Is MSH2 p.Lys90= (c.270A>G) pathogenic?

MSH2 p.Lys90= (c.270A>G) is classified Likely benign in MSH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-17). Very rare (popmax 8.48e-05%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with MSH2 p.Lys90= (c.270A>G)?

MSH2 p.Lys90= (c.270A>G) is associated with hereditary neoplastic syndrome (ClinVar).

How common is MSH2 p.Lys90= (c.270A>G) in the general population?

MSH2 p.Lys90= (c.270A>G) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

MSH2 p.Lys90=

c.270A>G · VCV4111036

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.33	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 5.1	GERP 2.6, phastCons 1
Overall
CADD	16.34	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,420 alleles

Overall 6.2e-05% 1/1,613,196 alleles · very rare exomes 1/1,461,022 · genomes 0/152,174 · joint denominator

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.Lys90=
Coding: c.270A>G
MANE Select: NM_000251
Type: single nucleotide variant
Location: chr2:47408459 (GRCh38)
Gene constraint: LOEUF 0.672 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.60 · 30 PDB
Residue 90: 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

Similar variants

MSH2 p.Lys90Glu Uncertain significance ★★ ⚠ same residue
MSH2 p.Lys90Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
MSH2 p.Lys90Asn 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-lys90 (accessed [today's date]).

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