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MSX1 msh homeobox 1 [ Homo sapiens (human) ]

Gene ID: 4487, updated on 11-Jun-2025
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
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See MSX1 in Genome Data Viewer
Location:
4p16.2
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (4859665..4863936)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (4829290..4833545)
RS_2024_09 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

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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
Products Interactant Other Gene Complex Source Pubs Description

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables p53 binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to transcription cis-regulatory region binding IEA
Inferred from Electronic Annotation
more info
 
enables transcription cis-regulatory region binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within BMP signaling pathway IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within activation of meiosis IEA
Inferred from Electronic Annotation
more info
 
involved_in animal organ morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within anterior/posterior pattern specification IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within 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 development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cartilage morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in cell morphogenesis IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within cell surface receptor signaling pathway involved in heart development IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to nicotine IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic digit morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic hindlimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within embryonic limb 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 IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic nail plate morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in epithelial to mesenchymal transition IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within epithelial to mesenchymal transition involved in endocardial cushion formation IEA
Inferred from Electronic Annotation
more info
 
involved_in face morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in face morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within forebrain development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within heart development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within heart morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
involved_in inner ear development IEA
Inferred from Electronic Annotation
more info
 
involved_in inner ear development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within mammary gland epithelium development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of mesenchymal cell apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in mesenchymal cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within midbrain development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within middle ear morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within muscle organ development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within 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 
acts_upstream_of_or_within negative regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of negative regulation of gene expression 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 IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of odontoblast differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within negative regulation of striated muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in nose development IEA
Inferred from Electronic Annotation
more info
 
involved_in nose development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in odontogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
 
involved_in odontogenesis of dentin-containing tooth IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in pituitary gland development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within 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 IEA
Inferred from Electronic Annotation
more info
 
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 
acts_upstream_of_or_within positive regulation of mesenchymal cell apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of odontogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of odontogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within 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 DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of odontogenesis IEA
Inferred from Electronic Annotation
more info
 
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
 
acts_upstream_of_or_within roof of mouth development IEA
Inferred from Electronic Annotation
more info
 
involved_in roof of mouth development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within signal transduction involved in regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within stem cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
is_active_in nuclear periphery IEA
Inferred from Electronic Annotation
more info
 
is_active_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 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
part_of transcription regulator complex IEA
Inferred from Electronic Annotation
more info
 
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

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_2024_08

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)