Is PMS2 p.Phe620Ser (c.1859T>C) pathogenic?

PMS2 p.Phe620Ser (c.1859T>C) is classified Uncertain significance in PMS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-01). AlphaMissense: likely pathogenic (0.9297); Absent from gnomAD v4.1; Associated with Lynch syndrome 4.

What condition is associated with PMS2 p.Phe620Ser (c.1859T>C)?

PMS2 p.Phe620Ser (c.1859T>C) is associated with Lynch syndrome 4 (ClinVar).

How common is PMS2 p.Phe620Ser (c.1859T>C) in the general population?

PMS2 p.Phe620Ser (c.1859T>C) 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.

What do computational predictors say about PMS2 p.Phe620Ser (c.1859T>C)?

AlphaMissense predicts likely pathogenic (score 0.9297) — an in-silico prediction, not a clinical call.

PMS2 p.Phe620Ser

c.1859T>C · rs2128722234 · VCV3240161

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9297 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Lynch syndrome 4

Computational evidence

Protein change
AlphaMissense	0.9297	likely pathogenic
REVEL	0.374	indeterminate
SaProt	LLR -8.41	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 22 kb · p 0.015 · regional, not allelic
Overall
CADD	22.7	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.Phe620Ser
Coding: c.1859T>C
MANE Select: NM_000535
dbSNP: rs2128722234
Type: single nucleotide variant
Location: chr7:5986906 (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

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.Phe620= Benign/Likely benign ★★ same residue
PMS2 p.Phe620fs Pathogenic/Likely pathogenic ★★ same residue
PMS2 p.Phe620Ile Uncertain significance ★ same residue
PMS2 p.Phe620Tyr Uncertain significance ★ same residue
PMS2 p.Phe620Val Uncertain significance ★ same residue
PMS2 c.1144+2T>A 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-phe620ser (accessed [today's date]).

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