004239 SMD Hs.546327 SAGE Hs.546327 Amigo component|Golgi apparatus Amigo function|protein binding Amigo function|transcription coactivator activity Amigo process|transcription from Pol II promoter PubGene TRIP11


Probe CEV14 Related clones (RZPD - Berlin) PubMed


BibliographyFusion of the platelet-derived growth factor receptor beta to a novel gene CEV14 in acute myelogenous leukemia after clonal evolution.Abe A, Emi N, Tanimoto M, Terasaki H, Marunouchi T, Saito H Blood 1997 Dec 1;90(11):4271-7 Medline 98043615 REVIEW articles automatic search in PubMed Last year publications automatic search in PubMed

BiblioGene - INIST


CitationThis paper should be referenced as such : Huret JL . TRIP11 (thyroid hormone receptor interactor 11). Atlas Genet Cytogenet Oncol Haematol. February 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/CEV14.html



FACC (Fanconi anaemia complementation group C) (updated: old version not available)

IdentityOther names FAC Hugo FANCC Location 9q22.3 next to PTCH and XPAC !!

DNA/RNADescription 14 exons; spans 80 kb Transcription mRNA of 2.3, 3.2, and 4.6 kb (alternative splicing in 5Õ, variable 3' untranslated

region, exon 13 skipping)

Protein

Description 558 amino acids; 63 kDa Expression wide, in particular in the bones; high expression in proliferating cells, low in

differentiated cells Localisation cytoplasmic (mostly) and nuclear Function • part of the FA complex with FANCA, FANCE, FANCF, and FANCG; this

complex is only found in the nucleus. • FANCA and FANCG form a complex in the cytoplasm, through a N-term FANCA (involving the nuclear localization signal) - FANCG interaction; FANCC join the complex; phosphorylation of FANCA would induce its translocation into the nucleus.This FA complex translocates into the nucleus, where FANCE and FANCF are present; FANCE and FANCF join the complex. The FA complex subsequently interacts with FANCD2 by monoubiquitination of FANCD2 during S phase or following DNA damage. Activated (ubiquinated ) FANCD2, downstream in the FA pathway, will then interact with other proteins involved in DNA repair, possibly BRCA1; after DNA repair, FANCD2 return to the non-ubiquinated form. • FANCC may have mutlifunctional roles, in addition to its involvement in the FA pathway. FANCC binds to cdc2 (mitotic cyclin-dependent kinase), STAT1, GRP94 (a chaperon protein), NADPH, and a number of other proteins; involved in DNA repair and in suppressing interferon gamma induced cellular apoptosis

Homology no known homology


MutationsGerminal most mutations are found in exon1, intron 4, and exon 14

Implicated inEntity Fanconi anaemia (FA); FACC is implicated in the FA complementation group C;

it represents about 15% of FA cases Disease Fanconi anaemia is a chromosome instability syndrome/cancer prone disease (at

risk of leukaemia) Prognosis • Fanconi anaemia's prognosis is poor; mean survival is 16 years: patients die of

bone marrow failure (infections, haemorrhages), leukaemia, or androgen therapy related liver tumours • It has recently been shown that significant phenotypic differences were found between the various complementation groups. FA group C patients had less somatic abnormalities. However, there is a certain clinical heterogeneity.

Cytogenetics spontaneous,chromatid/chromosome breaks; increased rate of breaks compared to control, when induced by breaking agent


Hugo FANCC GDB FANCC Entrez_Gene FANCC 2176 Fanconi anemia, complementation group C

Cards Atlas FACC101 GeneCards FANCC Ensembl FANCC CancerGene FANCC Genatlas FANCC GeneLynx FANCC eGenome FANCC euGene 2176

Genomic and cartography GoldenPath FANCC - 9q22.3 chr9:94940891-95159546 - 9q22.32 (hg17-May_2004) Ensembl FANCC - 9q22.32 [CytoView] NCBI Genes Cyto Gene Seq [Map View - NCBI] OMIM Disease map [OMIM] HomoloGene FANCC


Gene and transcription Genbank AL354893 [ SRS ] AL354893 [ ENTREZ ] Genbank AY220878 [ SRS ] AY220878 [ ENTREZ ] Genbank L02664 [ SRS ] L02664 [ ENTREZ ] Genbank BC006303 [ SRS ] BC006303 [ ENTREZ ] Genbank BC015748 [ SRS ] BC015748 [ ENTREZ ] RefSeq NM_000136 [ SRS ] NM_000136 [ ENTREZ ] RefSeq NT_086752 [ SRS ] NT_086752 [ ENTREZ ] AceView FANCC AceView - NCBI TRASER FANCC Traser - Stanford Unigene Hs.494529 [ SRS ] Hs.494529 [ NCBI ] HS494529 [ spliceNest ]

