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SMCHD1 structural maintenance of chromosomes flexible hinge domain containing 1 [ Homo sapiens (human) ]

Gene ID: 23347, updated on 11-Apr-2024

Summary

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Official Symbol
SMCHD1provided by HGNC
Official Full Name
structural maintenance of chromosomes flexible hinge domain containing 1provided by HGNC
Primary source
HGNC:HGNC:29090
See related
Ensembl:ENSG00000101596 MIM:614982; AllianceGenome:HGNC:29090
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BAMS; FSHD2
Summary
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]
Expression
Ubiquitous expression in lymph node (RPKM 16.1), bone marrow (RPKM 16.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
18p11.32
Exon count:
51
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (2655726..2805017)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (2811308..2960649)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (2655725..2805015)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:2653904-2654533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9247 Neighboring gene Sharpr-MPRA regulatory region 12050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13027 Neighboring gene RNA, U6 small nuclear 340, pseudogene Neighboring gene CBX3 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:2716737-2717237 Neighboring gene uncharacterized LOC124904372 Neighboring gene Sharpr-MPRA regulatory region 3375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9249 Neighboring gene Sharpr-MPRA regulatory region 4434 Neighboring gene elastin microfibril interfacer 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:2919273-2920004 Neighboring gene lipin 2 Neighboring gene CHORDC1 pseudogene 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Nasal Construction in Congenital Arhinia Due to Novel SMCHD1 Gene Variant. Bargiela M, et al. J Craniofac Surg, 2023 May 1. PMID 36944600,
  2. Cross-sectional Neuromuscular Phenotyping Study of Patients With Arhinia With SMCHD1 Variants. Mohassel P, et al. Neurology, 2022 Mar 29. PMID 35121673, Free PMC Article
  3. A novel start codon variant in SMCHD1 from a Chinese family causes facioscapulohumeral muscular dystrophy type 2. Qiu LL, et al. Chin Med J (Engl), 2021 Mar 23. PMID 34845997, Free PMC Article
  4. SMCHD1's ubiquitin-like domain is required for N-terminal dimerization and chromatin localization. Gurzau AD, et al. Biochem J, 2021 Jul 16. PMID 34109974, Free PMC Article
  5. Relating SMCHD1 structure to its function in epigenetic silencing. Gurzau AD, et al. Biochem Soc Trans, 2020 Aug 28. PMID 32779700, Free PMC Article

See all (151) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. In skeletal muscle and neural crest cells, SMCHD1 regulates biological pathways relevant for Bosma syndrome and facioscapulohumeral dystrophy phenotype.
    Title: In skeletal muscle and neural crest cells, SMCHD1 regulates biological pathways relevant for Bosma syndrome and facioscapulohumeral dystrophy phenotype.
  2. SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action.
    Title: SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action.
  3. Nasal Construction in Congenital Arhinia Due to Novel SMCHD1 Gene Variant.
    Title: Nasal Construction in Congenital Arhinia Due to Novel SMCHD1 Gene Variant.
  4. DUX4 double whammy: The transcription factor that causes a rare muscular dystrophy also kills the precursors of the human nose.
    Title: DUX4 double whammy: The transcription factor that causes a rare muscular dystrophy also kills the precursors of the human nose.
  5. Cross-sectional Neuromuscular Phenotyping Study of Patients With Arhinia With SMCHD1 Variants.
    Title: Cross-sectional Neuromuscular Phenotyping Study of Patients With Arhinia With SMCHD1 Variants.
  6. A novel start codon variant in SMCHD1 from a Chinese family causes facioscapulohumeral muscular dystrophy type 2.
    Title: A novel start codon variant in SMCHD1 from a Chinese family causes facioscapulohumeral muscular dystrophy type 2.
  7. A proteomics study identifying interactors of the FSHD2 gene product SMCHD1 reveals RUVBL1-dependent DUX4 repression.
    Title: A proteomics study identifying interactors of the FSHD2 gene product SMCHD1 reveals RUVBL1-dependent DUX4 repression.
  8. SMCHD1's ubiquitin-like domain is required for N-terminal dimerization and chromatin localization.
    Title: SMCHD1's ubiquitin-like domain is required for N-terminal dimerization and chromatin localization.
  9. Relating SMCHD1 structure to its function in epigenetic silencing.
    Title: Relating SMCHD1 structure to its function in epigenetic silencing.
  10. A Three Protein-Coding Gene Prognostic Model Predicts Overall Survival in Bladder Cancer Patients.
    Title: A Three Protein-Coding Gene Prognostic Model Predicts Overall Survival in Bladder Cancer Patients.
Submit: New GeneRIF Correction See all GeneRIFs (46)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of maternal and inherited loci for conotruncal heart defects.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0650, DKFZp686O0631

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in chromosome organization IEA
Inferred from Electronic Annotation
more info
  
involved_in dosage compensation by inactivation of X chromosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in double-strand break repair IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nose development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of DNA repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in Barr body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Barr body IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
structural maintenance of chromosomes flexible hinge domain-containing protein 1
Names
SMC hinge domain-containing protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_031972.2 RefSeqGene

    Range
    5002..154293
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_015295.3 → NP_056110.2  structural maintenance of chromosomes flexible hinge domain-containing protein 1

    See identical proteins and their annotated locations for NP_056110.2

    Status: REVIEWED

    Source sequence(s)
    AB014550, AI904018, AP001011, AP005061, AW503637, BC006008, BP872870, BU153211, BU509173, DA283721, DA675822, DB071574, DN913642
    Consensus CDS
    CCDS45822.1
    UniProtKB/Swiss-Prot
    A6NHR9, O75141, Q6AHX6, Q6ZTQ8, Q9H6Q2, Q9UG39
    UniProtKB/TrEMBL
    A0A8I5KRS9
    Related
    ENSP00000326603.7, ENST00000320876.11
    Conserved Domains (3) summary
    smart00968
    Location:1720 → 1846
    SMC_hinge; SMC proteins Flexible Hinge Domain
    pfam15898
    Location:1640 → 1703
    PRKG1_interact; cGMP-dependent protein kinase interacting domain
    cl00075
    Location:143 → 275
    HATPase_c; Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    2655726..2805017
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011525642.2 → XP_011523944.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A8I5KRS9
    Conserved Domains (3) summary
    smart00968
    Location:1720 → 1846
    SMC_hinge; SMC proteins Flexible Hinge Domain
    pfam15898
    Location:1640 → 1703
    PRKG1_interact; cGMP-dependent protein kinase interacting domain
    cl00075
    Location:143 → 275
    HATPase_c; Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins

  2. XM_047437427.1 → XP_047293383.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X4

  3. XM_047437426.1 → XP_047293382.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X3

  4. XM_047437428.1 → XP_047293384.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X5

  5. XM_047437429.1 → XP_047293385.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X6

  6. XM_047437425.1 → XP_047293381.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X2

RNA

  1. XR_001753172.2 RNA Sequence

  2. XR_935055.3 RNA Sequence

  3. XR_007066135.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    2811308..2960649
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054318425.1 → XP_054174400.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X1

  2. XM_054318428.1 → XP_054174403.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X4

  3. XM_054318427.1 → XP_054174402.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X3

  4. XM_054318429.1 → XP_054174404.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X5

  5. XM_054318430.1 → XP_054174405.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X6

  6. XM_054318426.1 → XP_054174401.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X2

RNA

  1. XR_008484992.1 RNA Sequence

  2. XR_008484994.1 RNA Sequence

  3. XR_008484993.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A6NHR9.2 GenPept UniProtKB/Swiss-Prot:A6NHR9

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