Is PRCD p.Arg17Cys (c.49C>T) pathogenic?

PRCD p.Arg17Cys (c.49C>T) is classified Benign/Likely benign in PRCD (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-02). AlphaMissense: likely benign (0.296); Low-frequency (popmax 2.26%, sas); Associated with retinitis pigmentosa.

What condition is associated with PRCD p.Arg17Cys (c.49C>T)?

PRCD p.Arg17Cys (c.49C>T) is associated with retinitis pigmentosa (ClinVar).

How common is PRCD p.Arg17Cys (c.49C>T) in the general population?

PRCD p.Arg17Cys (c.49C>T) is low-frequency (popmax 2.26%, sas) (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.Arg17Cys (c.49C>T)?

AlphaMissense predicts likely benign (score 0.296) — an in-silico prediction, not a clinical call.

PRCD p.Arg17Cys

c.49C>T · rs375181336 · VCV325472

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.296 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.26%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

retinitis pigmentosa

Computational evidence

Protein change
AlphaMissense	0.296	likely benign
REVEL	0.207	benign-leaning
SaProt	LLR -8.63	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4.8	GERP 0.49, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 2,429 bp · p 0.19 · regional, not allelic
Overall
CADD	28.2	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

Grpmax group 2.26% South Asian · 2,022/89,632 alleles

Filtering AF 2.17% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.14%

Overall 0.135% 2,171/1,603,082 alleles · low-frequency

Ancestry group	Frequency	1 in
South Asiangrpmax	2.26%	44
Remaining individualsnot grpmax-eligible	0.127%	786
Middle Eastern	0.0331%	3,018
African / African-American	0.00543%	18,417
European (non-Finnish)	0.00536%	18,669
Finnishnot grpmax-eligible	0.00161%	62,068

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.Arg17Cys
Coding: c.49C>T
MANE Select: NM_134268 · reported on NM_001077620
dbSNP: rs375181336
Type: single nucleotide variant
Location: chr17:76540190 (GRCh38)

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

Disease context

retinitis pigmentosa — 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-arg17cys (accessed [today's date]).

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