Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1)

Identity

Alias (NCBI)BAMS
FSHD2
HGNC (Hugo) SMCHD1
HGNC Alias symbKIAA0650
FSHD2
LocusID (NCBI) 23347
Atlas_Id 53305
Location 18p11.32  [Link to chromosome band 18p11]
Location_base_pair Starts at 2655726 and ends at 2805017 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)
ANKRD12 (18p11.22) / SMCHD1 (18p11.32)CTSC (11q14.2) / SMCHD1 (18p11.32)IFNGR1 (6q23.3) / SMCHD1 (18p11.32)
SMCHD1 (18p11.32) / AKAP10 (17p11.2)SMCHD1 (18p11.32) / FBXL7 (5p15.1)SMCHD1 (18p11.32) / NDC80 (18p11.32)
IFNGR1 6q23.3 / SMCHD1 18p11.32SMCHD1 18p11.32 / NDC80 18p11.32

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 ]
  del(18)(p11)

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(6;18)(q23;p11) IFNGR1/SMCHD1
SMCHD1/NDC80 (18p11)

External links

Nomenclature
HGNC (Hugo)SMCHD1   29090
Cards
Entrez_Gene (NCBI)SMCHD1    structural maintenance of chromosomes flexible hinge domain containing 1
AliasesBAMS; FSHD2
GeneCards (Weizmann)SMCHD1
Ensembl hg19 (Hinxton)ENSG00000101596 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000101596 [Gene_View]  ENSG00000101596 [Sequence]  chr18:2655726-2805017 [Contig_View]  SMCHD1 [Vega]
ICGC DataPortalENSG00000101596
TCGA cBioPortalSMCHD1
AceView (NCBI)SMCHD1
Genatlas (Paris)SMCHD1
SOURCE (Princeton)SMCHD1
Genetics Home Reference (NIH)SMCHD1
Genomic and cartography
GoldenPath hg38 (UCSC)SMCHD1  -     chr18:2655726-2805017 +  18p11.32   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMCHD1  -     18p11.32   [Description]    (hg19-Feb_2009)
GoldenPathSMCHD1 - 18p11.32 [CytoView hg19]  SMCHD1 - 18p11.32 [CytoView hg38]
ImmunoBaseENSG00000101596
genome Data Viewer NCBISMCHD1 [Mapview hg19]  
OMIM158901   603457   614982   
Gene and transcription
Genbank (Entrez)AB014550 AI904018 AK025646 AK126324 AL080138
RefSeq transcript (Entrez)NM_015295
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMCHD1
Alternative Splicing GalleryENSG00000101596
Gene ExpressionSMCHD1 [ NCBI-GEO ]   SMCHD1 [ EBI - ARRAY_EXPRESS ]   SMCHD1 [ SEEK ]   SMCHD1 [ MEM ]
Gene Expression Viewer (FireBrowse)SMCHD1 [ Firebrowse - Broad ]
GenevisibleExpression of SMCHD1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23347
GTEX Portal (Tissue expression)SMCHD1
Human Protein AtlasENSG00000101596-SMCHD1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtA6NHR9   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtA6NHR9  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProA6NHR9
Splice isoforms : SwissVarA6NHR9
PhosPhoSitePlusA6NHR9
Domains : Interpro (EBI)HATPase_C_sf    SMC_hinge    SMC_hinge_sf    SMCHD1   
Domain families : Pfam (Sanger)SMC_hinge (PF06470)   
Domain families : Pfam (NCBI)pfam06470   
Domain families : Smart (EMBL)SMC_hinge (SM00968)  
Conserved Domain (NCBI)SMCHD1
Blocks (Seattle)SMCHD1
PDB (RSDB)6MW7   
PDB Europe6MW7   
PDB (PDBSum)6MW7   
PDB (IMB)6MW7   
Structural Biology KnowledgeBase6MW7   
SCOP (Structural Classification of Proteins)6MW7   
CATH (Classification of proteins structures)6MW7   
SuperfamilyA6NHR9
Human Protein Atlas [tissue]ENSG00000101596-SMCHD1 [tissue]
Peptide AtlasA6NHR9
IPIIPI00890837   IPI00465022   IPI00645162   
Protein Interaction databases
DIP (DOE-UCLA)A6NHR9
IntAct (EBI)A6NHR9
BioGRIDSMCHD1
STRING (EMBL)SMCHD1
ZODIACSMCHD1
Ontologies - Pathways
QuickGOA6NHR9