Protein : pattern, domain, 3D structure SwissProt Q00597 [ SRS] Q00597 [ EXPASY ] Q00597 [ INTERPRO ] Interpro IPR000686 Fanconi [ SRS ] IPR000686 Fanconi [ EBI ] CluSTr Q00597 Pfam PF02106 Fanconi_C [ SRS ] PF02106 Fanconi_C [ Sanger ] pfam02106 [ NCBI-CDD ]Blocks Q00597

Polymorphism : SNP, mutations, diseases OMIM 227645 [ map ] GENECLINICS 227645 SNP FANCC [dbSNP-NCBI] SNP NM_000136 [SNP-NCI] SNP FANCC [GeneSNPs - Utah] FANCC [SNP - CSHL] FANCC] [HGBASE - SRS]

General knowledge Family Browser FANCC [UCSC Family Browser] SOURCE NM_000136 SMD Hs.494529 SAGE Hs.494529 Amigo process|DNA repair Amigo component|cytoplasm Amigo component|nucleus Amigo process|protein complex assembly BIOCARTA Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility BIOCARTA BRCA1-dependent Ub-ligase activity PubGene FANCC


Other databases Other database Fanconi Anemia Mutation Database

Probes Probe Cancer Cytogenetics (Bari) Probe FANCC Related clones (RZPD - Berlin)


BibliographyCloning of cDNAs for Fanconi's anaemia by functional complementation.Strathdee CA, Gavish H, Shannon WR, Buchwald M Nature 1992; 356: 763-767. Medline 92244337 Characterisation of the exon structure of the Fanconi anaemia group C gene by vectorette PCR.Gibson RA, Buchwald M, Roberts RG, Mathew CG Hum Mol Genet 1993; 2: 35-38. Medline 93258346 Molecular biology of Fanconi anemia: implications for diagnosis and therapyD'Andrea AD, Grompe M Blood 1997;90(5):1725-36 Medline 97436532 Fanconi anemia proteins FANCA, FANCC, and FANCG/XRCC9 interact in a functional nuclear complex.Garcia-Higuera I, Kuang Y, Naf D, Wasik J, D'Andrea AD. Mol Cell Biol 1999;19(7):4866-73 Medline 10373536 Association of complementation group and mutation type with clinical outcome in fanconi anemia. European Fanconi Anemia Research Group.Faivre L, Guardiola P, Lewis C, Dokal I, Ebell W, Zatterale A, Altay C, Poole J, Stones D, Kwee ML, van Weel-Sipman M, Havenga C, Morgan N, de Winter J, Digweed M, Savoia A, Pronk J, de Ravel T, Jansen S, Joenje H, Gluckman E, Mathew CG. Blood 2000;96(13):4064-70 Medline 11110674 Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway.Garcia-Higuera I, Taniguchi T, Ganesan S, Meyn MS, Timmers C, Hejna J, Grompe M, D'Andrea AD.


Mol Cell 2001;7(2):249-62 Medline 11239454 Fanconi anemia and DNA repair.Grompe M, D'Andrea A. Hum Mol Genet 2001;10(20):2253-9 Medline 11673408 The fanconi anemia complementation group C gene product : structural evidence of multifunctionalityQishen P, Christianson TA, Keeble W, Diaz J, Faulkner GR, Reifsteck C, Olson S, Baby GC. Blood 2001; 98(5): 1392-1401 Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway.Medhurst AL, Huber PA, Waisfisz Q, de Winter JP, Mathew CG Hum Mol Genet 2001;10(4):423-9 Medline 11157805 Fanconi anemia proteins localize to chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner.Qiao F, Moss A, Kupfer GM. J Biol Chem 2001;276(26):23391-6 Medline 11297559 Current knowledge on the pathophysiology of Fanconi anemia: from genes to phenotypes.Yamashita T, Nakahata T. Int J Hematol 2001;74(1):33-41 Medline 11530803 Breaks at telomeres and TRF2-independent end fusions in Fanconi anemia.Callen E, Samper E, Ramirez MJ, Creus A, Ortega JJ, Olive T, Badell I, Blasco MA, Surralles J. Hum Mol Genet 2002; 11(4): 439-444. Medline 11854176 REVIEW articles automatic search in PubMed Last year publications automatic search in PubMed

