Is PRKCQ p.Arg600Pro (c.1799G>C) pathogenic?

PRKCQ p.Arg600Pro (c.1799G>C) is classified Uncertain significance in PRKCQ (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-18). AlphaMissense: ambiguous (0.3439); Absent from gnomAD v4.1.

How common is PRKCQ p.Arg600Pro (c.1799G>C) in the general population?

PRKCQ p.Arg600Pro (c.1799G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PRKCQ p.Arg600Pro (c.1799G>C)?

AlphaMissense predicts ambiguous (score 0.3439) — an in-silico prediction, not a clinical call.

PRKCQ p.Arg600Pro

c.1799G>C · VCV4572093

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3439 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.3439	ambiguous
REVEL	0.182	moderately benign-leaning
SaProt	LLR -6.34	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.7	GERP 2.1, phastCons 1
Regional constraint	o/e 0.75	unconstrained · MANE · 87 kb · p 8.3e-14 · regional, not allelic
Overall
CADD	25.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PRKCQ
Protein: p.Arg600Pro
Coding: c.1799G>C
MANE Select: NM_006257
Type: single nucleotide variant
Location: chr10:6441930 (GRCh38)
Gene constraint: LOEUF 0.571 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.20 · 8 PDB
Residue 600: the protein kinase domain

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

Similar variants

PRKCQ p.Arg600Gln Uncertain significance ★ ⚠ same residue
PRKCQ p.Ile214Val Benign ★★ same type
PRKCQ p.Ser479Cys Benign ★★ same type
PRKCQ p.Thr442= Benign ★★ same type
PRKCQ p.Ala152Thr Uncertain significance ★ same type
PRKCQ p.Ala407Thr Uncertain significance ★ ⚠ same type
PRKCQ p.Ala410Ser Uncertain significance ★ ⚠ same type
PRKCQ p.Ala521Thr 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/prkcq-p-arg600pro (accessed [today's date]).

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