Is PRCD p.Leu5= (c.15T>G) pathogenic?

PRCD p.Leu5= (c.15T>G) is classified Likely benign in PRCD (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-08). Absent from gnomAD v4.1.

How common is PRCD p.Leu5= (c.15T>G) in the general population?

PRCD p.Leu5= (c.15T>G) is absent from gnomAD v4.1 (gnomAD).

PRCD p.Leu5=

c.15T>G · rs1266824232 · VCV2862048

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 0.23	GERP -0.87, phastCons 0.13
Overall
CADD	10.21	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.Leu5=
Coding: c.15T>G
MANE Select: NM_001077620
dbSNP: rs1266824232
Type: single nucleotide variant
Location: chr17:76540156 (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-leu5 (accessed [today's date]).

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