BiblioGene - INIST



Updated 06-2002 Jean-Loup Huret

CitationThis paper should be referenced as such : Huret JL . FACC (Fanconi anaemia complementation group C). Atlas Genet Cytogenet Oncol Haematol. February 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/FACC101.html Huret JL . FACC (Fanconi anaemia complementation group C). Atlas Genet Cytogenet Oncol Haematol. June 2002 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/FACC101.html




FGFR3 (Fibroblast Growth Factor Receptor 3)

IdentityHugo FGFR3 Location 4p16.3 centromere - IT 15 - FGFR 3 - IDUA - MYL 5 - ZNF 141 - telomere

DNA/RNA

c-FGFR3 (4p16.3) in normal cells: PAC 1054L13 (above) and PAC 1174P18 (below) - Courtesy

Mariano Rocchi, Resources for Molecular Cytogenetics. Laboratories willing to validate the probes are wellcome: contact M Rocchi

Description 16.5 Kb; 19 exons; exon 1 unknown in human Transcription 4.0 Kb mRNA; large 3' untranslated region (1.4 kb); alternative splicing of exons

7 and 8 gives rise to two isoforms IIIb and IIIc

Protein


Protein Diagram

Description 806 amino acids; 115 kDa; tyrosine kinase receptor; contains three major domains: an extracellular domain with 3 Ig-like loops, a highly hydrophobic transmembrane domain (22 amino acids) and an intracellular domain with tyrosine kinase activity

Expression mostly in brain, cartilage, liver, inner ear, kidney Localisation plasma membrane Function FGF receptor with tyrosine kinase activity; binding of ligand (FGF) induces

receptor dimerization, autophosphorylation and signal transduction Homology with other FGFR (1, 2 and 4); Cek 2 in chicken

Implicated inEntity t(4;14)(p16.3;q32.3)/multiple myeloma --> FGFR3 -IgH Disease plasma cell leukaemia and multiple myeloma Prognosis unknown: found in 11 cases, but with no data on clinics Abnormal Protein no fusion protein, but promoter exchange between both partner genes

Oncogenesis overexpression and activation of FGFR 3 provides an oncogenic signal Entity squeletal dysplasia (inborn diseases) Disease hypochondroplasia, achondroplasia, thanatophoric dwarfism (TD I and II),

Crouzon syndrome with acanthosis nigricans and coronal craniosynostosis; endochondral and membranous ossification defects are caused by recurrent missense mutations

Breakpoints


Note Chromosome 4 breakpoints are clustured in a 50-70 kb region centromeric to

FGFR 3


Hugo FGFR3 GDB FGFR3

Entrez_Gene FGFR3 2261 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) Cards

Atlas FGFR99 GeneCards FGFR3 Ensembl FGFR3 CancerGene FGFR3 Genatlas FGFR3 GeneLynx FGFR3 eGenome FGFR3 euGene 2261

Genomic and cartography GoldenPath FGFR3 - 4p16.3 chr4:1762854-1777829 + 4p16.3 (hg17-May_2004) Ensembl FGFR3 - 4p16.3 [CytoView] NCBI Genes Cyto Gene Seq [Map View - NCBI] OMIM Disease map [OMIM] HomoloGene FGFR3

Gene and transcription


Genbank AF487554 [ SRS ] AF487554 [ ENTREZ ] Genbank S76733 [ SRS ] S76733 [ ENTREZ ] Genbank U22410 [ SRS ] U22410 [ ENTREZ ] Genbank AF238374 [ SRS ] AF238374 [ ENTREZ ] Genbank AF245114 [ SRS ] AF245114 [ ENTREZ ] RefSeq NM_000142 [ SRS ] NM_000142 [ ENTREZ ] RefSeq NM_022965 [ SRS ] NM_022965 [ ENTREZ ] RefSeq NT_086649 [ SRS ] NT_086649 [ ENTREZ ] AceView FGFR3 AceView - NCBI TRASER FGFR3 Traser - Stanford Unigene Hs.1420 [ SRS ] Hs.1420 [ NCBI ] HS1420 [ spliceNest ]

Protein : pattern, domain, 3D structure SwissProt P22607 [ SRS] P22607 [ EXPASY ] P22607 [ INTERPRO ] Prosite PS50835 IG_LIKE [ SRS ] PS50835 IG_LIKE [ Expasy ]

Prosite PS00107 PROTEIN_KINASE_ATP [ SRS ] PS00107 PROTEIN_KINASE_ATP [ Expasy ]

Prosite PS50011 PROTEIN_KINASE_DOM [ SRS ] PS50011 PROTEIN_KINASE_DOM [ Expasy ]

