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Aliases for SMCHD1 Gene

Aliases for SMCHD1 Gene

  • Structural Maintenance Of Chromosomes Flexible Hinge Domain Containing 1 2 3 5
  • SMC Hinge Domain-Containing Protein 1 4
  • KIAA0650 4

External Ids for SMCHD1 Gene

Summaries for SMCHD1 Gene

Entrez Gene Summary for SMCHD1 Gene

  • This gene encodes a protein which contains a hinge region domain found in members of the SMC (structural maintenance of chromosomes) protein family. [provided by RefSeq, Dec 2011]

GeneCards Summary for SMCHD1 Gene

SMCHD1 (Structural Maintenance Of Chromosomes Flexible Hinge Domain Containing 1) is a Protein Coding gene. Diseases associated with SMCHD1 include fascioscapulohumeral muscular dystrophy 2, digenic and facioscapulohumeral muscular dystrophy 1.

UniProtKB/Swiss-Prot for SMCHD1 Gene

  • Required for maintenance of X inactivation in females and hypermethylation of CpG islands associated with inactive X. Involved in a pathway that mediates the methylation of a subset of CpG islands slowly and requires the de novo methyltransferase DNMT3B (By similarity). Required for DUX4 silencing in somatic cells.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMCHD1 Gene

Genomics for SMCHD1 Gene

Regulatory Elements for SMCHD1 Gene

Promoters for SMCHD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SMCHD1 on UCSC Golden Path with GeneCards custom track

Genomic Location for SMCHD1 Gene

Chromosome:
18
Start:
2,655,738 bp from pter
End:
2,805,017 bp from pter
Size:
149,280 bases
Orientation:
Plus strand

Genomic View for SMCHD1 Gene

Genes around SMCHD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMCHD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMCHD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMCHD1 Gene

Proteins for SMCHD1 Gene

  • Protein details for SMCHD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A6NHR9-SMHD1_HUMAN
    Recommended name:
    Structural maintenance of chromosomes flexible hinge domain-containing protein 1
    Protein Accession:
    A6NHR9
    Secondary Accessions:
    • O75141
    • Q6AHX6
    • Q6ZTQ8
    • Q9H6Q2
    • Q9UG39

    Protein attributes for SMCHD1 Gene

    Size:
    2005 amino acids
    Molecular mass:
    226374 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB15202.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BC035774; Type=Frameshift; Positions=1730; Evidence={ECO:0000305}; Sequence=CAH10538.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for SMCHD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMCHD1 Gene

Proteomics data for SMCHD1 Gene at MOPED

Post-translational modifications for SMCHD1 Gene

  • Sumoylated with SUMO1.
  • Ubiquitination at Lys 192, Lys 580, Lys 619, Lys 784, Lys 812, Lys 1048, Lys 1256, Lys 1266, Lys 1802, and Lys 1958
  • Modification sites at PhosphoSitePlus

Other Protein References for SMCHD1 Gene

No data available for DME Specific Peptides for SMCHD1 Gene

Domains & Families for SMCHD1 Gene

Protein Domains for SMCHD1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SMCHD1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SMCHD1: view

No data available for Gene Families and UniProtKB/Swiss-Prot for SMCHD1 Gene

Function for SMCHD1 Gene

Molecular function for SMCHD1 Gene

UniProtKB/Swiss-Prot Function:
Required for maintenance of X inactivation in females and hypermethylation of CpG islands associated with inactive X. Involved in a pathway that mediates the methylation of a subset of CpG islands slowly and requires the de novo methyltransferase DNMT3B (By similarity). Required for DUX4 silencing in somatic cells.
genes like me logo Genes that share phenotypes with SMCHD1: view

Human Phenotype Ontology for SMCHD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for SMCHD1 Gene

Localization for SMCHD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMCHD1 Gene

Chromosome. Note=Localizes to Barr body. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMCHD1 Gene COMPARTMENTS Subcellular localization image for SMCHD1 gene
Compartment Confidence
nucleus 4

Gene Ontology (GO) - Cellular Components for SMCHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001740 Barr body IEA --
genes like me logo Genes that share ontologies with SMCHD1: view

Pathways & Interactions for SMCHD1 Gene

SuperPathways for SMCHD1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SMCHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009048 dosage compensation by inactivation of X chromosome IEA --
GO:0051276 chromosome organization IEA --
genes like me logo Genes that share ontologies with SMCHD1: view

No data available for Pathways by source and SIGNOR curated interactions for SMCHD1 Gene

Drugs & Compounds for SMCHD1 Gene

No Compound Related Data Available

Transcripts for SMCHD1 Gene

Unigene Clusters for SMCHD1 Gene

Structural maintenance of chromosomes flexible hinge domain containing 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SMCHD1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
SP1: - - -
SP2: - -
SP3:
SP4:
SP5: -

ExUns: 24 ^ 25a · 25b
SP1: -
SP2: -
SP3:
SP4:
SP5:

Relevant External Links for SMCHD1 Gene

GeneLoc Exon Structure for
SMCHD1
ECgene alternative splicing isoforms for
SMCHD1

Expression for SMCHD1 Gene

mRNA expression in normal human tissues for SMCHD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMCHD1 Gene

This gene is overexpressed in Whole Blood (x5.9).

