PRKCA p.Asn279=
c.837C>T · rs150522438 · VCV790185
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.93%, afr)
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 3.9 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 12.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.93%
African / African-American · 1,445/74,682 alleles
Filtering AF
1.85%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.82%
Overall
0.159%
2,555/1,603,624 alleles · low-frequency
exomes 1,636/1,451,552 · genomes 919/152,072 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.93% | 52 |
| Middle Eastern | 1.29% | 78 |
| Remaining individualsnot grpmax-eligible | 0.312% | 320 |
| Admixed American | 0.293% | 342 |
| Ashkenazi Jewishnot grpmax-eligible | 0.241% | 415 |
| European (non-Finnish) | 0.0476% | 2,102 |
| South Asian | 0.0401% | 2,491 |
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.Asn279=
- Coding
- c.837C>T
- MANE Select
- NM_002737
- dbSNP
- rs150522438
- Type
- single nucleotide variant
- Location
- chr17:66688966 (GRCh38)
- Gene constraint
- LOEUF 0.397 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.90 · 6 PDB
Similar variants
- PRKCA p.Gly129= Benign ★★ same type
- PRKCA p.Leu277= Benign ★★ same type
- PRKCA p.Ala356Thr Uncertain significance ★ ⚠ same type
- PRKCA p.Arg324Lys Uncertain significance ★ ⚠ same type
- PRKCA p.Arg333Gln Uncertain significance ★ ⚠ same type
- PRKCA p.Arg496Gly Uncertain significance ★ ⚠ same type
- PRKCA p.Asn468Asp Uncertain significance ★ ⚠ same type
- PRKCA p.Asn554Ser 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-asn279 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown