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
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: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 4p16.2

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
109.20210514	current	GRCh38.p13 (GCF_000001405.39)	4	NC_000004.12 (4859665..4863936)
105.20201022	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

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Homeoprotein Msx1-PIASy Interaction Inhibits Angiogenesis.
Title: Homeoprotein Msx1-PIASy Interaction Inhibits Angiogenesis.
MSX1-A Potential Marker for Uterus-Preserving Therapy of Endometrial Carcinomas.
Title: MSX1-A Potential Marker for Uterus-Preserving Therapy of Endometrial Carcinomas.
Novel MSX1 variants identified in families with nonsyndromic oligodontia.
Title: Novel MSX1 variants identified in families with nonsyndromic oligodontia.
A Wnt-BMP4 Signaling Axis Induces MSX and NOTCH Proteins and Promotes Growth Suppression and Differentiation in Neuroblastoma.
Title: A Wnt-BMP4 Signaling Axis Induces MSX and NOTCH Proteins and Promotes Growth Suppression and Differentiation in Neuroblastoma.
MSX1 is differentially expressed in the deepest impacted maxillary third molars.
Title: MSX1 is differentially expressed in the deepest impacted maxillary third molars.
Msx1 loss suppresses formation of the ectopic crypts developed in the Apc-deficient small intestinal epithelium.
Title: Msx1 loss suppresses formation of the ectopic crypts developed in the Apc-deficient small intestinal epithelium.
Study of two unrelated Chinese individuals with non-syndromic tooth agenesis and their families identified two novel mutations: a missense mutation c.572 T>C and a frameshift mutation c.590_594 dup TGTCC, which were both detected in the homeodomain of MSX1.
Title: Two novel mutations in MSX1 causing oligodontia.
the variant genotype of the MSX1 rs8670 SNP was the most frequent in frontal agenesis; meanwhile in the lateral agenesis nonsyndromic hypodontia (NSH)As far as PAX9 rs61754301 and rs4904155 SNPs are considered, our findings were not significant as it seems that these polymorphisms have no influen group, the AXIN2 rs2240308 SNP showed a higher frequency of the variant genotype, with a trend towards statistical significance
Title: Study of rs12532, rs8670 Polymorphism of Msh Homeobox 1 (MSX1), rs61754301, rs4904155 Polymorphism of Paired Box Gene 9 (PAX9), and rs2240308 Polymorphism of Axis Inhibitor Protein 2 (AXIN2) Genes in Nonsyndromic Hypodontia.
synonymous change in MSX1 (rs34165410) showed association with NSCL+/-P, which may create an alternative splice site or lead to low codon usage
Title: TGFβ3, MSX1, and MMP3 as Candidates for NSCL±P in an Indian Population.
lack of association of MSX1 rs12532 and the risk of nonsyndromic unilateral complete cleft lip and palate and tooth agenesis
Title: Association between MSX1 rs12532 polymorphism with nonsyndromic unilateral complete cleft lip and palate and tooth agenesis.

Submit: New GeneRIF Correction See all GeneRIFs (114)

Phenotypes

Go to the top of the page Help

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
Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae. GeneReviews: Not available
Genome-wide association study of multiple congenital heart disease phenotypes identifies a susceptibility locus for atrial septal defect at chromosome 4p16. GeneReviews: Not available
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
Selective tooth agenesis 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

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

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

Homology

Homologs of the MSX1 gene: The MSX1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 331 organisms have orthologs with human gene MSX1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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	PubMed
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	PubMed
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 double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in BMP signaling pathway involved in heart development	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 cellular response to nicotine	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	PubMed
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 in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in mammary gland epithelium development	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
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	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription regulatory region DNA binding	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
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 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 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	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in roof of mouth development	IEA Inferred from Electronic Annotation 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

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment 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	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

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)

Go to the top of the page Help

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.