PRKCG p.Pro524=
c.1572G>A · rs760092806 · VCV3068993
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, 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 -20 | GERP -3.9 |
| Overall | ||
| CADD | 1.454 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
Admixed American · 12/60,006 alleles
Filtering AF
0.0115%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00898%
Overall
0.000743%
12/1,614,038 alleles · ultra-rare
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
- PRKCG
- Protein
- p.Pro524=
- Coding
- c.1572G>A
- MANE Select
- NM_002739
- dbSNP
- rs760092806
- Type
- single nucleotide variant
- Location
- chr19:53900746 (GRCh38)
- Gene constraint
- LOEUF 0.476 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 82.32 · 2 PDB
- Residue 524
- the protein kinase domain
Similar variants
- PRKCG p.Pro524Arg Uncertain significance ★ ⚠ same residue
- PRKCG p.Asn642Lys Likely pathogenic ★★ same type
- PRKCG p.Gln127Arg Pathogenic ★★ same type
- PRKCG p.Gln127Lys Likely pathogenic ★★ same type
- PRKCG p.Gly63Val Likely pathogenic ★★ same type
- PRKCG p.His101Tyr Pathogenic/Likely pathogenic ★★ same type
- PRKCG p.His74Asn Likely pathogenic ★★ same type
- PRKCG p.His74Tyr 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/prkcg-p-pro524 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown