Is PRKD2 p.Val384= (c.1152G>A) pathogenic?

PRKD2 p.Val384= (c.1152G>A) is classified Likely benign in PRKD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-23). Ultra-rare (popmax 0.0367%, amr).

How common is PRKD2 p.Val384= (c.1152G>A) in the general population?

PRKD2 p.Val384= (c.1152G>A) is ultra-rare (popmax 0.0367%, amr) (gnomAD).

PRKD2 p.Val384=

c.1152G>A · VCV3783374

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0367%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.19	GERP -0.6, phastCons 0.96
Overall
CADD	11.31	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0367% Admixed American · 22/59,996 alleles

Filtering AF 0.0248% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0209%

Overall 0.0018% 29/1,613,956 alleles · ultra-rare exomes 14/1,461,804 · genomes 15/152,152 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0367%	2,727
Remaining individualsnot grpmax-eligible	0.0096%	10,414
European (non-Finnish)	8.47e-05%	1,179,980

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: PRKD2
Protein: p.Val384=
Coding: c.1152G>A
MANE Select: NM_016457
Type: single nucleotide variant
Location: chr19:46697820 (GRCh38)
Gene constraint: LOEUF 0.381 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 69.85 · 4 PDB

Full PRKD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PKD2 p.Ala384Glu Uncertain significance ★★ same residue
PKD2 p.Ala384Thr Uncertain significance ★ ⚠ same residue
PKD2 p.Ala384= Likely benign ★ same residue
PKD2 p.Ala384fs Pathogenic ★ same residue
PKD2 c.1094+1G>A Pathogenic ★★ same type
PKD2 c.1094+1G>C Pathogenic ★★ same type
PKD2 c.1319+1G>A Pathogenic/Likely pathogenic ★★ same type
PKD2 c.1320-2A>C Pathogenic/Likely pathogenic ★★ same type

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/prkd2-p-val384 (accessed [today's date]).

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