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Gene

MSH3

mutS homolog 3

Summary

Cytogenetic location
5q14.1
Coordinates
Chromosome 5: 80,654,652–80,876,815 (GRCh38)
Exons
24 exons across 222.2 kb
Protein
1,137 amino acids
Inheritance
Autosomal dominant
Also known as
DUP, MRP1
MANE Select transcript
ENST00000265081.7NM_002439.5
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

  • Colorectal Cancer & Polyposis

    • Familial adenomatous polyposis (classic or attenuated)Autosomal dominant

      Hundreds to thousands of colorectal adenomas with a near-certain risk of colorectal cancer without treatment; includes APC-related FAP and MUTYH-, NTHL1- and MSH3-related polyposis.

      • ClinGen rates the link definitive
      • 4 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 MSH3 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 MSH3 sits. MSH3 and 7 genes near it on chromosome 5, from 80,265,734 to 81,265,733.Chromosome 55q14.1p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.380.4 Mb80.6 Mb80.8 Mb81 Mb81.2 MbSPZ1: 80,319,625–80,321,842, forward strandSPZ1ZFYVE16: 80,407,149–80,483,379, forward strandZFYVE16FAM151B: 80,487,954–80,542,563, forward strandFAM151BANKRD34B: 80,556,755–80,570,479, reverse strandANKRD34BDHFR: 80,626,226–80,655,002, reverse strandDHFRMSH3: 80,654,652–80,876,815, forward strandMSH3RASGRF2: 80,960,234–81,230,166, forward strandRASGRF2CKMT2: 81,232,673–81,266,400, forward strandCKMT2Diagram of MSH3: 24 exons on the forward strand of chromosome 5Exon 1: 28 known disease-causing sitesExon 2: 25 known disease-causing sitesExon 3: 22 known disease-causing sitesExon 4: 29 known disease-causing sitesExon 5: 15 known disease-causing sitesExon 6: 12 known disease-causing sitesExon 7: 15 known disease-causing sitesExon 8: 19 known disease-causing sitesExon 9: 12 known disease-causing sitesExon 10: 16 known disease-causing sitesExon 11: 11 known disease-causing sitesExon 12: 15 known disease-causing sitesExon 13: 17 known disease-causing sitesExon 14: 19 known disease-causing sitesExon 15: 25 known disease-causing sitesExon 16: 8 known disease-causing sitesExon 17: 13 known disease-causing sitesExon 18: 7 known disease-causing sitesExon 19: 12 known disease-causing sitesExon 20: 16 known disease-causing sitesExon 21: 23 known disease-causing sitesExon 22: 12 known disease-causing sitesExon 23: 12 known disease-causing sitesExon 1: 80,654,652–80,654,964, 313 basesExon 2: 80,656,411–80,656,531, 121 basesExon 3: 80,665,143–80,665,363, 221 basesExon 4: 80,670,097–80,670,309, 213 basesExon 5: 80,672,244–80,672,360, 117 basesExon 6: 80,672,741–80,672,858, 118 basesExon 7: 80,674,983–80,675,128, 146 basesExon 8: 80,678,927–80,679,093, 167 basesExon 9: 80,725,453–80,725,565, 113 basesExon 10: 80,728,851–80,728,965, 115 basesExon 11: 80,741,464–80,741,548, 85 basesExon 12: 80,744,506–80,744,615, 110 basesExon 13: 80,761,546–80,761,678, 133 basesExon 14: 80,767,933–80,768,120, 188 basesExon 15: 80,768,835–80,769,003, 169 basesExon 16: 80,775,694–80,775,758, 65 basesExon 17: 80,778,720–80,778,836, 117 basesExon 18: 80,787,565–80,787,672, 108 basesExon 19: 80,792,733–80,792,844, 112 basesExon 20: 80,813,584–80,813,741, 158 basesExon 21: 80,854,130–80,854,316, 187 basesExon 22: 80,864,813–80,864,942, 130 basesExon 23: 80,873,116–80,873,287, 172 basesExon 24: 80,875,751–80,876,815, 1,065 bases15101520245′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 4.4 kb of the gene's 222.2 kb; 3,414 of those bases code for the protein.

How a genome test reads MSH3

446

positions in MSH3 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 222.2 kb of MSH3, introns included, not only the 4.4 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.). MSH3 gene: mutS homolog 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/msh3

Vancouver

Dante Labs. MSH3 gene: mutS homolog 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/msh3

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