Is PPCS p.Ser274Trp (c.821C>G) pathogenic?

PPCS p.Ser274Trp (c.821C>G) is classified Uncertain significance in PPCS (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-13). AlphaMissense: likely benign (0.2451); Absent from gnomAD v4.1.

How common is PPCS p.Ser274Trp (c.821C>G) in the general population?

PPCS p.Ser274Trp (c.821C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PPCS p.Ser274Trp (c.821C>G)?

AlphaMissense predicts likely benign (score 0.2451) — an in-silico prediction, not a clinical call.

PPCS p.Ser274Trp

c.821C>G · rs756903119 · VCV2111185

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2451 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2451	likely benign
REVEL	0.343	indeterminate
SaProt	LLR -12.35	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.7	GERP 1.4, phastCons 1
Regional constraint	o/e 0.69	unconstrained · MANE · 2,669 bp · p 5.9e-05 · regional, not allelic
Overall
CADD	26.4	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: PPCS
Protein: p.Ser274Trp
Coding: c.821C>G
MANE Select: NM_001395517 · reported on NM_024664
dbSNP: rs756903119
Type: single nucleotide variant
Location: chr1:42459811 (GRCh38)

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

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/ppcs-p-ser274trp (accessed [today's date]).

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