MSX1 msh homeobox 1 [Homo sapiens (human)] - Gene

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: all
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Genomic context

Location:: 4p16.2

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (4859665..4863936)
RS_2025_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_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Orodental malformations associated with human MSX1 sequence variants.
Title: Orodental malformations associated with human MSX1 sequence variants.
Intrahepatic homeobox protein MSX-1 is a novel host restriction factor of hepatitis B virus.
Title: Intrahepatic homeobox protein MSX-1 is a novel host restriction factor of hepatitis B virus.
Characterization of novel MSX1 variants causally associated with non-syndromic oligodontia in Chinese families.
Title: Characterization of novel MSX1 variants causally associated with non-syndromic oligodontia in Chinese families.
MSX1 involved selective tooth agenesis and abnormal labial frenum, pedigree, and retrospective study.
Title: MSX1 involved selective tooth agenesis and abnormal labial frenum, pedigree, and retrospective study.
MSX1-expression during the different phases in healthy human endometrium.
Title: MSX1-expression during the different phases in healthy human endometrium.
LINC01021 maintains tumorigenicity by enhancing N6-methyladenosine reader IMP2 dependent stabilization of MSX1 and JARID2: implication in colorectal cancer.
Title: LINC01021 maintains tumorigenicity by enhancing N6-methyladenosine reader IMP2 dependent stabilization of MSX1 and JARID2: implication in colorectal cancer.
Hypermethylation of PDX1, EN2, and MSX1 predicts the prognosis of colorectal cancer.
Title: Hypermethylation of PDX1, EN2, and MSX1 predicts the prognosis of colorectal cancer.
Family and case-control genetic study of MSX1 polymorphisms in peg-shaped teeth Jordanian population.
Title: Family and case-control genetic study of MSX1 polymorphisms in peg-shaped teeth Jordanian population.
IRF6, MSX1, TGFA, dental anomalies, and skeletal malocclusion.
Title: IRF6, MSX1, TGFA, dental anomalies, and skeletal malocclusion.
Association of Polymorphic and Haplotype Variants of the MSX1 Gene and the Impacted Teeth Phenomenon.
Title: Association of Polymorphic and Haplotype Variants of the MSX1 Gene and the Impacted Teeth Phenomenon.

Submit: New GeneRIF Correction See all GeneRIFs (124)

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
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 MedGen: C3489529 OMIM: 106600 GeneReviews: Nonsyndromic Tooth Agenesis Overview	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 EBI GWAS CatalogPubMed
Genome-wide association study of multiple congenital heart disease phenotypes identifies a susceptibility locus for atrial septal defect at chromosome 4p16. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Msx1 (e-PCR), detects polymorphism
- UniSTS:532515

SHGC4-464 (e-PCR)
- UniSTS:90449

G33875 (e-PCR)
- UniSTS:71783

G62104 (e-PCR)
- UniSTS:139140

D4S3135 (e-PCR)
- UniSTS:37074

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
involved_in animal organ morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cardiac conduction system development	NAS Non-traceable Author Statement more info	PubMed
involved_in cell morphogenesis	IDA Inferred from Direct Assay more info	PubMed
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
involved_in face morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in face morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
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
involved_in mesenchymal cell proliferation	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 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
involved_in 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 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
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
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 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
involved_in roof of mouth development	ISS Inferred from Sequence or Structural Similarity 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

General protein information

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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)

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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.