Ontology : AmiGOnuclear chromosome, telomeric region  Barr body  DNA binding  protein binding  ATP binding  double-strand break repair  dosage compensation by inactivation of X chromosome  ATPase activity  site of double-strand break  protein homodimerization activity  nose development  positive regulation of DNA repair  inactivation of X chromosome by heterochromatin assembly  inactivation of X chromosome by DNA methylation  heterochromatin organization involved in chromatin silencing  negative regulation of double-strand break repair via homologous recombination  positive regulation of double-strand break repair via nonhomologous end joining  
Ontology : EGO-EBInuclear chromosome, telomeric region  Barr body  DNA binding  protein binding  ATP binding  double-strand break repair  dosage compensation by inactivation of X chromosome  ATPase activity  site of double-strand break  protein homodimerization activity  nose development  positive regulation of DNA repair  inactivation of X chromosome by heterochromatin assembly  inactivation of X chromosome by DNA methylation  heterochromatin organization involved in chromatin silencing  negative regulation of double-strand break repair via homologous recombination  positive regulation of double-strand break repair via nonhomologous end joining  
NDEx NetworkSMCHD1
Atlas of Cancer Signalling NetworkSMCHD1
Wikipedia pathwaysSMCHD1
Orthology - Evolution
OrthoDB23347
GeneTree (enSembl)ENSG00000101596
Phylogenetic Trees/Animal Genes : TreeFamSMCHD1
HOGENOMA6NHR9
Homologs : HomoloGeneSMCHD1
Homology/Alignments : Family Browser (UCSC)SMCHD1
Gene fusions - Rearrangements
Fusion : MitelmanIFNGR1/SMCHD1 [6q23.3/18p11.32]  
Fusion : MitelmanSMCHD1/NDC80 [18p11.32/18p11.32]  
Fusion PortalIFNGR1 6q23.3 SMCHD1 18p11.32 PRAD
Fusion PortalSMCHD1 18p11.32 NDC80 18p11.32 LUAD
Fusion Cancer (Beijing)CTSC [11q14.2]  -  SMCHD1 [18p11.32]  [FUSC002488]
Fusion : QuiverSMCHD1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMCHD1 [hg38]
dbVarSMCHD1
ClinVarSMCHD1
MonarchSMCHD1
1000_GenomesSMCHD1 
Exome Variant ServerSMCHD1
GNOMAD BrowserENSG00000101596
Varsome BrowserSMCHD1
Genomic Variants (DGV)SMCHD1 [DGVbeta]
DECIPHERSMCHD1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMCHD1 
Mutations
ICGC Data PortalSMCHD1 
TCGA Data PortalSMCHD1 
Broad Tumor PortalSMCHD1
OASIS PortalSMCHD1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMCHD1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSMCHD1
Mutations and Diseases : HGMDSMCHD1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)Leiden Muscular Dystrophy pages
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SMCHD1
DgiDB (Drug Gene Interaction Database)SMCHD1
DoCM (Curated mutations)SMCHD1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMCHD1 (select a term)
intoGenSMCHD1
Cancer3DSMCHD1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM158901    603457    614982   
Orphanet62    62   
DisGeNETSMCHD1
MedgenSMCHD1
Genetic Testing Registry SMCHD1
NextProtA6NHR9 [Medical]
GENETestsSMCHD1
Target ValidationSMCHD1
Huge Navigator SMCHD1 [HugePedia]
ClinGenSMCHD1
Clinical trials, drugs, therapy
MyCancerGenomeSMCHD1
Protein Interactions : CTD
Pharm GKB GenePA128395776
PharosA6NHR9
Clinical trialSMCHD1
Miscellaneous
canSAR (ICR)SMCHD1 (select the gene name)
HarmonizomeSMCHD1
DataMed IndexSMCHD1
Probes
Litterature
PubMed88 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXSMCHD1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Jan 1 18:38:20 CET 2021
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