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Gene

MSX1

msh homeobox 1

Summary

Cytogenetic location
4p16.2
Coordinates
Chromosome 4: 4,859,665–4,863,936 (GRCh38)
Exons
2 exons across 4.3 kb
Protein
303 amino acids
Inheritance
Autosomal dominant
Also known as
HYD1, OFC5
Previous symbols
HOX7
MANE Select transcript
ENST00000382723.5NM_002448.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Hereditary Orofacial Clefting

    • Orofacial Cleft 5 (MSX1-related)Autosomal dominant

      Cleft lip and/or palate, sometimes with missing teeth, caused by variants in the MSX1 gene.

      • 1 GenCC submitter rates it definitive or strong

  • Hypodontia and Anodontia

    • Tooth Agenesis (Hypodontia)
      • ClinGen rates the link definitive
      • 3 GenCC submitters rate it definitive or strong

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How MSX1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 4, with a bracket where MSX1 sits. MSX1 and 4 genes near it on chromosome 4, from 4,361,801 to 5,361,800.Chromosome 44p16.2p16.3p16.2p16.1p15.33p15.32p15.31p15.2p15.1p14p13p12p11q11q12q13.1q13.2q13.3q21.1q21.21q21.22q21.23q21.3q22.1q22.2q22.3q23q24q25q26q27q28.1q28.2q28.3q31.1q31.21q31.22q31.23q31.3q32.1q32.2q32.3q33q34.1q34.2q34.3q35.1q35.24.4 Mb4.6 Mb4.8 Mb5 Mb5.2 MbNSG1: 4,348,140–4,479,327, forward strandNSG1STX18: 4,414,973–4,542,346, reverse strandSTX18MSX1: 4,859,665–4,863,936, forward strandMSX1CYTL1: 5,014,586–5,019,487, reverse strandCYTL1STK32B: 5,051,400–5,500,994, forward strandSTK32BDiagram of MSX1: 2 exons on the forward strand of chromosome 4Exon 1: 5 known disease-causing sitesExon 2: 12 known disease-causing sitesExon 1: 4,859,665–4,860,368, 704 basesExon 2: 4,862,701–4,863,936, 1,236 bases125′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 1.9 kb of the gene's 4.3 kb; 912 of those bases code for the protein.

How a genome test reads MSX1

18

positions in MSX1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 4.3 kb of MSX1, introns included, not only the 1.9 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). MSX1 gene: msh homeobox 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/msx1

Vancouver

Dante Labs. MSX1 gene: msh homeobox 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/msx1

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