Is PRCD p.Thr3Ala (c.7A>G) pathogenic?

PRCD p.Thr3Ala (c.7A>G) is classified Uncertain significance in PRCD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-09). AlphaMissense: likely benign (0.34); No allele count reported in gnomAD v4.1 (AN 1,599,444); Associated with Inborn genetic diseases.

What condition is associated with PRCD p.Thr3Ala (c.7A>G)?

PRCD p.Thr3Ala (c.7A>G) is associated with Inborn genetic diseases (ClinVar).

How common is PRCD p.Thr3Ala (c.7A>G) in the general population?

PRCD p.Thr3Ala (c.7A>G) is no allele count reported in gnomAD v4.1 (AN 1,599,444) (gnomAD).

What do computational predictors say about PRCD p.Thr3Ala (c.7A>G)?

AlphaMissense predicts likely benign (score 0.34) — an in-silico prediction, not a clinical call.

PRCD p.Thr3Ala

c.7A>G · VCV3424585

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.34 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,599,444)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

⚠ 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
AlphaMissense	0.34	likely benign
REVEL	0.504	indeterminate
SaProt	LLR -5.70	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 9.2	GERP 0.47, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 2,429 bp · p 0.19 · regional, not allelic
Overall
CADD	24.0	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

No allele count reported in gnomAD v4.1 (AN 1,599,444). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PRCD
Protein: p.Thr3Ala
Coding: c.7A>G
MANE Select: NM_001077620
Type: single nucleotide variant
Location: chr17:76540148 (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

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-thr3ala (accessed [today's date]).

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