Is MSH2 p.Arg382Ser (c.1144C>A) pathogenic?

MSH2 p.Arg382Ser (c.1144C>A) is classified Uncertain significance in MSH2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-04-24). AlphaMissense: likely pathogenic (0.925); Absent from gnomAD v4.1; Associated with Hereditary nonpolyposis colorectal neoplasms.

What condition is associated with MSH2 p.Arg382Ser (c.1144C>A)?

MSH2 p.Arg382Ser (c.1144C>A) is associated with Hereditary nonpolyposis colorectal neoplasms, hereditary neoplastic syndrome (ClinVar).

How common is MSH2 p.Arg382Ser (c.1144C>A) in the general population?

MSH2 p.Arg382Ser (c.1144C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MSH2 p.Arg382Ser (c.1144C>A)?

AlphaMissense predicts likely pathogenic (score 0.925) — an in-silico prediction, not a clinical call.

MSH2 p.Arg382Ser

c.1144C>A · rs752373431 · VCV584534

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.925 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Hereditary nonpolyposis colorectal neoplasms

Computational evidence

Protein change
AlphaMissense	0.925	likely pathogenic
REVEL	0.793	moderately pathogenic-leaning
SaProt	LLR -11.39	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>T here scores Δ0.23 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.5	GERP 1.7, phastCons 1
Regional constraint	o/e 1.30	unconstrained · MANE · 80 kb · p 4.9e-24 · regional, not allelic
Overall
CADD	27.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MSH2
Protein: p.Arg382Ser
Coding: c.1144C>A
MANE Select: NM_000251
dbSNP: rs752373431
Type: single nucleotide variant
Location: chr2:47429809 (GRCh38)
Gene constraint: LOEUF 0.672 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.60 · 30 PDB
Residue 382: an α-helix

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

Disease context

Hereditary nonpolyposis colorectal neoplasms — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome

Similar variants

MSH2 p.Arg382Leu Uncertain significance ★★ ⚠ same residue
MSH2 p.Arg382Pro Uncertain significance ★★ ⚠ same residue
MSH2 p.Arg382Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
MSH2 p.Arg382Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
MSH2 p.Arg382His Conflicting classifications of pathogenicity ★ ⚠ same residue
MSH2 p.Arg382fs Pathogenic ★ same residue
MSH2 p.Arg382= Benign ★ same residue
MSH2 c.1076+1G>A 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-arg382ser (accessed [today's date]).

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