Is PMS2 p.Ser238= (c.714C>T) pathogenic?

PMS2 p.Ser238= (c.714C>T) is classified Benign in PMS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-28). Absent from gnomAD v4.1; Associated with Lynch syndrome 4.

What condition is associated with PMS2 p.Ser238= (c.714C>T)?

PMS2 p.Ser238= (c.714C>T) is associated with Lynch syndrome 4 (ClinVar).

How common is PMS2 p.Ser238= (c.714C>T) in the general population?

PMS2 p.Ser238= (c.714C>T) is absent from gnomAD v4.1 (gnomAD).

How is Lynch syndrome inherited?

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

PMS2 p.Ser238=

c.714C>T · VCV3903801

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Lynch syndrome 4

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 4.5	phastCons 1
Overall
CADD	10.66	PHRED · no single calibrated threshold — expert panels disagree

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.Ser238=
Coding: c.714C>T
MANE Select: NM_000535
Type: single nucleotide variant
Location: chr7:5997415 (GRCh38)
Gene constraint: LOEUF 0.898 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.37 · 9 PDB
Residue 238: a UniProt-annotated variant site (in lynch4; uncertain significance; no effect on dna mismatch repair activity in an in vitro assay, compared to wild-type; no effect on atpase activity; no effect on protein stability)

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

Disease context

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

For Lynch syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult

Similar variants

PMS2 p.Ser238Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
PMS2 p.Ser238Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
PMS2 p.Ser238Gly Uncertain significance ★★ ⚠ same residue
PMS2 p.Ser238Thr Uncertain significance ★★ ⚠ same residue
PMS2 p.Ser238Cys Uncertain significance ★ ⚠ same residue
PMS2 p.Ser238Ile Uncertain significance ★ ⚠ same residue
PMS2 c.1144+2T>A 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-ser238 (accessed [today's date]).

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