Aliases for SMCHD1 Gene
Aliases for SMCHD1 Gene
External Ids for SMCHD1 Gene
- HGNC: 29090
- Entrez Gene: 23347
- Ensembl: ENSG00000101596
- OMIM: 614982
- UniProtKB: A6NHR9
Summaries 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
-
Non-canonical member of the structural maintenance of chromosomes (SMC) protein family that plays a key role in epigenetic silencing by regulating chromatin architecture (By similarity). Promotes heterochromatin formation in both autosomes and chromosome X, probably by mediating the merge of chromatin compartments (By similarity). Plays a key role in chromosome X inactivation in females by promoting the spreading of heterochromatin (PubMed:23542155). Recruited to inactivated chromosome X by Xist RNA and acts by mediating the merge of chromatin compartments: promotes random chromatin interactions that span the boundaries of existing structures, leading to create a compartment-less architecture typical of inactivated chromosome X (By similarity). Required to facilitate Xist RNA spreading (By similarity). Also required for silencing of a subset of clustered autosomal loci in somatic cells, such as the DUX4 locus (PubMed:23143600). Has ATPase activity; may participate in structural manipulation of chromatin in an ATP-dependent manner as part of its role in gene expression regulation (PubMed:29748383). Also plays a role in DNA repair: localizes to sites of DNA double-strand breaks in response to DNA damage to promote the repair of DNA double-strand breaks (PubMed:25294876, PubMed:24790221). Acts by promoting non-homologous end joining (NHEJ) and inhibiting homologous recombination (HR) repair (PubMed:25294876).
Additional gene information for SMCHD1 Gene
- Monarch Initiative
- Search for SMCHD1 at DataMed
- Search for SMCHD1 at HumanCyc
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
- 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:
-
- AML1a
- C/EBPbeta
- ISGF-3
- Pbx1a
- RREB-1
- SRY
- STAT1
- STAT1alpha
- STAT1beta
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:
-
- 18p11.32 by HGNC
- 18p11.32 by Entrez Gene
- 18p11.32 by Ensembl
SMCHD1 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene 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
- O75141
- Q6AHX6
- Q6ZTQ8
- Q9H6Q2
- Q9UG39
Protein attributes for SMCHD1 Gene
- Size:
- 2005 amino acids
- Molecular mass:
- 226374 Da
- Quaternary structure:
-
- Homodimer; homodimerizes via its SMC hinge domain (By similarity). Interacts with LRIF1 (PubMed:23542155).
- 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};
Protein Expression for SMCHD1 Gene
Post-translational modifications for SMCHD1 Gene
- Sumoylated with SUMO1.
- Ubiquitination at posLast=10481048, posLast=12561256, Lys812, Lys619, Lys1958, Lys192, Lys1266, Lys580, Lys1802, and Lys784
- Modification sites at PhosphoSitePlus
Other Protein References for SMCHD1 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
- Novus Biologicals Antibodies for SMCHD1
-
Abcam antibodies for SMCHD1
- Invitrogen Antibodies for SMCHD1 (AFLGC-SMCHD1)
Protein Products
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for SMCHD1
- Origene Custom Protein Services for SMCHD1
- Novus Biologicals proteins for SMCHD1
-
Abcam proteins for SMCHD1
Assay Products
- antibodies-online: Search results for 2 available SMCHD1 Elisa Kits ranked by validation data
- Compare Top SMCHD1 Elisa Kits
-
Quality Products:
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
- InterPro:
- ProtoNet:
Suggested Antigen Peptide Sequences for SMCHD1 Gene
- GenScript: Design optimal peptide antigens:
-
- Structural maintenance of chromosomes flexible hinge domain-containing protein 1 (SMHD1_HUMAN)
Graphical View of Domain Structure for InterPro Entry
A6NHR9UniProtKB/Swiss-Prot:
SMHD1_HUMAN :- Atypical member of the structural maintenance of chromosomes (SMC) protein family. Like other members of the SMC family, has ATPase activity, which is probably necessary for its engagement with chromatin, and a SMC hinge domain. However, the SMC hinge domain adopts an unconventional homodimeric arrangement augmented by an intermolecular coiled coil formed between the two monomers. This suggests that protein may assemble as a head-to-head parallel dimer without adopting a hairpin shape at the hinge domain, unlike the dimeric arrangement conventionally found in other members of the SMC protein family. The SMC hinge domain binds DNA and RNA.
- Belongs to the SMC family. Highly divergent.
