Is PRCD p.Cys2Tyr (c.5G>A) pathogenic?

PRCD p.Cys2Tyr (c.5G>A) is classified Uncertain significance in PRCD (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-07-17). AlphaMissense: likely pathogenic (0.8828); Absent from gnomAD v4.1; Associated with retinitis pigmentosa 36.

What condition is associated with PRCD p.Cys2Tyr (c.5G>A)?

PRCD p.Cys2Tyr (c.5G>A) is associated with retinitis pigmentosa 36 (ClinVar).

How common is PRCD p.Cys2Tyr (c.5G>A) in the general population?

PRCD p.Cys2Tyr (c.5G>A) is absent from gnomAD v4.1 (gnomAD).

How is Retinitis pigmentosa inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about PRCD p.Cys2Tyr (c.5G>A)?

AlphaMissense predicts likely pathogenic (score 0.8828) — an in-silico prediction, not a clinical call.

PRCD p.Cys2Tyr

c.5G>A · rs121918369 · VCV1188

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.8828 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

retinitis pigmentosa 36

Computational evidence

Protein change
AlphaMissense	0.8828	likely pathogenic
REVEL	0.825	moderately pathogenic-leaning
SaProt	LLR -4.61	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 12	GERP 1.5, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 2,429 bp · p 0.19 · regional, not allelic
Overall
CADD	27.3	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: PRCD
Protein: p.Cys2Tyr
Coding: c.5G>A
MANE Select: NM_134268 · reported on NM_001077620
dbSNP: rs121918369
Type: single nucleotide variant
Location: chr17:76540146 (GRCh38)

Full PRCD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

retinitis pigmentosa 36 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

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-cys2tyr (accessed [today's date]).

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