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Gene

MSH5

mutS homolog 5

Summary

Cytogenetic location
6p21.33
Coordinates
Chromosome 6: 31,740,005–31,762,676 (GRCh38)
Exons
25 exons across 22.7 kb
Protein
834 amino acids
Also known as
G7
MANE Select transcript
ENST00000375750.9NM_172166.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Male Infertility

    • The inability of the male to effect fertilization of an ovum after a specified period of unprotected intercourse. Male sterility is permanent infertility.

      • 2 GenCC submitters rate it definitive or strong

How MSH5 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 6, with a bracket where MSH5 sits. MSH5 and 70 genes near it on chromosome 6, from 31,251,341 to 32,251,340.Chromosome 66p21.33p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q2731.4 Mb31.6 Mb31.8 Mb32 Mb32.2 MbHLA-C: 31,268,746–31,272,171, reverse strandHLA-CHLA-B: 31,353,195–31,367,067, reverse strandHLA-BMICA: 31,399,784–31,415,315, forward strandMICAMICB: 31,494,881–31,511,124, forward strandMICBMCCD1: 31,528,962–31,530,232, forward strandMCCD1DDX39B: 31,530,217–31,542,451, reverse strandDDX39BATP6V1G2-DDX39B: 31,530,219–31,546,608, reverse strandATP6V1G2: 31,544,444–31,548,427, reverse strandNFKBIL1: 31,546,870–31,558,829, forward strandLTA: 31,572,054–31,574,324, forward strandTNF: 31,575,558–31,578,336, forward strandLTB: 31,580,525–31,582,522, reverse strandLTBLST1: 31,581,065–31,588,911, forward strandLST1NCR3: 31,588,895–31,593,217, reverse strandNCR3AIF1: 31,615,214–31,617,025, forward strandAIF1PRRC2A: 31,620,675–31,637,771, forward strand: 31,622,774–31,622,860, forward strand: 31,623,874–31,625,499, forward strandBAG6: 31,638,543–31,652,747, reverse strandAPOM: 31,652,416–31,658,214, forward strandC6orf47: 31,658,298–31,660,778, reverse strandGPANK1: 31,661,228–31,666,283, reverse strandCSNK2B: 31,665,227–31,670,343, forward strandCSNK2B: 31,666,102–31,673,546, forward strandLY6G5B: 31,669,976–31,673,776, forward strandLY6G5BLY6G5C: 31,676,684–31,684,040, reverse strandABHD16A: 31,686,954–31,703,391, reverse strandLY6G6F: 31,706,863–31,710,801, forward strandLY6G6F-LY6G6D: 31,706,904–31,717,918, forward strandLY6G6D: 31,715,285–31,717,919, forward strandMPIG6B: 31,718,594–31,726,714, forward strandLY6G6C: 31,718,648–31,721,746, reverse strandDDAH2: 31,726,586–31,730,617, reverse strandCLIC1: 31,730,579–31,740,558, reverse strandCLIC1MSH5: 31,740,005–31,762,676, forward strandMSH5MSH5-SAPCD1: 31,740,020–31,764,851, forward strandMSH5-SAPCD1SAPCD1: 31,762,656–31,764,851, forward strandSAPCD1VWA7: 31,765,590–31,777,328, reverse strandVARS1: 31,777,518–31,795,975, reverse strandLSM2: 31,797,019–31,806,992, reverse strandHSPA1L: 31,809,619–31,815,788, reverse strandHSPA1A: 31,815,543–31,817,994, forward strandHSPA1AHSPA1B: 31,827,738–31,830,254, forward strandHSPA1BNEU1: 31,857,063–31,862,905, reverse strandNEU1SLC44A4: 31,863,173–31,879,198, reverse strandSLC44A4EHMT2: 31,879,758–31,897,723, reverse strandEHMT2C2: 31,897,785–31,945,677, forward strandC2ZBTB12: 31,899,065–31,902,103, reverse strandZBTB12: 31,927,698–31,952,048, forward strandCFB: 31,945,650–31,952,086, forward strandCFBNELFE: 