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SMARCD1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1)

Identity

Alias_symbol (synonym)BAF60A
Rsc6p
CRACD1
Other alias
HGNC (Hugo) SMARCD1
LocusID (NCBI) 6602
Atlas_Id 42336
Location 12q13.12  [Link to chromosome band 12q13]
Location_base_pair Starts at 50085200 and ends at 50100711 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
NR1H2 (19q13.33) / SMARCD1 (12q13.12)SMARCD1 (12q13.12) / ATP2C2 (16q24.1)

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 Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Breast: Ductal carcinoma


External links

Nomenclature
HGNC (Hugo)SMARCD1   11106
Cards
Entrez_Gene (NCBI)SMARCD1  6602  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
AliasesBAF60A; CRACD1; Rsc6p
GeneCards (Weizmann)SMARCD1
Ensembl hg19 (Hinxton)ENSG00000066117 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000066117 [Gene_View]  chr12:50085200-50100711 [Contig_View]  SMARCD1 [Vega]
ICGC DataPortalENSG00000066117
TCGA cBioPortalSMARCD1
AceView (NCBI)SMARCD1
Genatlas (Paris)SMARCD1
WikiGenes6602
SOURCE (Princeton)SMARCD1
Genetics Home Reference (NIH)SMARCD1
Genomic and cartography
GoldenPath hg38 (UCSC)SMARCD1  -     chr12:50085200-50100711 +  12q13.12   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMARCD1  -     12q13.12   [Description]    (hg19-Feb_2009)
EnsemblSMARCD1 - 12q13.12 [CytoView hg19]  SMARCD1 - 12q13.12 [CytoView hg38]
Mapping of homologs : NCBISMARCD1 [Mapview hg19]  SMARCD1 [Mapview hg38]
OMIM601735   
Gene and transcription
Genbank (Entrez)AA610093 AF109733 AK130517 AK292700 AK293932
RefSeq transcript (Entrez)NM_003076 NM_139071
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMARCD1
Cluster EST : UnigeneHs.79335 [ NCBI ]
CGAP (NCI)Hs.79335
Alternative Splicing GalleryENSG00000066117
Gene ExpressionSMARCD1 [ NCBI-GEO ]   SMARCD1 [ EBI - ARRAY_EXPRESS ]   SMARCD1 [ SEEK ]   SMARCD1 [ MEM ]
Gene Expression Viewer (FireBrowse)SMARCD1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6602
GTEX Portal (Tissue expression)SMARCD1
Human Protein AtlasENSG00000066117-SMARCD1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96GM5   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ96GM5  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96GM5
Splice isoforms : SwissVarQ96GM5
PhosPhoSitePlusQ96GM5
Domains : Interpro (EBI)SWIB_domain    SWIB_MDM2_domain   
Domain families : Pfam (Sanger)SWIB (PF02201)   
Domain families : Pfam (NCBI)pfam02201   
Domain families : Smart (EMBL)SWIB (SM00151)  
Conserved Domain (NCBI)SMARCD1
DMDM Disease mutations6602
Blocks (Seattle)SMARCD1
SuperfamilyQ96GM5
Human Protein Atlas [tissue]ENSG00000066117-SMARCD1 [tissue]
Peptide AtlasQ96GM5
HPRD03438
IPIIPI00852816   IPI00853408   IPI01015894   IPI01021758   IPI01021621   IPI01021430   IPI01021270   IPI01022482   
Protein Interaction databases
DIP (DOE-UCLA)Q96GM5
IntAct (EBI)Q96GM5
FunCoupENSG00000066117
BioGRIDSMARCD1
STRING (EMBL)SMARCD1
ZODIACSMARCD1
Ontologies - Pathways
QuickGOQ96GM5
Ontology : AmiGOchromatin binding  transcription coactivator activity  receptor binding  protein binding  nucleoplasm  nucleosome disassembly  chromatin remodeling  chromatin remodeling  regulation of transcription from RNA polymerase II promoter  nervous system development  SWI/SNF complex  covalent chromatin modification  protein complex scaffold  intracellular membrane-bounded organelle  chromatin-mediated maintenance of transcription  cellular response to fatty acid  npBAF complex  nBAF complex  
Ontology : EGO-EBIchromatin binding  transcription coactivator activity  receptor binding  protein binding  nucleoplasm  nucleosome disassembly  chromatin remodeling  chromatin remodeling  regulation of transcription from RNA polymerase II promoter  nervous system development  SWI/SNF complex  covalent chromatin modification  protein complex scaffold  intracellular membrane-bounded organelle  chromatin-mediated maintenance of transcription  cellular response to fatty acid  npBAF complex  nBAF complex  
Pathways : BIOCARTAChromatin Remodeling by hSWI/SNF ATP-dependent Complexes [Genes]    Control of Gene Expression by Vitamin D Receptor [Genes]   
NDEx NetworkSMARCD1
Atlas of Cancer Signalling NetworkSMARCD1
Wikipedia pathwaysSMARCD1
Orthology - Evolution
OrthoDB6602
GeneTree (enSembl)ENSG00000066117
Phylogenetic Trees/Animal Genes : TreeFamSMARCD1
HOVERGENQ96GM5
HOGENOMQ96GM5
Homologs : HomoloGeneSMARCD1
Homology/Alignments : Family Browser (UCSC)SMARCD1
Gene fusions - Rearrangements
Fusion: Tumor Portal SMARCD1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMARCD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMARCD1
dbVarSMARCD1
ClinVarSMARCD1
1000_GenomesSMARCD1 
Exome Variant ServerSMARCD1
ExAC (Exome Aggregation Consortium)ENSG00000066117
GNOMAD BrowserENSG00000066117
Genetic variants : HAPMAP6602
Genomic Variants (DGV)SMARCD1 [DGVbeta]
DECIPHERSMARCD1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMARCD1 
Mutations
ICGC Data PortalSMARCD1 
TCGA Data PortalSMARCD1 
Broad Tumor PortalSMARCD1
OASIS PortalSMARCD1 [ Somatic mutations - Copy number]
Cancer Gene: CensusSMARCD1 
Somatic Mutations in Cancer : COSMICSMARCD1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSMARCD1
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
BioMutasearch SMARCD1
DgiDB (Drug Gene Interaction Database)SMARCD1
DoCM (Curated mutations)SMARCD1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMARCD1 (select a term)
intoGenSMARCD1
Cancer3DSMARCD1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601735   
Orphanet
MedgenSMARCD1
Genetic Testing Registry SMARCD1
NextProtQ96GM5 [Medical]
TSGene6602
GENETestsSMARCD1
Target ValidationSMARCD1
Huge Navigator SMARCD1 [HugePedia]
snp3D : Map Gene to Disease6602
BioCentury BCIQSMARCD1
ClinGenSMARCD1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6602
Chemical/Pharm GKB GenePA35956
Clinical trialSMARCD1
Miscellaneous
canSAR (ICR)SMARCD1 (select the gene name)
Probes
Litterature
PubMed61 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMARCD1
EVEXSMARCD1
GoPubMedSMARCD1
iHOPSMARCD1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Thu Nov 9 13:11:46 CET 2017

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