Prosite PS00109 PROTEIN_KINASE_TYR [ SRS ] PS00109 PROTEIN_KINASE_TYR [ Expasy ] Interpro IPR007110 Ig-like [ SRS ] IPR007110 Ig-like [ EBI ] Interpro IPR011009 Kinase_like [ SRS ] IPR011009 Kinase_like [ EBI ] Interpro IPR000719 Prot_kinase [ SRS ] IPR000719 Prot_kinase [ EBI ] Interpro IPR001245 Tyr_pkinase [ SRS ] IPR001245 Tyr_pkinase [ EBI ] Interpro IPR008266 Tyr_pkinase_AS [ SRS ] IPR008266 Tyr_pkinase_AS [ EBI ] CluSTr P22607 Pfam PF00047 ig [ SRS ] PF00047 ig [ Sanger ] pfam00047 [ NCBI-CDD ] Pfam PF00069 Pkinase [ SRS ] PF00069 Pkinase [ Sanger ] pfam00069 [ NCBI-CDD ] Prodom PD000001 Prot_kinase[INRA-Toulouse]

Prodom P22607 FGR3_HUMAN [ Domain structure ] P22607 FGR3_HUMAN [ sequences sharing at least 1 domain ]

Blocks P22607 PDB 1RY7 [ SRS ] 1RY7 [ PdbSum ], 1RY7 [ IMB ]

Polymorphism : SNP, mutations, diseases OMIM 134934 [ map ] GENECLINICS 134934


SNP FGFR3 [dbSNP-NCBI] SNP NM_000142 [SNP-NCI] SNP NM_022965 [SNP-NCI] SNP FGFR3 [GeneSNPs - Utah] FGFR3 [SNP - CSHL] FGFR3] [HGBASE - SRS]

General knowledge Family Browser FGFR3 [UCSC Family Browser] SOURCE NM_000142 SOURCE NM_022965 SMD Hs.1420 SAGE Hs.1420 Enzyme 2.7.1.112 [ Enzyme-SRS ] 2.7.1.112 [ Brenda-SRS ] 2.7.1.112 [ KEGG ] 2.7.1.112 [ WIT ] Amigo function|ATP binding Amigo process|JAK-STAT cascade Amigo process|MAPKKK cascade Amigo process|cell growth Amigo function|fibroblast growth factor receptor activity Amigo process|fibroblast growth factor receptor signaling pathway Amigo component|integral to plasma membrane Amigo process|protein amino acid phosphorylation Amigo function|protein-tyrosine kinase activity Amigo function|receptor activity Amigo process|skeletal development Amigo function|transferase activity PubGene FGFR3

Other databases Other database Somatic mutation (COSMIC-CGP-Sanger)

Probes Probe FGFR3 (4p16.3) in normal cells (Bari) Probe FGFR3 Related clones (RZPD - Berlin)


BibliographyMutations in the gene encoding fibroblast growth factor receptor-3 in achondroplasia.Rousseau F, Bonaventure J, Legeai-Mallet L, Pelet A, Rozet JM, Maroteaux P, Le Merrer M,


Munnich A Nature 1994 Sep 15;371(6494):252-4 Medline 94359611 FGFR activation in skeletal disorders: too much of a good thing.Webster MK, Donoghue DJ Trends Genet 1997 May;13(5):178-82 Medline 97298558 Frequent translocation t(4;14)(p16.3;q32.3) in multiple myeloma is associated with increased expression and activating mutations of fibroblast growth factor receptor 3.Chesi M, Nardini E, Brents LA, Schrock E, Ried T, Kuehl WM, Bergsagel PL Nat Genet 1997 Jul;16(3):260-4 Medline 97351509 A novel chromosomal translocation t(4; 14)(p16.3; q32) in multiple myeloma involves the fibroblast growth-factor receptor 3 gene.Richelda R, Ronchetti D, Baldini L, Cro L, Viggiano L, Marzella R, Rocchi M, Otsuki T, Lombardi L, Maiolo AT, Neri A Blood 1997 Nov 15;90(10):4062-70 Medline 98022801 REVIEW articles automatic search in PubMed Last year publications automatic search in PubMed

BiblioGene - INIST

Contributor(s)Written 02-1998 Jacky Bonaventure

CitationThis paper should be referenced as such : Bonaventure J . FGFR3 (Fibroblast Growth Factor Receptor 3). Atlas Genet Cytogenet Oncol Haematol. February 1998 . URL : http://www.infobiogen.fr/services/chromcancer/Genes/FGFR99.html




JAK2 (janus kinase 2) (updated: old version not available)