Protein differential expression in normal tissues from HIPED for SMCHD1 Gene

This gene is overexpressed in Lymph node (19.3), Peripheral blood mononuclear cells (13.0), and Liver (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for SMCHD1 Gene



SOURCE GeneReport for Unigene cluster for SMCHD1 Gene Hs.8118

genes like me logo Genes that share expression patterns with SMCHD1: view

Protein tissue co-expression partners for SMCHD1 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for SMCHD1 Gene

Orthologs for SMCHD1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SMCHD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMCHD1 35
  • 99.58 (n)
  • 99.45 (a)
SMCHD1 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SMCHD1 36
  • 92 (a)
OneToOne
SMCHD1 35
  • 91.57 (n)
  • 92.99 (a)
dog
(Canis familiaris)
Mammalia SMCHD1 35
  • 93.35 (n)
  • 93.79 (a)
SMCHD1 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smchd1 35
  • 85.99 (n)
  • 87.11 (a)
Smchd1 16
Smchd1 36
  • 86 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMCHD1 36
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMCHD1 36
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smchd1 35
  • 86.4 (n)
  • 88.42 (a)
chicken
(Gallus gallus)
Aves SMCHD1 35
  • 76.08 (n)
  • 77.19 (a)
SMCHD1 36
  • 76 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 61 (a)
OneToMany
-- 36
  • 72 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia smchd1 35
  • 67.61 (n)
  • 64 (a)
zebrafish
(Danio rerio)
Actinopterygii smchd1 36
  • 41 (a)
OneToMany
SMCHD1 (2 of 2) 36
  • 39 (a)
OneToMany
LOC570784 35
  • 57.45 (n)
  • 52.43 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 45 (a)
OneToMany
-- 36
  • 38 (a)
OneToMany
Species with no ortholog for SMCHD1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SMCHD1 Gene

ENSEMBL:
Gene Tree for SMCHD1 (if available)
TreeFam:
Gene Tree for SMCHD1 (if available)

Paralogs for SMCHD1 Gene

No data available for Paralogs for SMCHD1 Gene

Variants for SMCHD1 Gene

Sequence variations from dbSNP and Humsavar for SMCHD1 Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
rs2276092 - 2,707,621(-) CCTAA(C/T)CTCAT nc-transcript-variant, reference, missense
rs633422 - 2,724,932(+) ACCAA(A/C/T)GGACC nc-transcript-variant, reference, missense
rs9961682 - 2,728,561(+) ACAAC(A/G)TAACA nc-transcript-variant, reference, missense
VAR_069067 Facioscapulohumeral muscular dystrophy 2 (FSHD2)
VAR_069068 Facioscapulohumeral muscular dystrophy 2 (FSHD2)

Structural Variations from Database of Genomic Variants (DGV) for SMCHD1 Gene

Variant ID Type Subtype PubMed ID
nsv909315 CNV Loss 21882294
esv2677635 CNV Deletion 23128226
nsv909316 CNV Gain 21882294
esv2716680 CNV Deletion 23290073

Variation tolerance for SMCHD1 Gene

Residual Variation Intolerance Score: 7.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.02; 90.05% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMCHD1 Gene

HapMap Linkage Disequilibrium report
SMCHD1
Human Gene Mutation Database (HGMD)
SMCHD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMCHD1 Gene

Disorders for SMCHD1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SMCHD1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
fascioscapulohumeral muscular dystrophy 2, digenic
  • facioscapulohumeral muscular dystrophy 2
facioscapulohumeral muscular dystrophy 1
  • facioscapulohumeral muscular dystrophy
18p deletion syndrome
  • chromosome 18p deletion syndrome
muscular dystrophy
  • muscular dystrophies
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SMHD1_HUMAN
  • Facioscapulohumeral muscular dystrophy 2 (FSHD2) [MIM:158901]: A degenerative muscle disease characterized by slowly progressive weakness of the muscles of the face, upper-arm, and shoulder girdle. The onset of symptoms usually occurs in the first or second decade of life. Affected individuals usually present with impairment of upper extremity elevation. This tends to be followed by facial weakness, primarily involving the orbicularis oris and orbicularis oculi muscles. {ECO:0000269 PubMed:23143600}. Note=The disease is caused by mutations affecting the gene represented in this entry. SMCHD1 mutations lead to DUX4 expression in somatic tissues, including muscle cells, when an haplotype on chromosome 4 is permissive for DUX4 expression. Ectopic expression of DUX4 in skeletal muscle activates the expression of stem cell and germline genes, and, when overexpressed in somatic cells, DUX4 can ultimately lead to cell death.

Relevant External Links for SMCHD1

Genetic Association Database (GAD)
SMCHD1
Human Genome Epidemiology (HuGE) Navigator
SMCHD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMCHD1
genes like me logo Genes that share disorders with SMCHD1: view

No data available for Genatlas for SMCHD1 Gene

Publications for SMCHD1 Gene

  1. Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9734811) Ishikawa K. … Ohara O. (DNA Res. 1998) 2 3 4 67
  2. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3
  3. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3
  4. Hemizygosity for SMCHD1 in Facioscapulohumeral Muscular Dystrophy Type 2: Consequences for 18p Deletion Syndrome. (PMID: 25820463) Lemmers R.J. … van der Maarel S.M. (Hum. Mutat. 2015) 3
  5. The central role of EED in the orchestration of polycomb group complexes. (PMID: 24457600) Cao Q. … Chinnaiyan A.M. (Nat Commun 2014) 3

Products for SMCHD1 Gene

Sources for SMCHD1 Gene

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