Is PRCD p.Pro25Gln (c.74C>A) pathogenic?

PRCD p.Pro25Gln (c.74C>A) is classified Uncertain significance in PRCD (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-26). AlphaMissense: ambiguous (0.5324); Very rare (popmax 0.00623%, amr).

How common is PRCD p.Pro25Gln (c.74C>A) in the general population?

PRCD p.Pro25Gln (c.74C>A) is very rare (popmax 0.00623%, amr) (gnomAD).

What do computational predictors say about PRCD p.Pro25Gln (c.74C>A)?

AlphaMissense predicts ambiguous (score 0.5324) — an in-silico prediction, not a clinical call.

PRCD p.Pro25Gln

c.74C>A · rs757471313 · VCV2115565

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5324 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00623%, amr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.5324	ambiguous
REVEL	0.279	benign-leaning
SaProt	LLR -6.91	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 2,429 bp · p 0.19 · regional, not allelic
Overall
CADD	32.0	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

Grpmax group 0.00623% Admixed American · 3/48,176 alleles

Filtering AF 0.00165% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000858%

Overall 0.000206% 3/1,454,554 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PRCD
Protein: p.Pro25Gln
Coding: c.74C>A
MANE Select: NM_001077620
dbSNP: rs757471313
Type: single nucleotide variant
Location: chr17:76540215 (GRCh38)

Full PRCD 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/prcd-p-pro25gln (accessed [today's date]).

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