Is PRCD p.Met1Thr (c.2T>C) pathogenic?

PRCD p.Met1Thr (c.2T>C) is classified Pathogenic/Likely pathogenic in PRCD (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-02). Ultra-rare (popmax 0.0247%, eas); Associated with inherited retinal dystrophy.

What condition is associated with PRCD p.Met1Thr (c.2T>C)?

PRCD p.Met1Thr (c.2T>C) is associated with inherited retinal dystrophy, retinitis pigmentosa 36, retinitis pigmentosa (ClinVar).

How common is PRCD p.Met1Thr (c.2T>C) in the general population?

PRCD p.Met1Thr (c.2T>C) is ultra-rare (popmax 0.0247%, eas) (gnomAD).

PRCD p.Met1Thr

c.2T>C · rs527236092 · VCV143095

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

Consequence

start-loss

predicted LoF

gnomAD v4.1

Rare

ultra-rare (popmax 0.0247%, eas)

Conditions

inherited retinal dystrophy

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	start-loss	predicted loss-of-function
REVEL	0.456	indeterminate
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.8	GERP 1.5, phastCons 1
Overall
CADD	23.2	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0247% East Asian · 11/44,492 alleles

Filtering AF 0.0138% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0106%

Overall 0.000936% 15/1,602,530 alleles · ultra-rare exomes 15/1,451,200 · genomes 0/151,330 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0247%	4,045
Remaining individualsnot grpmax-eligible	0.00161%	62,060
African / African-American	0.00134%	74,634
European (non-Finnish)	0.00017%	587,731

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.Met1Thr
Coding: c.2T>C
MANE Select: NM_001077620
dbSNP: rs527236092
Type: single nucleotide variant
Location: chr17:76540143 (GRCh38)

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

Disease context

inherited retinal dystrophy — 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-met1thr (accessed [today's date]).

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