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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 3 4
  • Structural Maintenance Of Chromosomes Flexible Hinge Domain-Containing Protein 1 3
  • KIAA0650 4
  • FSHD2 3
  • BAMS 3

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 Bosma Arhinia Microphthalmia Syndrome and Facioscapulohumeral Muscular Dystrophy 2.

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 methyltransferase DNMT3B (By similarity). Required for DUX4 silencing in somatic cells (PubMed:23143600).

Additional gene information for SMCHD1 Gene

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

Genomics for SMCHD1 Gene

GeneHancer (GH) Regulatory Elements for SMCHD1 Gene

Promoters and enhancers for SMCHD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18J002653 Promoter/Enhancer 2.3 FANTOM5 Ensembl ENCODE dbSUPER 684.9 +1.0 1031 6.5 HDGF PKNOX1 CLOCK FOXA2 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 SMCHD1 CBX3P2 METTL4 EMILIN2 NDC80 ENSG00000266783 LPIN2 GC18M002508
GH18J002569 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 26.9 -83.8 -83804 4.1 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 METTL4 NDC80 SMCHD1 CBX3P2 KATNBL1P3 GC18M002508
GH18J003011 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 16.8 +358.8 358805 6.4 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF213 ZNF416 LPIN2 SMCHD1 METTL4 EMILIN2 CBX3P2 TGIF1 MYL12A GC18P003018
GH18J003245 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.1 +600.3 600343 22.1 CLOCK ZFP64 FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 E2F8 MYOM1 MYL12B MYL12A METTL4 CBX3P2 LOC104968399 LOC101927044 LPIN2 EMILIN2 SMCHD1
GH18J003591 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE dbSUPER 10.9 +940.3 940259 9.2 HDGF PKNOX1 SMAD1 FOXA2 MLX ARID4B SIN3A FEZF1 YY1 ZNF143 DLGAP1-AS2 TGIF1 DLGAP1-AS1 SMCHD1 CBX3P2 MYL12B DLGAP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMCHD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SMCHD1 gene promoter:
  • SRY
  • Pbx1a
  • AML1a
  • ISGF-3
  • C/EBPbeta
  • STAT1beta
  • STAT1alpha
  • STAT1
  • RREB-1

Genomic Locations for SMCHD1 Gene

Genomic Locations for SMCHD1 Gene
chr18:2,655,738-2,805,017
(GRCh38/hg38)
Size:
149,280 bases
Orientation:
Plus strand
chr18:2,655,737-2,805,015
(GRCh37/hg19)
Size:
149,279 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:
    • Active as a monomer.
    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

Post-translational modifications for SMCHD1 Gene

  • Sumoylated with SUMO1.
  • Ubiquitination at isoforms=1958, isoforms=2, 31802, isoforms=2, 31266, posLast=12561256, isoforms=21048, isoforms=2812, isoforms=2784, isoforms=2619, isoforms=2580, and posLast=192192
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SMCHD1 Gene

Domains & Families for SMCHD1 Gene

Gene Families for SMCHD1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SMCHD1 Gene

Suggested Antigen Peptide Sequences for SMCHD1 Gene

Graphical View of Domain Structure for InterPro Entry

A6NHR9

UniProtKB/Swiss-Prot:

SMHD1_HUMAN :
  • The ATPase activity domain is probably necessary for its engagement with chromatin (By similarity).
Domain:
  • The ATPase activity domain is probably necessary for its engagement with chromatin (By similarity).
genes like me logo Genes that share domains with SMCHD1: view

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 methyltransferase DNMT3B (By similarity). Required for DUX4 silencing in somatic cells (PubMed:23143600).

Phenotypes From GWAS Catalog for SMCHD1 Gene

Gene Ontology (GO) - Molecular Function for SMCHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0005524 ATP binding IEA --
GO:0016887 ATPase activity ISS,IEA --
genes like me logo Genes that share ontologies with SMCHD1: view
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

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMCHD1 gene
Compartment Confidence
nucleus 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SMCHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000784 colocalizes_with nuclear chromosome, telomeric region IDA 24270157
GO:0001740 Barr body IEA --
GO:0005694 chromosome 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:0043584 nose development IMP 28067909
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 and SIGNOR curated interactions for SMCHD1 Gene

Drugs & Compounds for SMCHD1 Gene

No Compound Related Data Available

Transcripts for SMCHD1 Gene

mRNA/cDNA for SMCHD1 Gene

(4) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(17) Selected AceView cDNA sequences:
(15) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SMCHD1 Gene

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

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for SMCHD1 Gene



Protein tissue co-expression partners for SMCHD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SMCHD1 Gene:

SMCHD1

SOURCE GeneReport for Unigene cluster for SMCHD1 Gene:

Hs.8118

Evidence on tissue expression from TISSUES for SMCHD1 Gene

  • Eye(4.5)
  • Nervous system(4.3)
  • Blood(3.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SMCHD1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • eyelid
  • face
  • head
  • mouth
  • tongue
Thorax:
  • clavicle
  • lung
  • scapula
Abdomen:
  • abdominal wall
Pelvis:
  • pelvis
Limb:
  • arm
  • humerus
  • lower limb
  • shin
  • shoulder
  • upper limb
General:
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SMCHD1: view

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 34 33
  • 99.58 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SMCHD1 34 33
  • 93.35 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SMCHD1 34 33
  • 91.57 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMCHD1 34
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smchd1 33
  • 86.4 (n)
mouse
(Mus musculus)
Mammalia Smchd1 16 34 33
  • 85.99 (n)
oppossum
(Monodelphis domestica)
Mammalia SMCHD1 34
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMCHD1 34 33
  • 76.08 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 72 (a)
OneToMany
-- 34
  • 61 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia smchd1 33
  • 67.61 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC570784 33
  • 57.45 (n)
smchd1 34
  • 41 (a)
OneToMany
SMCHD1 (2 of 2) 34
  • 39 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 45 (a)
OneToMany
-- 34
  • 38 (a)
OneToMany
Species where no ortholog for SMCHD1 was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SMCHD1: view image

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 Variation AA Info Type
rs1057519614 pathogenic, Facioscapulohumeral muscular dystrophy 2 2,700,877(+) AAA/AA coding_sequence_variant, frameshift, non_coding_transcript_variant
rs1057519639 pathogenic, Arhinia choanal atresia microphthalmia, Anosmia 2,694,687(+) A/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1057519640 pathogenic, Arhinia choanal atresia microphthalmia 2,697,034(+) A/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1057519641 pathogenic, Arhinia choanal atresia microphthalmia 2,667,030(+) G/A/C/T 5_prime_UTR_variant, coding_sequence_variant, missense_variant, non_coding_transcript_variant, synonymous_variant
rs1057519642 pathogenic, Arhinia choanal atresia microphthalmia, Anosmia, Short nose 2,697,898(+) A/T coding_sequence_variant, missense_variant, non_coding_transcript_variant

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

Variant ID Type Subtype PubMed ID
dgv3314n100 CNV loss 25217958
dgv596e214 CNV loss 21293372
esv2677635 CNV deletion 23128226
esv2716680 CNV deletion 23290073
esv2761986 CNV gain 21179565
esv3641565 CNV loss 21293372
esv3641566 CNV gain 21293372
esv3641567 CNV loss 21293372
esv3641568 CNV gain 21293372
esv3641569 CNV gain 21293372
esv3641570 CNV loss 21293372
esv3641572 CNV gain 21293372
esv3893063 CNV loss 25118596
nsv1063715 CNV loss 25217958
nsv1065848 CNV gain 25217958
nsv1116247 CNV deletion 24896259
nsv1138592 CNV deletion 24896259
nsv1138593 CNV deletion 24896259
nsv1138594 CNV deletion 24896259
nsv482935 CNV loss 15286789
nsv576251 CNV gain 21841781

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)

Additional Variant Information for SMCHD1 Gene

Human Gene Mutation Database (HGMD)
SMCHD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMCHD1

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

Disorders for SMCHD1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for SMCHD1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- 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, ECO:0000269 PubMed:24075187, ECO:0000269 PubMed:25256356, ECO:0000269 PubMed:27059856, ECO:0000269 PubMed:28067911}. 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 (PubMed:23143600). FSHD2 and FSHD1 share a common pathophysiological pathway in which the FSHD2 gene SMCHD1 can act as a modifier for disease severity in families affected by FSHD1 (PubMed:24075187).
  • Bosma arhinia microphthalmia syndrome (BAMS) [MIM:603457]: An autosomal dominant syndrome characterized by severe hypoplasia of the nose, palatal abnormalities, hypoplasia of the eyes, sensory abnormalities of taste and smell, hypogonadotropic hypogonadism with cryptorchidism, and normal intelligence. {ECO:0000269 PubMed:28067909, ECO:0000269 PubMed:28067911}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SMCHD1

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

No data available for Genatlas for SMCHD1 Gene

Publications for SMCHD1 Gene

  1. The FSHD2 gene SMCHD1 is a modifier of disease severity in families affected by FSHD1. (PMID: 24075187) Sacconi S … van der Maarel SM (American journal of human genetics 2013) 2 3 4 58
  2. De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome and abrogate nasal development. (PMID: 28067911) Gordon CT … Reversade B (Nature genetics 2017) 3 4 58
  3. SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome. (PMID: 28067909) Shaw ND … Talkowski ME (Nature genetics 2017) 3 4 58
  4. Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2. (PMID: 23143600) Lemmers RJ … van der Maarel SM (Nature genetics 2012) 3 4 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for SMCHD1 Gene

Sources for SMCHD1 Gene

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