- Domain:
-
- Atypical member of the structural maintenance of chromosomes (SMC) protein family. Like other members of the SMC family, has ATPase activity, which is probably necessary for its engagement with chromatin, and a SMC hinge domain. However, the SMC hinge domain adopts an unconventional homodimeric arrangement augmented by an intermolecular coiled coil formed between the two monomers. This suggests that protein may assemble as a head-to-head parallel dimer without adopting a hairpin shape at the hinge domain, unlike the dimeric arrangement conventionally found in other members of the SMC protein family. The SMC hinge domain binds DNA and RNA.
- Family:
-
- Belongs to the SMC family. Highly divergent.
Function for SMCHD1 Gene
Molecular function for SMCHD1 Gene
- UniProtKB/Swiss-Prot Function:
- Non-canonical member of the structural maintenance of chromosomes (SMC) protein family that plays a key role in epigenetic silencing by regulating chromatin architecture (By similarity). Promotes heterochromatin formation in both autosomes and chromosome X, probably by mediating the merge of chromatin compartments (By similarity). Plays a key role in chromosome X inactivation in females by promoting the spreading of heterochromatin (PubMed:23542155). Recruited to inactivated chromosome X by Xist RNA and acts by mediating the merge of chromatin compartments: promotes random chromatin interactions that span the boundaries of existing structures, leading to create a compartment-less architecture typical of inactivated chromosome X (By similarity). Required to facilitate Xist RNA spreading (By similarity). Also required for silencing of a subset of clustered autosomal loci in somatic cells, such as the DUX4 locus (PubMed:23143600). Has ATPase activity; may participate in structural manipulation of chromatin in an ATP-dependent manner as part of its role in gene expression regulation (PubMed:29748383). Also plays a role in DNA repair: localizes to sites of DNA double-strand breaks in response to DNA damage to promote the repair of DNA double-strand breaks (PubMed:25294876, PubMed:24790221). Acts by promoting non-homologous end joining (NHEJ) and inhibiting homologous recombination (HR) repair (PubMed:25294876).
- UniProtKB/Swiss-Prot CatalyticActivity:
- ATP + H(2)O = ADP + phosphate.
Enzyme Numbers (IUBMB) for SMCHD1 Gene
Phenotypes From GWAS Catalog for SMCHD1 Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0003677 | DNA binding | IEA | -- |
| GO:0005515 | protein binding | IPI | 23542155 |
| GO:0005524 | ATP binding | IEA | -- |
| GO:0016787 | hydrolase activity | IEA | -- |
| GO:0016887 | ATPase activity | IEA,ISS | -- |
Phenotypes for SMCHD1 Gene
- MGI mutant phenotypes for SMCHD1:
- inferred from 2 alleles
- GenomeRNAi human phenotypes for SMCHD1:
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
- Cyagen custom Knockout/knockin (KOKI) mouse models for SMCHD1
-
CRISPR Products
-
OriGene CRISPR knockouts for SMCHD1
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for SMCHD1
- genomics-online: gRNA clones - Search results for 55 available SMCHD1 gene related products
- Overview of 55 available SMCHD1 gene related products
- Applied Biological Materials (abm): CRISPR Clones for SMCHD1 - Now 50% OFF >
- * SMCHD1 CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
- * SMCHD1 CRISPR applications: KO, Activation, Repression, and more - Browse All
-
Santa Cruz Biotechnology (SCBT) CRISPR for SMCHD1
miRNA for SMCHD1 Gene
- miRTarBase miRNAs that target SMCHD1
-
- hsa-mir-210-3p (MIRT003173)
- hsa-mir-132-3p (MIRT021727)
- hsa-mir-128-3p (MIRT021952)
- hsa-mir-181a-5p (MIRT025085)
- hsa-mir-877-5p (MIRT037356)
- hsa-mir-421 (MIRT039446)
- hsa-mir-149-5p (MIRT045406)
- hsa-mir-221-3p (MIRT046851)
- hsa-mir-10b-5p (MIRT047425)
- hsa-mir-10a-5p (MIRT047549)
- hsa-mir-100-5p (MIRT048562)
- hsa-mir-30a-5p (MIRT049938)
- hsa-mir-18a-5p (MIRT050718)
- hsa-mir-6768-5p (MIRT148257)
- hsa-mir-1277-5p (MIRT615832)
- hsa-mir-4789-5p (MIRT615833)
- hsa-mir-3941 (MIRT615834)
- hsa-mir-5011-5p (MIRT615835)
- hsa-mir-603 (MIRT615836)
- hsa-mir-362-3p (MIRT615837)
- hsa-mir-329-3p (MIRT615838)
- hsa-mir-8485 (MIRT615839)
- hsa-mir-1264 (MIRT615840)
- hsa-mir-3184-3p (MIRT615841)
- hsa-mir-510-3p (MIRT653358)
- hsa-mir-203a-3p (MIRT653359)
- hsa-mir-190a-3p (MIRT784007)
miRNA Products
Inhibitory RNA Products
