Is PRCD c.*643C>T pathogenic?

PRCD c.643C>T is classified Uncertain significance in PRCD (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Ultra-rare (popmax 0.0605%, sas); Associated with retinitis pigmentosa.

What condition is associated with PRCD c.*643C>T?

PRCD c.*643C>T is associated with retinitis pigmentosa (ClinVar).

How common is PRCD c.*643C>T in the general population?

PRCD c.*643C>T is ultra-rare (popmax 0.0605%, sas) (gnomAD).

How is Retinitis pigmentosa inherited?

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

PRCD c.*643C>T

rs745814897 · VCV325484

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0605%, sas)

Conditions

retinitis pigmentosa

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 -1.3	GERP -0.14
Overall
CADD	12.71	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0605% South Asian · 39/64,480 alleles

Filtering AF 0.0454% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0402%

Overall 0.0088% 40/454,496 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0605%	1,653
Remaining individualsnot grpmax-eligible	0.00619%	16,162

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
Coding: c.*643C>T
MANE Select: NM_134268 · reported on NM_001077620
dbSNP: rs745814897
Type: single nucleotide variant
Location: chr17:76544293 (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-c-star-643c-t (accessed [today's date]).

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