Is PRCD p.Arg17= (c.51C>A) pathogenic?

PRCD p.Arg17= (c.51C>A) is classified Likely benign in PRCD (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-08). Very rare (popmax 0.00335%, sas).

How common is PRCD p.Arg17= (c.51C>A) in the general population?

PRCD p.Arg17= (c.51C>A) is very rare (popmax 0.00335%, sas) (gnomAD).

PRCD p.Arg17=

c.51C>A · rs776386516 · VCV2792085

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00335%, sas)

⚠ 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
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -1.1	GERP -3.2
Overall
CADD	6.644	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00335% South Asian · 3/89,610 alleles

Filtering AF 0.000889% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000447%

Overall 0.000188% 3/1,598,116 alleles · very rare exomes 3/1,451,510 · genomes 0/146,606 · joint denominator

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.Arg17=
Coding: c.51C>A
MANE Select: NM_001077620
dbSNP: rs776386516
Type: single nucleotide variant
Location: chr17:76540192 (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-arg17 (accessed [today's date]).

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