Is PMS2 p.Thr511= (c.1533G>A) pathogenic?

PMS2 p.Thr511= (c.1533G>A) is classified Benign/Likely benign in PMS2 (ClinVar, Multiple submitters, 11 submitters; last evaluated 2026-01-26). Ultra-rare (popmax 0.0467%, amr); Associated with Hereditary nonpolyposis colorectal neoplasms.

What condition is associated with PMS2 p.Thr511= (c.1533G>A)?

PMS2 p.Thr511= (c.1533G>A) is associated with Hereditary nonpolyposis colorectal neoplasms, Lynch syndrome 4, hereditary neoplastic syndrome (ClinVar).

How common is PMS2 p.Thr511= (c.1533G>A) in the general population?

PMS2 p.Thr511= (c.1533G>A) is ultra-rare (popmax 0.0467%, amr) (gnomAD).

PMS2 p.Thr511=

c.1533G>A · rs542520309 · VCV186001

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0467%, amr)

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 -4.4
Overall
CADD	0.44	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0467% Admixed American · 28/59,996 alleles

Filtering AF 0.0331% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0286%

Overall 0.00415% 67/1,614,044 alleles · ultra-rare exomes 50/1,461,816 · genomes 17/152,228 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0467%	2,143
Remaining individualsnot grpmax-eligible	0.0048%	20,833
European (non-Finnish)	0.00288%	34,706
African / African-American	0.00133%	75,028
South Asian	0.0011%	91,076

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.Thr511=
Coding: c.1533G>A
MANE Select: NM_000535
dbSNP: rs542520309
Type: single nucleotide variant
Location: chr7:5987232 (GRCh38)
Gene constraint: LOEUF 0.898 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.37 · 9 PDB
Residue 511: the 'disordered' region; a UniProt-annotated variant site (in lynch4; benign; normal dna mismatch repair activity); a UniProt-annotated variant site (normal dna mismatch repair activity); a UniProt-annotated variant site (in)

Full PMS2 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 4 hereditary neoplastic syndrome

Similar variants

PMS2 p.Thr511Ala Benign ★★★ same residue
PMS2 p.Thr511Met Benign ★★★ same residue
PMS2 p.Thr511Ser Uncertain significance ★★ ⚠ same residue
PMS2 p.Thr511fs Pathogenic ★★ same residue
PMS2 p.Thr511Val 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

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-thr511 (accessed [today's date]).

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