PRKCB p.Lys29=
c.87G>A · rs146177740 · VCV735257
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.843%, nfe)
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 | GERP -0.37, phastCons 1 |
| Overall | ||
| CADD | 13.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.843%
European (non-Finnish) · 9,902/1,175,196 alleles
Filtering AF
0.829%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.823%
Overall
0.68%
10,894/1,603,234 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.843% | 119 |
| Remaining individualsnot grpmax-eligible | 0.61% | 164 |
| Middle Eastern | 0.409% | 244 |
| Admixed American | 0.332% | 301 |
| Finnishnot grpmax-eligible | 0.293% | 342 |
| African / African-American | 0.139% | 719 |
| South Asian | 0.102% | 976 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0274% | 3,643 |
| East Asian | 0.00694% | 14,399 |
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
- PRKCB
- Protein
- p.Lys29=
- Coding
- c.87G>A
- MANE Select
- NM_002738
- dbSNP
- rs146177740
- Type
- single nucleotide variant
- Location
- chr16:23836262 (GRCh38)
- Gene constraint
- LOEUF 0.241 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.95 · 8 PDB
Similar variants
- PRKCB c.1395-4A>G Benign ★★ same type
- PRKCB p.Ile174= Benign ★★ same type
- PRKCB p.Pro400= Likely benign ★★ same type
- PRKCB p.Ala2Pro Uncertain significance ★ ⚠ same type
- PRKCB p.Ala395Thr Uncertain significance ★ ⚠ same type
- PRKCB p.Ala539Thr Uncertain significance ★ ⚠ same type
- PRKCB p.Ala6Thr Uncertain significance ★ ⚠ same type
- PRKCB p.Ala6Val 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/prkcb-p-lys29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown