Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SMC1A (structural maintenance of chromosomes 1A)

Identity

Other namesCDLS2
DXS423E
SB1.8
SMC1
SMC1L1
SMC1alpha
SMCB
HGNC (Hugo) SMC1A
LocusID (NCBI) 8243
Atlas_Id 42339
Location Xp11.22
Location_base_pair Starts at 53401070 and ends at 53449677 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
ALDH3A2 (17p11.2) / SMC1A (Xp11.22)BRWD1 (21q22.2) / SMC1A (Xp11.22)FOXP1 (3p13) / SMC1A (Xp11.22)
SMC1A (Xp11.22) / SEC31A (4q21.22)SMC1A (Xp11.22) / XIAP (Xq25)BRWD1 21q22.2 / SMC1A Xp11.22

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  Chronic Myelomonocytic Leukemia (CMML)

External links

Nomenclature
HGNC (Hugo)SMC1A   11111
Cards
Entrez_Gene (NCBI)SMC1A  8243  structural maintenance of chromosomes 1A
GeneCards (Weizmann)SMC1A
Ensembl hg19 (Hinxton)ENSG00000072501 [Gene_View]  chrX:53401070-53449677 [Contig_View]  SMC1A [Vega]
Ensembl hg38 (Hinxton)ENSG00000072501 [Gene_View]  chrX:53401070-53449677 [Contig_View]  SMC1A [Vega]
ICGC DataPortalENSG00000072501
TCGA cBioPortalSMC1A
AceView (NCBI)SMC1A
Genatlas (Paris)SMC1A
WikiGenes8243
SOURCE (Princeton)SMC1A
Genomic and cartography
GoldenPath hg19 (UCSC)SMC1A  -     chrX:53401070-53449677 -  Xp11.22   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SMC1A  -     Xp11.22   [Description]    (hg38-Dec_2013)
EnsemblSMC1A - Xp11.22 [CytoView hg19]  SMC1A - Xp11.22 [CytoView hg38]
Mapping of homologs : NCBISMC1A [Mapview hg19]  SMC1A [Mapview hg38]
OMIM300040   300590   
Gene and transcription
Genbank (Entrez)AF176781 AK055575 AK056308 AK091458 AK291921
RefSeq transcript (Entrez)NM_001281463 NM_006306
RefSeq genomic (Entrez)NC_000023 NC_018934 NG_006988 NT_011630 NW_004929442
Consensus coding sequences : CCDS (NCBI)SMC1A
Cluster EST : UnigeneHs.211602 [ NCBI ]
CGAP (NCI)Hs.211602
Alternative Splicing GalleryENSG00000072501
Gene ExpressionSMC1A [ NCBI-GEO ]   SMC1A [ EBI - ARRAY_EXPRESS ]   SMC1A [ SEEK ]   SMC1A [ MEM ]
Gene Expression Viewer (FireBrowse)SMC1A [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8243
GTEX Portal (Tissue expression)SMC1A
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ14683 (Uniprot)
NextProtQ14683  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ14683
Splice isoforms : SwissVarQ14683 (Swissvar)
PhosPhoSitePlusQ14683
Domains : Interpro (EBI)P-loop_NTPase    RecF/RecN/SMC_N    SMC    SMC1A_metazoan    SMC_hinge   
Domain families : Pfam (Sanger)SMC_hinge (PF06470)    SMC_N (PF02463)   
Domain families : Pfam (NCBI)pfam06470    pfam02463   
Domain families : Smart (EMBL)SMC_hinge (SM00968)  
DMDM Disease mutations8243
Blocks (Seattle)SMC1A
SuperfamilyQ14683
Human Protein AtlasENSG00000072501
Peptide AtlasQ14683
HPRD02077
IPIIPI00291939   IPI00922333   IPI00385082   IPI00553151   
Protein Interaction databases
DIP (DOE-UCLA)Q14683
IntAct (EBI)Q14683
FunCoupENSG00000072501
BioGRIDSMC1A
STRING (EMBL)SMC1A
ZODIACSMC1A
Ontologies - Pathways
QuickGOQ14683
Ontology : AmiGOmitotic sister chromatid segregation  chromosome, centromeric region  kinetochore  condensed chromosome kinetochore  condensed nuclear chromosome  chromatin binding  protein binding  ATP binding  nucleus  nucleoplasm  nucleoplasm  chromosome  cytoplasm  cytosol  DNA repair  mitotic spindle organization  sister chromatid cohesion  sister chromatid cohesion  mitotic sister chromatid cohesion  mitotic cell cycle checkpoint  meiotic nuclear division  cohesin core heterodimer  response to radiation  protein sumoylation  stem cell population maintenance  meiotic cohesin complex  negative regulation of DNA endoreduplication  mediator complex binding  signal transduction in response to DNA damage  poly(A) RNA binding  protein heterodimerization activity  cell division  
Ontology : EGO-EBImitotic sister chromatid segregation  chromosome, centromeric region  kinetochore  condensed chromosome kinetochore  condensed nuclear chromosome  chromatin binding  protein binding  ATP binding  nucleus  nucleoplasm  nucleoplasm  chromosome  cytoplasm  cytosol  DNA repair  mitotic spindle organization  sister chromatid cohesion  sister chromatid cohesion  mitotic sister chromatid cohesion  mitotic cell cycle checkpoint  meiotic nuclear division  cohesin core heterodimer  response to radiation  protein sumoylation  stem cell population maintenance  meiotic cohesin complex  negative regulation of DNA endoreduplication  mediator complex binding  signal transduction in response to DNA damage  poly(A) RNA binding  protein heterodimerization activity  cell division  
Pathways : KEGGCell cycle    Oocyte meiosis   
NDEx Network
Atlas of Cancer Signalling NetworkSMC1A
Wikipedia pathwaysSMC1A
Orthology - Evolution
OrthoDB8243
GeneTree (enSembl)ENSG00000072501
Phylogenetic Trees/Animal Genes : TreeFamSMC1A
Homologs : HomoloGeneSMC1A
Homology/Alignments : Family Browser (UCSC)SMC1A
Gene fusions - Rearrangements
Fusion: TCGABRWD1 21q22.2 SMC1A Xp11.22 LUAD
Polymorphisms : SNP, variants
NCBI Variation ViewerSMC1A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMC1A
dbVarSMC1A
ClinVarSMC1A
1000_GenomesSMC1A 
Exome Variant ServerSMC1A
ExAC (Exome Aggregation Consortium)SMC1A (select the gene name)
Genetic variants : HAPMAP8243
Genomic Variants (DGV)SMC1A [DGVbeta]
Mutations
ICGC Data PortalSMC1A 
TCGA Data PortalSMC1A 
Broad Tumor PortalSMC1A
OASIS PortalSMC1A [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMC1A 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)MRC Human Genetics Unit LOVD at MRC IGMM
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
BioMutasearch SMC1A
DgiDB (Drug Gene Interaction Database)SMC1A
DoCM (Curated mutations)SMC1A (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMC1A (select a term)
intoGenSMC1A
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)X:53401070-53449677  ENSG00000072501
CONAN: Copy Number AnalysisSMC1A 
Mutations and Diseases : HGMDSMC1A
OMIM300040    300590   
MedgenSMC1A
Genetic Testing Registry SMC1A
NextProtQ14683 [Medical]
TSGene8243
GENETestsSMC1A
Huge Navigator SMC1A [HugePedia]
snp3D : Map Gene to Disease8243
BioCentury BCIQSMC1A
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8243
Chemical/Pharm GKB GenePA35961
Clinical trialSMC1A
Miscellaneous
canSAR (ICR)SMC1A (select the gene name)
Probes
Litterature
PubMed137 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMC1A
EVEXSMC1A
GoPubMedSMC1A
iHOPSMC1A
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sun May 8 19:06:32 CEST 2016

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