Is MSH2 p.Ser860= (c.2580G>A) pathogenic?

MSH2 p.Ser860= (c.2580G>A) is classified Conflicting classifications of pathogenicity in MSH2 (ClinVar, Conflicting submitters, 13 submitters; last evaluated 2026-01-25). Very rare (popmax 0.00801%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with MSH2 p.Ser860= (c.2580G>A)?

MSH2 p.Ser860= (c.2580G>A) is associated with hereditary neoplastic syndrome, Lynch syndrome, Lynch syndrome 1 (ClinVar).

How common is MSH2 p.Ser860= (c.2580G>A) in the general population?

MSH2 p.Ser860= (c.2580G>A) is very rare (popmax 0.00801%, afr) (gnomAD).

MSH2 p.Ser860=

c.2580G>A · rs752428475 · VCV232231

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 13 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00801%, afr)

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 -2.1	GERP -4.1
Overall
CADD	4.547	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00801% African / African-American · 6/74,910 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00229%

Overall 0.00136% 22/1,613,672 alleles · very rare exomes 16/1,461,528 · genomes 6/152,144 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00801%	12,485
Remaining individualsnot grpmax-eligible	0.0048%	20,823
Admixed American	0.00167%	60,000
European (non-Finnish)	0.00102%	98,309

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.Ser860=
Coding: c.2580G>A
MANE Select: NM_000251
dbSNP: rs752428475
Type: single nucleotide variant
Location: chr2:47480817 (GRCh38)
Gene constraint: LOEUF 0.672 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.60 · 30 PDB
Residue 860: a UniProt-annotated variant site (in lynch1; likely benign; normal mismatch repair activity)

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 Lynch syndrome 1 Muir-Torre syndrome

Similar variants

MSH2 p.Ser860Ter Pathogenic ★★★ same residue
MSH2 p.Ser860Leu Likely benign ★★★ same residue
MSH2 p.Ser860Trp Likely benign ★ ⚠ same residue
MSH2 p.Ser860Ala Uncertain significance ★ ⚠ same residue
MSH2 p.Ser860Thr 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

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-ser860 (accessed [today's date]).

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