Is PRKD1 p.Pro314= (c.942G>A) pathogenic?

PRKD1 p.Pro314= (c.942G>A) is classified Benign in PRKD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-11-07). Common (popmax 8.84%, afr) — too common for a highly-penetrant pathogenic allele; Associated with PRKD1-related disorder.

What condition is associated with PRKD1 p.Pro314= (c.942G>A)?

PRKD1 p.Pro314= (c.942G>A) is associated with PRKD1-related disorder (ClinVar).

PRKD1 p.Pro314=

Q: How common is PRKD1 p.Pro314= (c.942G>A) in the general population?

PRKD1 p.Pro314= (c.942G>A) is common (popmax 8.84%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.942G>A · rs2273807 · VCV3044767

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 8.84%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

PRKD1-related disorder

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 -7.1	GERP -4.8
Overall
CADD	6.103	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.84% African / African-American · 6,632/75,028 alleles

Filtering AF 8.66% ClinGen BA1/BS1 input FAF95, joint · FAF99 8.59%

Overall 0.639% 10,313/1,614,166 alleles · common exomes 6,085/1,461,866 · genomes 4,228/152,300 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	8.84%	11
East Asian	1.96%	51
Ashkenazi Jewishnot grpmax-eligible	1.17%	86
Remaining individualsnot grpmax-eligible	1.08%	93
Middle Eastern	1.04%	96
Admixed American	0.823%	121
South Asian	0.747%	134
European (non-Finnish)	0.0458%	2,181
Finnishnot grpmax-eligible	0.00468%	21,346

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: PRKD1
Protein: p.Pro314=
Coding: c.942G>A
MANE Select: NM_002742
dbSNP: rs2273807
Type: single nucleotide variant
Location: chr14:29638532 (GRCh38)
Gene constraint: LOEUF 0.762 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 68.99

Full PRKD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PRKD1-related disorder

Similar variants

PRKD1 p.Pro545Ser Uncertain significance ★★ ⚠ same condition
PRKD1 p.Tyr252His Uncertain significance ★★ ⚠ same condition
PRKD1 p.Ala21Pro Uncertain significance ★ ⚠ same condition
PRKD1 p.Lys268Ter Uncertain significance ★ same condition
PRKD1 p.Gln297Arg Uncertain significance ⚠ same condition
PRKD1 p.Gln537Ter Uncertain significance same condition
PRKD1 p.Ala873= Likely benign same condition
PRKD1 p.Glu646= Likely benign same condition

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/prkd1-p-pro314 (accessed [today's date]).

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