- Origene sirna, shrna, and RNAi products in human, mouse, rat for SMCHD1
- Browse OriGene Inhibitory RNA Products For SMCHD1
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMCHD1
- genomics-online: shRNA clones - Search results for 55 available SMCHD1 gene related products
- Overview of 55 available SMCHD1 gene related products
Clone Products
- Applied Biological Materials (abm): Clones for SMCHD1 - Now 50% OFF >
- * SMCHD1 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
- * SMCHD1 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All
- Sino Biological Human cDNA Clone for SMCHD1
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SMCHD1
Cell Line Products
-
Horizon Cell Lines for SMCHD1
No data available for 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=Recruited to inactivated chromosome X in females by Xist RNA (By similarity). Localizes at sites of DNA damage at double-strand breaks (DSBs) (PubMed:25294876, PubMed:24790221). {ECO:0000250 UniProtKB:Q6P5D8, ECO:0000269 PubMed:24790221, ECO:0000269 PubMed:25294876}.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
- Nuclear bodies (2)
- Nucleoplasm (2)
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0000784 | colocalizes_with nuclear chromosome, telomeric region | IDA | 24270157 |
| GO:0001740 | Barr body | IDA | 23542155 |
| GO:0005694 | chromosome | IEA | -- |
| GO:0035861 | site of double-strand break | IDA | 24790221 |
Pathways & Interactions for SMCHD1 Gene
No Data Available
Interacting Proteins for SMCHD1 Gene
Selected Interacting proteins:
A6NHR9-SMHD1_HUMAN
ENSP00000326603
for SMCHD1 Gene via
MINT
STRING
IID
GPS-Prot Interaction Network for SMCHD1
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0006281 | DNA repair | IEA | -- |
| GO:0006302 | double-strand break repair | IEA | -- |
| GO:0006325 | chromatin organization | IEA | -- |
| GO:0006974 | cellular response to DNA damage stimulus | IEA | -- |
| GO:0009048 | dosage compensation by inactivation of X chromosome | IDA | 23542155 |
No data available for Pathways by source and SIGNOR curated interactions for SMCHD1 Gene
Transcripts for SMCHD1 Gene
mRNA/cDNA for SMCHD1 Gene
- (1) REFSEQ mRNAs :
- (16) Additional mRNA sequences :
- (194) Selected AceView cDNA sequences:
- (15) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
-
- ENST00000320876 8821 bps (uc002klm.5)
- ENST00000581226 459 bps (uc060mwb.1)
- ENST00000585229 555 bps (uc060mwc.1)
- ENST00000577880 4951 bps (uc060mwd.1)
- ENST00000577300 506 bps (uc060mwe.1)
Unigene Clusters for SMCHD1 Gene
CRISPR Products
-
OriGene CRISPR knockouts for SMCHD1
- Search GeneCopoeia for CRISPR/Cas9 clones, lentivirus and AAV products for SMCHD1
- genomics-online: gRNA clones - Search results for 55 available SMCHD1 gene related products
- Overview of 55 available SMCHD1 gene related products
- Applied Biological Materials (abm): CRISPR Clones for SMCHD1 - Now 50% OFF >
- * SMCHD1 CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
- * SMCHD1 CRISPR applications: KO, Activation, Repression, and more - Browse All
-
Santa Cruz Biotechnology (SCBT) CRISPR for SMCHD1
miRNA Products
Inhibitory RNA Products
- Origene sirna, shrna, and RNAi products in human, mouse, rat for SMCHD1
- Browse OriGene Inhibitory RNA Products For SMCHD1
- Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMCHD1
- genomics-online: shRNA clones - Search results for 55 available SMCHD1 gene related products
- Overview of 55 available SMCHD1 gene related products
Clone Products
- Applied Biological Materials (abm): Clones for SMCHD1 - Now 50% OFF >
- * SMCHD1 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
- * SMCHD1 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All
- Sino Biological Human cDNA Clone for SMCHD1
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles and/or promoter clone products for SMCHD1
| 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: |
Expression for SMCHD1 Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
-
Intermediate Mesoderm (Gastrulation Derivatives)
- Mesonephric cells Mesonephros
- Mesonephros
-
Blood (Hematopoietic System)
- Granulocytes Peripheral Blood
-
Gonad
- Mesonephric cells Mesonephros
- Bone (Muscoskeletal System)
-
Testis (Reproductive System)
mRNA differential expression in normal tissues according to GTEx for SMCHD1 Gene
This gene is overexpressed in Whole Blood (x5.9).
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
- Elite partner
NURSA nuclear receptor signaling pathways regulating expression of SMCHD1 Gene:
SMCHD1SOURCE GeneReport for Unigene cluster for SMCHD1 Gene:
Hs.8118Evidence 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
Primer Products
-
OriGene qPCR primer pairs for SMCHD1
- genomics-online: primer clones - Search results for 55 available SMCHD1 gene related products
- Overview of 55 available SMCHD1 gene related products
Gene Expression 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.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | SMCHD1 35 34 |
|
OneToOne | |
| dog (Canis familiaris) |
Mammalia | SMCHD1 35 34 |
|
OneToOne | |
| cow (Bos Taurus) |
Mammalia | SMCHD1 35 34 |
|
OneToOne | |
| platypus (Ornithorhynchus anatinus) |
Mammalia | SMCHD1 35 |
|
OneToOne | |
| rat (Rattus norvegicus) |
Mammalia | Smchd1 34 |
|
||
| mouse (Mus musculus) |
Mammalia | Smchd1 17 35 34 |
|
||
| oppossum (Monodelphis domestica) |
Mammalia | SMCHD1 35 |
|
OneToOne | |
| chicken (Gallus gallus) |
Aves | SMCHD1 35 34 |
|
OneToOne | |
| lizard (Anolis carolinensis) |
Reptilia | -- 35 |
|
OneToMany | |
| -- 35 |
|
OneToMany | |||
| tropical clawed frog (Silurana tropicalis) |
Amphibia | smchd1 34 |
|
||
| zebrafish (Danio rerio) |
Actinopterygii | LOC570784 34 |
|
||
| smchd1 35 |
|
OneToMany | |||
| SMCHD1 (2 of 2) 35 |
|
OneToMany | |||
| sea squirt (Ciona savignyi) |
Ascidiacea | -- 35 |
|
OneToMany | |
| -- 35 |
|
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
| 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, Bosma arhinia microphthalmia syndrome (BAMS) [MIM:603457] | 2,694,687(+) | A/G | coding_sequence_variant, missense_variant, non_coding_transcript_variant | |
| rs1057519640 | pathogenic, Arhinia choanal atresia microphthalmia, Bosma arhinia microphthalmia syndrome (BAMS) [MIM:603457] | 2,697,034(+) | A/G | coding_sequence_variant, missense_variant, non_coding_transcript_variant | |
| rs1057519641 | pathogenic, Arhinia choanal atresia microphthalmia, Bosma arhinia microphthalmia syndrome (BAMS) [MIM:603457] | 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, Bosma arhinia microphthalmia syndrome (BAMS) [MIM:603457] | 2,697,898(+) | A/T | coding_sequence_variant, missense_variant, non_coding_transcript_variant |
| 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 |
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
SNP Genotyping and Copy Number Assay Products
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMCHD1 Gene
Disorders for SMCHD1 Gene
(12) MalaCards diseases for SMCHD1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| bosma arhinia microphthalmia syndrome |
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| facioscapulohumeral muscular dystrophy 2 |
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| arhinia choanal atresia microphthalmia |
|
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| anosmia |
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| cryptorchidism, unilateral or bilateral |
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|
Search SMCHD1 in MalaCards
View complete list of genes associated with diseases
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:24128691, ECO:0000269 PubMed:25256356, ECO:0000269 PubMed:25370034, ECO:0000269 PubMed:27059856, ECO:0000269 PubMed:28067911, ECO:0000269 PubMed:29748383}. 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 (PubMed:23143600). 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, PubMed:25370034). {ECO:0000269 PubMed:23143600, ECO:0000269 PubMed:24075187, ECO:0000269 PubMed:25370034}.
- 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, ECO:0000269 PubMed:29748383}. 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
No data available for Genatlas for SMCHD1 Gene
Publications for SMCHD1 Gene
- 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
- 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
- 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
- Diagnostic approach for FSHD revisited: SMCHD1 mutations cause FSHD2 and act as modifiers of disease severity in FSHD1. (PMID: 25370034) Larsen M … Müller CR (European journal of human genetics : EJHG 2015) 3 4 58
- SMCHD1 accumulates at DNA damage sites and facilitates the repair of DNA double-strand breaks. (PMID: 24790221) Coker H … Brockdorff N (Journal of cell science 2014) 3 4 58
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Sources for SMCHD1 Gene
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