Is MSH2 p.Pro259= (c.777A>G) pathogenic?

MSH2 p.Pro259= (c.777A>G) is classified Benign/Likely benign in MSH2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-12-05). Very rare (popmax 0.0066%, sas); Associated with Hereditary nonpolyposis colorectal neoplasms.

What condition is associated with MSH2 p.Pro259= (c.777A>G)?

MSH2 p.Pro259= (c.777A>G) is associated with Hereditary nonpolyposis colorectal neoplasms, Lynch syndrome 1 (ClinVar).

How common is MSH2 p.Pro259= (c.777A>G) in the general population?

MSH2 p.Pro259= (c.777A>G) is very rare (popmax 0.0066%, sas) (gnomAD).

MSH2 p.Pro259=

c.777A>G · rs544212322 · VCV1561290

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.0066%, sas)

Conditions

Hereditary nonpolyposis colorectal neoplasms

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 -0.029	GERP -3.5, phastCons 0.025
Overall
CADD	5.489	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0066% South Asian · 6/90,846 alleles

Filtering AF 0.00287% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00196%

Overall 0.000435% 7/1,607,556 alleles · very rare exomes 5/1,455,324 · genomes 2/152,232 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0066%	15,141
Finnishnot grpmax-eligible	0.00157%	63,744

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.Pro259=
Coding: c.777A>G
MANE Select: NM_000251
dbSNP: rs544212322
Type: single nucleotide variant
Location: chr2:47412545 (GRCh38)
Gene constraint: LOEUF 0.672 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.60 · 30 PDB
Residue 259: 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: Lynch syndrome 1

Similar variants

MSH2 p.Pro259Arg Uncertain significance ★ ⚠ same residue
MSH2 p.Pro259Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
MSH2 p.Pro259fs Pathogenic ★ same residue
MSH2 p.Pro259Leu Conflicting classifications of pathogenicity ★ ⚠ 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

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-pro259 (accessed [today's date]).

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