Is PMS2 p.Ser669Ile (c.2006G>T) pathogenic?

PMS2 p.Ser669Ile (c.2006G>T) is classified Uncertain significance in PMS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-13). AlphaMissense: ambiguous (0.5332); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with PMS2 p.Ser669Ile (c.2006G>T)?

PMS2 p.Ser669Ile (c.2006G>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is PMS2 p.Ser669Ile (c.2006G>T) in the general population?

PMS2 p.Ser669Ile (c.2006G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PMS2 p.Ser669Ile (c.2006G>T)?

AlphaMissense predicts ambiguous (score 0.5332) — an in-silico prediction, not a clinical call.

PMS2 p.Ser669Ile

c.2006G>T · rs1417552718 · VCV1784327

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5332 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.5332	ambiguous
REVEL	0.251	benign-leaning
SaProt	LLR -11.75	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense is indeterminate.
Splicing
SpliceAI	Δ0.71	donor loss at this position · masked 0 · deltas
Pangolin	Δ0.52	loss · gain 0.03 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 7.7	phastCons 1
Regional constraint	o/e 0.40	unconstrained · MANE · 13 kb · p 2e-20 · regional, not allelic
Overall
CADD	34.0	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.Ser669Ile
Coding: c.2006G>T
MANE Select: NM_000535
dbSNP: rs1417552718
Type: single nucleotide variant
Location: chr7:5986759 (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

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

Similar variants

PMS2 p.Ser669Asn Uncertain significance ★★ ⚠ same residue
PMS2 p.Ser669Cys Uncertain significance ★★ ⚠ same residue
PMS2 p.Ser669Arg Uncertain significance ★ ⚠ same residue
PMS2 p.Ser669= Likely benign ★ same residue
PMS2 p.Ser669fs Pathogenic ★ same residue
PMS2 p.Ser669Gly Uncertain significance ★ ⚠ same residue
PMS2 p.Ser669Thr Uncertain significance ★ ⚠ same residue
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-ser669ile (accessed [today's date]).

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