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    MSX1 msh homeobox 1 [ Homo sapiens (human) ]

    Gene ID: 4487, updated on 17-Jun-2024

    Summary

    Official Symbol
    MSX1provided by HGNC
    Official Full Name
    msh homeobox 1provided by HGNC
    Primary source
    HGNC:HGNC:7391
    See related
    Ensembl:ENSG00000163132 MIM:142983; AllianceGenome:HGNC:7391
    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
    HOX7; HYD1; ECTD3; STHAG1
    Summary
    This gene encodes a member of the muscle segment homeobox gene family. The encoded protein functions as a transcriptional repressor during embryogenesis through interactions with components of the core transcription complex and other homeoproteins. It may also have roles in limb-pattern formation, craniofacial development, particularly odontogenesis, and tumor growth inhibition. Mutations in this gene, which was once known as homeobox 7, have been associated with nonsyndromic cleft lip with or without cleft palate 5, Witkop syndrome, Wolf-Hirschom syndrome, and autosomoal dominant hypodontia. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in endometrium (RPKM 10.8), fat (RPKM 4.4) and 8 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See MSX1 in Genome Data Viewer
    Location:
    4p16.2
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (4859665..4863936)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (4829290..4833545)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (4861392..4865663)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900165 Neighboring gene uncharacterized LOC101928279 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:4764243-4765442 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:4782258-4783457 Neighboring gene Sharpr-MPRA regulatory region 11147 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4853897-4854854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4854855-4855811 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15217 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:4864037-4864708 Neighboring gene long intergenic non-protein coding RNA 1396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:4866226-4867143 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:4872827-4873402 Neighboring gene Sharpr-MPRA regulatory region 11527 Neighboring gene uncharacterized LOC101928306 Neighboring gene lactate dehydrogenase A pseudogene 1 Neighboring gene RN7SK pseudogene 113

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Hypoplastic enamel-onycholysis-hypohidrosis syndrome
    MedGen: C0406735 OMIM: 189500 GeneReviews: Not available
    Compare labs
    Orofacial cleft 5
    MedGen: C1837210 OMIM: 608874 GeneReviews: Not available
    Compare labs
    Tooth agenesis, selective, 1 Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-01-12)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-01-12)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae.
    EBI GWAS Catalog
    Genome-wide association study of multiple congenital heart disease phenotypes identifies a susceptibility locus for atrial septal defect at chromosome 4p16.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in activation of meiosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in anterior/posterior pattern specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in bone morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cardiac conduction system development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in cartilage morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell morphogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell surface receptor signaling pathway involved in heart development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic forelimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic hindlimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in embryonic nail plate morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in epithelial to mesenchymal transition involved in endocardial cushion formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in face morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in forebrain development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inner ear development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mammary gland epithelium development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mesenchymal cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mesenchymal cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in midbrain development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in middle ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in muscle organ development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cell growth IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of negative regulation of gene expression ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of odontoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of striated muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in nose development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in odontogenesis of dentin-containing tooth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA damage response, signal transduction by p53 class mediator IC
    Inferred by Curator
    more info
    PubMed 
    involved_in positive regulation of cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of mesenchymal cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of odontogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein localization to nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein stabilization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of odontogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in roof of mouth development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in signal transduction involved in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stem cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    is_active_in nuclear periphery ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nuclear periphery ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    homeobox protein MSX-1
    Names
    homeobox 7
    homeobox protein Hox-7
    msh homeo box 1
    msh homeobox 1-like protein
    msh homeobox homolog 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_008121.1 RefSeqGene

      Range
      5001..9272
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1342

    mRNA and Protein(s)

    1. NM_002448.3NP_002439.2  homeobox protein MSX-1

      See identical proteins and their annotated locations for NP_002439.2

      Status: REVIEWED

      Source sequence(s)
      AC092437, AU117561, BC067353
      Consensus CDS
      CCDS3378.2
      UniProtKB/Swiss-Prot
      A0SZU5, A8K3M1, P28360, Q96NY4
      Related
      ENSP00000372170.4, ENST00000382723.5
      Conserved Domains (2) summary
      PTZ00449
      Location:105248
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      pfam00046
      Location:175229
      Homeobox; Homeobox domain

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      4859665..4863936
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      4829290..4833545
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)