Is MSH2 p.Val20= (c.60G>A) pathogenic?

MSH2 p.Val20= (c.60G>A) is classified Benign/Likely benign in MSH2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-08-07). Very rare (popmax 0.00451%, sas); Associated with hereditary neoplastic syndrome.

What condition is associated with MSH2 p.Val20= (c.60G>A)?

MSH2 p.Val20= (c.60G>A) is associated with hereditary neoplastic syndrome, Lynch syndrome 1 (ClinVar).

How common is MSH2 p.Val20= (c.60G>A) in the general population?

MSH2 p.Val20= (c.60G>A) is very rare (popmax 0.00451%, sas) (gnomAD).

MSH2 p.Val20=

c.60G>A · rs368874228 · VCV483709

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00451%, sas)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP -1.4, phastCons 1
Overall
CADD	11.6	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00451% South Asian · 4/88,630 alleles

Filtering AF 0.00145% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00091%

Overall 0.000312% 5/1,600,106 alleles · very rare exomes 5/1,447,716 · genomes 0/152,390 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00451%	22,158
European (non-Finnish)	8.51e-05%	1,174,949

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MSH2
Protein: p.Val20=
Coding: c.60G>A
MANE Select: NM_000251
dbSNP: rs368874228
Type: single nucleotide variant
Location: chr2:47403251 (GRCh38)
Gene constraint: LOEUF 0.672 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.60 · 30 PDB
Residue 20: an α-helix

Full MSH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Lynch syndrome 1

Similar variants

MSH2 p.Val20Leu Uncertain significance ★★ ⚠ same residue
MSH2 p.Val20Met Uncertain significance ★★ same residue
MSH2 p.Val20Ala Uncertain significance ★ ⚠ same residue
MSH2 c.1076+1G>A Pathogenic ★★★ same condition
MSH2 c.1076+1G>T Likely pathogenic ★★★ same condition
MSH2 c.1077-1G>C Likely pathogenic ★★★ same condition
MSH2 c.1077-1G>T Likely pathogenic ★★★ same condition
MSH2 c.1077-2A>C Pathogenic ★★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/msh2-p-val20 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown