Is PMS2 p.Ala520Val (c.1559C>T) pathogenic?

PMS2 p.Ala520Val (c.1559C>T) is classified Conflicting classifications of pathogenicity in PMS2 (ClinVar, Conflicting submitters, 18 submitters; last evaluated 2026-01-21). AlphaMissense: likely benign (0.0733); Ultra-rare (popmax 0.0417%, amr); Associated with mismatch repair cancer syndrome 4.

What condition is associated with PMS2 p.Ala520Val (c.1559C>T)?

PMS2 p.Ala520Val (c.1559C>T) is associated with mismatch repair cancer syndrome 4, Lynch syndrome, mismatch repair cancer syndrome 1 (ClinVar).

How common is PMS2 p.Ala520Val (c.1559C>T) in the general population?

PMS2 p.Ala520Val (c.1559C>T) is ultra-rare (popmax 0.0417%, amr) (gnomAD).

What do computational predictors say about PMS2 p.Ala520Val (c.1559C>T)?

AlphaMissense predicts likely benign (score 0.0733) — an in-silico prediction, not a clinical call.

PMS2 p.Ala520Val

Q: How is Constitutional mismatch repair deficiency syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.1559C>T · rs63751300 · VCV185185

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 18 submitters

AlphaMissense

likely benign

0.0733 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0417%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

mismatch repair cancer syndrome 4

Computational evidence

Protein change
AlphaMissense	0.0733	likely benign
REVEL	0.09	moderately benign-leaning
SaProt	LLR -6.35	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.22	gain · loss 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP -0.005
Regional constraint	o/e 1.09	unconstrained · MANE · 22 kb · p 0.015 · regional, not allelic
Overall
CADD	1.867	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

Grpmax group 0.0417% Admixed American · 25/59,998 alleles

Filtering AF 0.0289% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0247%

Overall 0.00471% 76/1,613,986 alleles · ultra-rare exomes 58/1,461,774 · genomes 18/152,212 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0417%	2,400
South Asian	0.00988%	10,120
African / African-American	0.00533%	18,756
Finnishnot grpmax-eligible	0.00313%	31,989
European (non-Finnish)	0.00297%	33,713
Remaining individualsnot grpmax-eligible	0.0016%	62,508

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: PMS2
Protein: p.Ala520Val
Coding: c.1559C>T
MANE Select: NM_000535
dbSNP: rs63751300
Type: single nucleotide variant
Location: chr7:5987206 (GRCh38)
Gene constraint: LOEUF 0.898 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.37 · 9 PDB
Residue 520: the 'disordered' region

Full PMS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

mismatch repair cancer syndrome 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Lynch syndrome mismatch repair cancer syndrome 1 Lynch syndrome 4 Lynch syndrome 5 hereditary neoplastic syndrome

For Constitutional mismatch repair deficiency syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood

Similar variants

PMS2 p.Ala520= Conflicting classifications of pathogenicity ★ same residue
PMS2 p.Ala520Thr Uncertain significance ★ ⚠ same residue
PMS2 c.1144+2T>A Likely pathogenic ★★★ same condition
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
PMS2 c.251-2A>G 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-ala520val (accessed [today's date]).

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