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Gene

MSX2

msh homeobox 2

Summary

Cytogenetic location
5q35.2
Coordinates
Chromosome 5: 174,724,582–174,730,896 (GRCh38)
Exons
2 exons across 6.3 kb
Protein
267 amino acids
Also known as
CRS2, FPP, HOX8, MSH, PFM
Previous symbols
PFM1
MANE Select transcript
ENST00000239243.7NM_002449.5
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 report relevant to this gene

  • Syndromic Craniosynostosis

    • Conditions combining early skull suture closure with other features, including Apert, Crouzon, Pfeiffer, Muenke and Saethre-Chotzen syndromes, caused by genes such as FGFR2, FGFR3, FGFR1, TWIST1, TCF12 and ERF.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Early diagnosis allows timely surgery and monitoring of head growth, vision and hearing; milder forms such as Muenke syndrome can go unrecognised in adults, which is relevant to family planning.

How MSX2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 5, with a bracket where MSX2 sits. MSX2 and 1 gene near it on chromosome 5, from 174,227,739 to 175,227,738.Chromosome 55q35.2p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.3174.4 Mb174.6 Mb174.8 Mb175 Mb175.2 MbNSG2: 174,045,706–174,243,501, forward strandNSG2MSX2: 174,724,582–174,730,896, forward strandMSX2Diagram of MSX2: 2 exons on the forward strand of chromosome 5Exon 2: 2 known disease-causing sitesExon 1: 174,724,582–174,725,038, 457 basesExon 2: 174,729,159–174,730,896, 1,738 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 2.2 kb of the gene's 6.3 kb; 804 of those bases code for the protein.

How a genome test reads MSX2

3

positions in MSX2 where ClinVar classes a change as pathogenic or likely pathogenic

2 of them (67%) fall in regions short reads find hard.

  • Segmental duplications (2 sites)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 6.3 kb of MSX2, introns included, not only the 2.2 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.). MSX2 gene: msh homeobox 2. Retrieved 16 October 2026, from https://dantelabs.com/genes/msx2

Vancouver

Dante Labs. MSX2 gene: msh homeobox 2 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/msx2

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