31,952,087–31,959,079, reverse strandSKIC2: 31,959,025–31,969,852, forward strandSKIC2DXO: 31,969,810–31,972,517, reverse strandWHR1: 31,971,091–31,982,821, forward strandC4A: 31,981,991–32,005,247, forward strandC4AC4B: 32,014,725–32,035,975, forward strandC4BCYP21A2: 32,038,297–32,042,321, forward strandCYP21A2TNXB: 32,041,153–32,115,334, reverse strandTNXBATF6B: 32,115,264–32,128,255, reverse strandATF6BFKBPL: 32,128,697–32,131,070, reverse strandFKBPLPPT2: 32,146,580–32,163,679, forward strandPRRT1: 32,147,292–32,153,083, reverse strandPRRT1: 32,150,495–32,154,373, reverse strandPPT2-EGFL8: 32,153,845–32,171,978, forward strandEGFL8: 32,163,918–32,171,980, forward strandAGPAT1: 32,167,118–32,178,112, reverse strandRNF5: 32,178,391–32,184,769, forward strandAGER: 32,180,963–32,184,365, reverse strandPBX2: 32,184,733–32,190,278, reverse strandGPSM3: 32,190,766–32,195,523, reverse strandNOTCH4: 32,194,843–32,224,111, reverse strandNOTCH4Diagram of MSH5: 25 exons on the forward strand of chromosome 6Exon 7: 1 known disease-causing siteExon 8: 2 known disease-causing sitesExon 18: 1 known disease-causing siteExon 1: 31,740,005–31,740,062, 58 basesExon 2: 31,740,454–31,740,613, 160 basesExon 3: 31,741,163–31,741,286, 124 basesExon 4: 31,742,877–31,742,957, 81 basesExon 5: 31,743,108–31,743,170, 63 basesExon 6: 31,743,904–31,744,025, 122 basesExon 7: 31,744,190–31,744,299, 110 basesExon 8: 31,744,546–31,744,581, 36 basesExon 9: 31,745,237–31,745,319, 83 basesExon 10: 31,747,387–31,747,432, 46 basesExon 11: 31,753,301–31,753,439, 139 basesExon 12: 31,753,567–31,753,629, 63 basesExon 13: 31,758,165–31,758,293, 129 basesExon 14: 31,758,548–31,758,620, 73 basesExon 15: 31,758,766–31,758,875, 110 basesExon 16: 31,759,097–31,759,177, 81 basesExon 17: 31,759,425–31,759,512, 88 basesExon 18: 31,759,786–31,759,975, 190 basesExon 19: 31,760,090–31,760,216, 127 basesExon 20: 31,760,690–31,760,839, 150 basesExon 21: 31,761,188–31,761,262, 75 basesExon 22: 31,761,472–31,761,615, 144 basesExon 23: 31,761,818–31,761,955, 138 basesExon 24: 31,762,112–31,762,185, 74 basesExon 25: 31,762,420–31,762,676, 257 bases15101520255′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 2.7 kb of the gene's 22.7 kb; 2,505 of those bases code for the protein.

Sequencing MSH5

4

positions in MSH5 where ClinVar classes a change as pathogenic or likely pathogenic

4 of them (100%) fall in regions short reads find hard.

  • MHC (4 sites)

A whole genome covers all 22.7 kb of MSH5, introns included, not only the 2.7 kb of exons.

Genes linked to the same conditions

Traits linked to MSH5

The Human Phenotype Ontology lists these as features of the rare conditions MSH5 can cause. Each trait's page lists the other genes linked to it.

External links

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 2026-10-17: 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 2026.10.17-8666dff2.

Cite this page

APA

Dante Labs. (n.d.). MSH5 gene: mutS homolog 5. Retrieved 17 October 2026, from https://dantelabs.com/genes/msh5

Vancouver

Dante Labs. MSH5 gene: mutS homolog 5 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/msh5

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