Is PRCD p.Arg16= (c.48C>T) pathogenic?

PRCD p.Arg16= (c.48C>T) is classified Likely benign in PRCD (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-22). Absent from gnomAD v4.1.

How common is PRCD p.Arg16= (c.48C>T) in the general population?

PRCD p.Arg16= (c.48C>T) is absent from gnomAD v4.1 (gnomAD).

PRCD p.Arg16=

c.48C>T · rs2510032534 · VCV2072045

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

⚠ 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 0.34	GERP -2.1, phastCons 0.99
Overall
CADD	10.75	PHRED · no single calibrated threshold — expert panels disagree

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: PRCD
Protein: p.Arg16=
Coding: c.48C>T
MANE Select: NM_001077620
dbSNP: rs2510032534
Type: single nucleotide variant
Location: chr17:76540189 (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-arg16 (accessed [today's date]).

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