Inherited MMR deficiency (Lynch syndrome): genes and variants
Inherited MMR deficiency (Lynch syndrome) is linked to 1 analyzed protein (MSH6). 1 DNA variants are known to cause it; 7 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Inherited MMR deficiency (Lynch syndrome)
MSH6: DNA mismatch repair protein Msh6
Together with MSH2, it recognizes single-base mismatches and small insertion-deletion loops during DNA replication and initiates mismatch repair. Germline loss-of-function variants cause Lynch syndrome, while biallelic variants can cause constitutional mismatch-repair deficiency.
1 disease-causing and 2 uncertain variants in MSH6 are linked to Inherited MMR deficiency (Lynch syndrome).
Weakly linked (only a few uncertain records): MLH1, MSH2 and PMS2.
Known disease-causing variants in Inherited MMR deficiency (Lynch syndrome)
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| MSH6 A1162D | 1162 | Disease-causing (★★) |
Same protein, different disease
- Hereditary nonpolyposis colorectal neoplasms is also caused by MSH6 variants; they fall mostly in different places as the Inherited MMR deficiency (Lynch syndrome) variants (14 disease-causing).
- Lynch syndrome is also caused by MSH6 variants; they fall mostly in different places as the Inherited MMR deficiency (Lynch syndrome) variants (12 disease-causing).
Diseases related to Inherited MMR deficiency (Lynch syndrome)
- Lynch syndrome, also linked to MSH6
- Hereditary nonpolyposis colorectal neoplasms, also linked to MSH6
- Ovarian cancer, also linked to MSH6
- Colorectal cancer, also linked to MSH6
- Gastric cancer, also linked to MSH6
- Hereditary nonpolyposis colon cancer, also linked to MSH6
- Mismatch repair cancer syndrome, also linked to MSH6
- Breast and/or ovarian cancer, also linked to MSH6
- Endometrial carcinoma, also linked to MSH6
- Lynch-like syndrome, also linked to MSH6
Frequently asked questions
Which genes are linked to Inherited MMR deficiency (Lynch syndrome)?
In CATVariant, Inherited MMR deficiency (Lynch syndrome) is linked to 1 analyzed protein: MSH6 (DNA mismatch repair protein Msh6).
How many genetic variants are linked to Inherited MMR deficiency (Lynch syndrome)?
8 variants: 1 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 7 are of uncertain significance or have conflicting reports.
Which uncertain variants in Inherited MMR deficiency (Lynch syndrome) look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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