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

    Gene ID: 23347, updated on 2-Nov-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
    mouse all
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    Genomic context

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    See SMCHD1 in Genome Data Viewer
    Location:
    18p11.32
    Exon count:
    51
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (2655726..2805017)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (2811308..2960649)
    RS_2024_09 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 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. Different clinicopathological features between Japanese siblings with facioscapulohumeral muscular dystrophy 2 with a novel nonsense SMCHD1 mutation (Arg552(∗)). Ohta Y, et al. J Clin Neurosci, 2018 Dec. PMID 30327220
    2. Remotely acting SMCHD1 gene regulatory elements: in silico prediction and identification of potential regulatory variants in patients with FSHD. Mayes MB, et al. Hum Genomics, 2015 Oct 7. PMID 26446085, Free PMC Article
    3. Clinical, muscle pathological, and genetic features of Japanese facioscapulohumeral muscular dystrophy 2 (FSHD2) patients with SMCHD1 mutations. Hamanaka K, et al. Neuromuscul Disord, 2016 Apr-May. PMID 27061275
    4. Many faces of SMCHD1. Wilkie AO. Nat Genet, 2017 Jan 31. PMID 28138148
    5. The Epigenetic Regulator SMCHD1 in Development and Disease. Jansz N, et al. Trends Genet, 2017 Apr. PMID 28222895

    See all (169) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMCHD1 activates the expression of genes required for the expansion of human myoblasts.
      Title: SMCHD1 activates the expression of genes required for the expansion of human myoblasts.
    2. DNMT3B splicing dysregulation mediated by SMCHD1 loss contributes to DUX4 overexpression and FSHD pathogenesis.
      Title: DNMT3B splicing dysregulation mediated by SMCHD1 loss contributes to DUX4 overexpression and FSHD pathogenesis.
    3. 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.
    4. 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.
    5. Nasal Construction in Congenital Arhinia Due to Novel SMCHD1 Gene Variant.
      Title: Nasal Construction in Congenital Arhinia Due to Novel SMCHD1 Gene Variant.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (48)

    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

    Associated conditions

    Description Tests
    Arrhinia with choanal atresia and microphthalmia syndrome
    MedGen: C1863878 OMIM: 603457 GeneReviews: Not available
    		not available
    Facioscapulohumeral muscular dystrophy 2
    MedGen: C1834671 OMIM: 158901 GeneReviews: Facioscapulohumeral Muscular Dystrophy
    		not available

    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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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