Is PMS2 p.Val858Asp (c.2573T>A) pathogenic?

PMS2 p.Val858Asp (c.2573T>A) is classified Uncertain significance in PMS2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-06-07). AlphaMissense: ambiguous (0.3712); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with PMS2 p.Val858Asp (c.2573T>A)?

PMS2 p.Val858Asp (c.2573T>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is PMS2 p.Val858Asp (c.2573T>A) in the general population?

PMS2 p.Val858Asp (c.2573T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PMS2 p.Val858Asp (c.2573T>A)?

AlphaMissense predicts ambiguous (score 0.3712) — an in-silico prediction, not a clinical call.

PMS2 p.Val858Asp

c.2573T>A · VCV3572136

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.3712 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.3712	ambiguous
REVEL	0.543	indeterminate
SaProt	LLR -5.90	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.23	gain · loss 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 6.1	phastCons 1
Regional constraint	o/e 0.40	unconstrained · MANE · 13 kb · p 2e-20 · regional, not allelic
Overall
CADD	23.1	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.Val858Asp
Coding: c.2573T>A
MANE Select: NM_000535
Type: single nucleotide variant
Location: chr7:5973415 (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.Val858Ala Uncertain significance ★★ ⚠ same residue
PMS2 p.Val858Ile Uncertain significance ★★ ⚠ same residue
PMS2 p.Val858fs Uncertain significance ★ same residue
PMS2 p.Val858= Likely benign ★ 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
PMS2 c.2174+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/pms2-p-val858asp (accessed [today's date]).

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