PIK3CB p.Arg1069=
c.3205A>C · rs28763907 · VCV731809
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.33%, eas) — too common for a highly-penetrant pathogenic allele
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 1 | GERP -0.4, phastCons 1 |
| Overall | ||
| CADD | 5.729 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.33%
East Asian · 2,839/44,882 alleles
Filtering AF
6.13%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.05%
Overall
0.206%
3,321/1,614,088 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 6.33% | 16 |
| Remaining individualsnot grpmax-eligible | 0.238% | 420 |
| South Asian | 0.234% | 428 |
| Middle Eastern | 0.181% | 551 |
| European (non-Finnish) | 0.0089% | 11,238 |
| Admixed American | 0.00666% | 15,006 |
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
- PIK3CB
- Protein
- p.Arg1069=
- Coding
- c.3205A>C
- MANE Select
- NM_006219
- dbSNP
- rs28763907
- Type
- single nucleotide variant
- Location
- chr3:138655397 (GRCh38)
- Gene constraint
- LOEUF 0.319 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.62
Similar variants
- PIK3CB c.1302+10T>C Benign ★★ same type
- PIK3CB p.Arg811= Benign ★★ same type
- PIK3CB p.Asn717Ser Likely benign ★★ same type
- PIK3CB p.Gln644= Benign ★★ same type
- PIK3CB p.Phe508= Likely benign ★★ same type
- PIK3CB p.Tyr618= Benign ★★ same type
- PIK3CB p.Ala490Val Uncertain significance ★ ⚠ same type
- PIK3CB p.Ala519Thr 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/pik3cb-p-arg1069 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown