Is PRCD p.Leu5Val (c.13C>G) pathogenic?

PRCD p.Leu5Val (c.13C>G) is classified Uncertain significance in PRCD (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-06-06). AlphaMissense: likely benign (0.1195); Ultra-rare (popmax 0.0305%, nfe); Associated with Inborn genetic diseases.

What condition is associated with PRCD p.Leu5Val (c.13C>G)?

PRCD p.Leu5Val (c.13C>G) is associated with Inborn genetic diseases, retinitis pigmentosa 36, retinitis pigmentosa (ClinVar).

How common is PRCD p.Leu5Val (c.13C>G) in the general population?

PRCD p.Leu5Val (c.13C>G) is ultra-rare (popmax 0.0305%, nfe) (gnomAD).

What do computational predictors say about PRCD p.Leu5Val (c.13C>G)?

AlphaMissense predicts likely benign (score 0.1195) — an in-silico prediction, not a clinical call.

PRCD p.Leu5Val

c.13C>G · rs200954045 · VCV891110

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.1195 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0305%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1195	likely benign
REVEL	0.061	moderately benign-leaning
SaProt	LLR -6.60	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 2.2	GERP 0.44, phastCons 0.98
Regional constraint	o/e 0.84	unconstrained · MANE · 2,429 bp · p 0.19 · regional, not allelic
Overall
CADD	22.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0305% European (non-Finnish) · 359/1,176,448 alleles

Filtering AF 0.0279% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0268%

Overall 0.0229% 368/1,603,570 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0305%	3,277
Remaining individualsnot grpmax-eligible	0.00644%	15,527
African / African-American	0.00538%	18,579
Admixed American	0.00171%	58,506

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.Leu5Val
Coding: c.13C>G
MANE Select: NM_134268 · reported on NM_001077620
dbSNP: rs200954045
Type: single nucleotide variant
Location: chr17:76540154 (GRCh38)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: retinitis pigmentosa 36 retinitis pigmentosa

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-leu5val (accessed [today's date]).

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