Is PMS2 p.Ser773Cys (c.2317A>T) pathogenic?

PMS2 p.Ser773Cys (c.2317A>T) is classified Uncertain significance in PMS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-29). AlphaMissense: likely pathogenic (0.5721); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with PMS2 p.Ser773Cys (c.2317A>T)?

PMS2 p.Ser773Cys (c.2317A>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is PMS2 p.Ser773Cys (c.2317A>T) in the general population?

PMS2 p.Ser773Cys (c.2317A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PMS2 p.Ser773Cys (c.2317A>T)?

AlphaMissense predicts likely pathogenic (score 0.5721) — an in-silico prediction, not a clinical call.

PMS2 p.Ser773Cys

c.2317A>T · VCV3890944

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5721 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.5721	likely pathogenic
REVEL	0.788	moderately pathogenic-leaning
SaProt	LLR -9.60	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	Δ0.71	acceptor loss, 2 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 7.8	phastCons 1
Regional constraint	o/e 0.40	unconstrained · MANE · 13 kb · p 2e-20 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

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: PMS2
Protein: p.Ser773Cys
Coding: c.2317A>T
MANE Select: NM_000535
Type: single nucleotide variant
Location: chr7:5977716 (GRCh38)
Gene constraint: LOEUF 0.898 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.37 · 9 PDB

Full PMS2 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

PMS2 p.Ser773Asn Uncertain significance ★★ ⚠ same residue
PMS2 p.Ser773Gly Uncertain significance ★★ ⚠ same residue
PMS2 p.Ser773Thr Uncertain significance ★★ same residue
PMS2 p.Ser773= Benign/Likely benign ★★ same residue
PMS2 p.Ser773Arg Uncertain significance ★ ⚠ same residue
PMS2 c.163+2T>C Likely pathogenic ★★★ same condition
PMS2 c.164-2A>G Likely pathogenic ★★★ same condition
PMS2 c.2007-1G>A 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/pms2-p-ser773cys (accessed [today's date]).

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