Is PRKCA p.Pro93= (c.279C>T) pathogenic?

PRKCA p.Pro93= (c.279C>T) is classified Likely benign in PRKCA (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-25). Very rare (popmax 0.0033%, sas); Associated with PRKCA-related disorder.

What condition is associated with PRKCA p.Pro93= (c.279C>T)?

PRKCA p.Pro93= (c.279C>T) is associated with PRKCA-related disorder (ClinVar).

How common is PRKCA p.Pro93= (c.279C>T) in the general population?

PRKCA p.Pro93= (c.279C>T) is very rare (popmax 0.0033%, sas) (gnomAD).

PRKCA p.Pro93=

c.279C>T · rs750302415 · VCV3046735

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0033%, sas)

Conditions

PRKCA-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 -20	GERP -4.1
Overall
CADD	0.317	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0033% South Asian · 3/91,042 alleles

Filtering AF 0.000875% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000443%

Overall 0.000558% 9/1,612,836 alleles · very rare exomes 9/1,460,630 · genomes 0/152,206 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0033%	30,347
Remaining individualsnot grpmax-eligible	0.0016%	62,466
European (non-Finnish)	0.000424%	235,779

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: PRKCA
Protein: p.Pro93=
Coding: c.279C>T
MANE Select: NM_002737
dbSNP: rs750302415
Type: single nucleotide variant
Location: chr17:66496274 (GRCh38)
Gene constraint: LOEUF 0.397 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 86.90 · 6 PDB

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

Disease context

PRKCA-related disorder

Similar variants

PRKCA p.Asp96Glu Uncertain significance ⚠ same condition
PRKCA p.Glu593= Benign same condition
PRKCA p.Gly257fs Uncertain significance same condition
PRKCA c.-4dup Likely benign same condition
PRKCA p.Asn279= Benign ★★ same type
PRKCA p.Gly129= Benign ★★ same type
PRKCA p.Leu277= Benign ★★ same type
PRKCA p.Ala356Thr Uncertain significance ★ ⚠ 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/prkca-p-pro93 (accessed [today's date]).

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