Is PPCS p.Gln251Pro (c.752A>C) pathogenic?

PPCS p.Gln251Pro (c.752A>C) is classified Uncertain significance in PPCS (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-24). AlphaMissense: likely benign (0.2191); Absent from gnomAD v4.1.

How common is PPCS p.Gln251Pro (c.752A>C) in the general population?

PPCS p.Gln251Pro (c.752A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PPCS p.Gln251Pro (c.752A>C)?

AlphaMissense predicts likely benign (score 0.2191) — an in-silico prediction, not a clinical call.

PPCS p.Gln251Pro

c.752A>C · rs1021499805 · VCV2160094

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2191 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.2191	likely benign
REVEL	0.111	moderately benign-leaning
SaProt	LLR -12.14	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.3	GERP 0.29, phastCons 1
Regional constraint	o/e 0.69	unconstrained · MANE · 2,669 bp · p 5.9e-05 · regional, not allelic
Overall
CADD	19.54	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.Gln251Pro
Coding: c.752A>C
MANE Select: NM_024664
dbSNP: rs1021499805
Type: single nucleotide variant
Location: chr1:42459742 (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-gln251pro (accessed [today's date]).

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