Is PMS2 p.Ser513= (c.1539T>C) pathogenic?

PMS2 p.Ser513= (c.1539T>C) is classified Benign/Likely benign in PMS2 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-12-21). Very rare (popmax 0.00534%, afr); Associated with Hereditary nonpolyposis colorectal neoplasms.

What condition is associated with PMS2 p.Ser513= (c.1539T>C)?

PMS2 p.Ser513= (c.1539T>C) is associated with Hereditary nonpolyposis colorectal neoplasms, Lynch syndrome 4, hereditary neoplastic syndrome (ClinVar).

How common is PMS2 p.Ser513= (c.1539T>C) in the general population?

PMS2 p.Ser513= (c.1539T>C) is very rare (popmax 0.00534%, afr) (gnomAD).

PMS2 p.Ser513=

c.1539T>C · rs786202950 · VCV186435

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00534%, afr)

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 0.33
Overall
CADD	0.823	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00534% African / African-American · 4/74,886 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.00031% 5/1,613,928 alleles · very rare exomes 2/1,461,854 · genomes 3/152,074 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00534%	18,722
European (non-Finnish)	8.47e-05%	1,180,032

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.Ser513=
Coding: c.1539T>C
MANE Select: NM_000535
dbSNP: rs786202950
Type: single nucleotide variant
Location: chr7:5987226 (GRCh38)
Gene constraint: LOEUF 0.898 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.37 · 9 PDB
Residue 513: the 'disordered' region

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.Ser513Cys Uncertain significance ★★ ⚠ same residue
PMS2 p.Ser513Asn Uncertain significance ★ ⚠ same residue
PMS2 p.Ser513Gly Uncertain significance ★ ⚠ same residue
PMS2 p.Ser513Thr Uncertain significance ★ ⚠ same residue
PMS2 p.Ser513Arg Likely benign ★ same residue
PMS2 p.Ser513fs Pathogenic ★★ same residue
PMS2 c.1144+2T>A Likely pathogenic ★★★ same condition
PMS2 c.163+2T>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/pms2-p-ser513 (accessed [today's date]).

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