IdentityHugo JAK2 Location 9p24

JAK2 (9p24) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics. Laboratories


DNA/RNADescription 25 exons spanning roughly 140 kb of genomic DNA; 5402 bp pre-mRNA; 6

different transcripts, putatively encoding 4 different protein isoforms

Protein

Description 1132 amino acids; 130,7 kDa; JAK2 contains a central Src homology 2 (SH2) domain, and two C-terminal domains: a tyrosine kinase domain JH1 (also termed PTK or TyrKc domain), and a tyrosine kinase-like domain JH2 (also termed STYKc)

Expression wide Localisation intracellular, possibly membrane associated Function protein tyrosine kinase of the non-receptor type that associates with the

intracellular domains of cytokine receptors; JAK2 is the predominant JAK kinase activated in response to several growth factors and cytokines such as IL-3, GM-


CSF and erythropoietin; it has been found to be constitutively associated with the prolactin receptor and is required for responses to gamma interferon

Homology JAK2 belongs to the janus kinase subfamily; so far four mammalian JAKs have been identified (JAK1, JAK2, JAK3, and TYK2); human JAK2 is > 90% identical to the mouse and the rat JAK2 homologs.

MutationsSomatic A high proportion (> 50%) of patients with myeloproliferative disorders (MPD;

(polycythemia vera, essential thrombocythemia, idiopathic myelofibrosis - see below) carry a dominant gain-of-function V617F mutation in the JH2 kinase-like domain of JAK2. This mutation leads to deregulation of the kinase activity, and thus to constitutive tyrosine phosphorylation activity. The incidence of the V617F mutation in different studies ranges from 65-97% in polycythemia vera, from 41-57% in patients with essential thrombocythemia, and from 23-95% in patients with idiopathic myelofibrosis. In MPD the mutation is heterozygous in most patients and homozygous only in a minor subset. Mitotic recombination probably causes both 9p LOH and the transition from heterozygosity to homozygosity. The same mutation was also found in roughly 20% of Ph-negative atypical CML, in more than 10% of CMML, in about 15% of patients with megakaryocytic AML (AML M7), and 1/5 patients with juvenile myelomonocytic leukemia (JMML). The V617F mutation seems to occur exclusively in hematopietic malignancies of the myeloid lineage.

Implicated inEntity t(8;9)(p21-22;p24) / acute leukaemias -- > PCM1-JAK2 Disease myeloid and lymphoid malignancies; predominantly atypical CML, but also

found in (CEL), (secondary) AML, and MDS/MPD; thirteen cases described to date, all male, except for one childhood female case with erythroid leukemia with multiple bone tumors

Prognosis highly variable; allogeneic stem cell transplantation may be the only curative treatment

Hybrid/Mutated Gene

5¹ PCM1 3¹ JAK2; only in some cases the reciprocal 5¹ JAK2 3¹ PCM1 is present

Abnormal Protein

almost the entire PCM1 protein containing multiple coiled-coil domains is fused to the tyrosine kinase C-terminal domains (JH2 and JH1) of JAK2

Oncogenesis dimerization or oligomerization of the PCM1-JAK2 chimera through one or more of the coiled-coil motifs of PCM1 probably results in the constitutive activation of the tyrosine kinase domain of JAK2

Entity t(9;12)(p24;p13) / acute leukaemias --> JAK2/ETV6 Disease myeloid and lymphoid leukemias; only three cases described to date; one case

each: childhood T-ALL, pre B-ALL, atypical CML Prognosis unknown


Hybrid/Mutated Gene 5' ETV6 - 3' JAK2

Abnormal Protein

in the atypical CML the N-terminal HLH of ETV6 is fused to the tyrosine kinase C-terminal domains (JH2 and JH1) of JAK2; in the B-ALL the same ETV6 domain is fused to part of the JH2 and the complete JH1 domain, and in the T-ALL case to the JH1 domain

Oncogenesis it may be speculated that the HLH domain of ETV6 provides a dimerization interface to the kinase domain of JAK2, which activates JAK2; ETV6-JAK2 transgenic mice generated using a T-ALL specific fusion construct - develop fatal CD8+ acute T-cell leukemia

Entity t(9;22)(p24;q11.2) /MPD-- > JAK2-BCR Disease atypical CML; only one case described to date Hybrid/Mutated Gene 5

Documents

Atlas of Genetics and Cytogenetics in Oncology and Haematologyatlasgeneticsoncology.org/Journal/Arch1998Vol2Num1.pdf · 2008. 12. 10. · Atlas of Genetics and Cytogenetics in Oncology