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Aliases for SMCHD1 Gene

Aliases for SMCHD1 Gene

  • Structural Maintenance Of Chromosomes Flexible Hinge Domain Containing 1 2 3
  • KIAA0650 4 6
  • SMC Hinge Domain-Containing Protein 1 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 facioscapulohumeral muscular dystrophy 1 and fascioscapulohumeral muscular dystrophy 2, digenic.

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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for SMCHD1 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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 Lys192, Lys580, Lys619, Lys784, Lys812, Lys1048, Lys1256, Lys1266, Lys1802, and Lys1958
  • Modification sites at PhosphoSitePlus

Other Protein References for SMCHD1 Gene

No data available for DME Specific Peptides for SMCHD1 Gene

Domains 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.

Gene Ontology (GO) - Molecular Function for SMCHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding --
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with SMCHD1: view
genes like me logo Genes that share phenotypes with SMCHD1: view

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SMCHD1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting 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
cytosol 2
nucleus 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SMCHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001740 Barr body IEA --
GO:0005694 chromosome --
genes like me logo Genes that share ontologies with SMCHD1: view

Pathways 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 --
GO:0051276 chromosome organization IEA --
GO:0060821 inactivation of X chromosome by DNA methylation IEA --
genes like me logo Genes that share ontologies with SMCHD1: view

No data available for Pathways by source for SMCHD1 Gene

Transcripts for SMCHD1 Gene

Unigene Clusters for SMCHD1 Gene

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

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SMCHD1

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for SMCHD1
  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

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 (5.9).

Integrated Proteomics: protein expression 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 expressions with SMCHD1: view

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 35
  • 91.57 (n)
  • 92.99 (a)
SMCHD1 36
  • 92 (a)
OneToOne
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 LOC570784 35
  • 57.45 (n)
  • 52.43 (a)
smchd1 36
  • 41 (a)
OneToMany
SMCHD1 (2 of 2) 36
  • 39 (a)
OneToMany
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 MAF
rs14409 -- 2,804,118(+) GAAAG(G/T)TTAAA utr-variant-3-prime
rs62579 -- 2,746,578(-) ACCAA(A/G)CACCC intron-variant
rs159757 -- 2,746,798(-) CTGGG(C/T)CAACA intron-variant
rs159825 -- 2,765,107(-) TGGTC(A/G)GTAAA intron-variant
rs159826 -- 2,747,226(-) TTTAT(A/G)TAAAA intron-variant

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

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

(1) OMIM Diseases for SMCHD1 Gene (614982)

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

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
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 48
  3. Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2. (PMID: 23143600) Lemmers R.J. … van der Maarel S.M. (Nat. Genet. 2012) 3 4
  4. Epigenetic regulator Smchd1 functions as a tumor suppressor. (PMID: 23269277) Leong H.S. … Blewitt M.E. (Cancer Res. 2013) 3
  5. Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway. (PMID: 23542155) Nozawa R.S. … Obuse C. (Nat. Struct. Mol. Biol. 2013) 3

Products for SMCHD1 Gene

Sources for SMCHD1 Gene

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