APOL6 p.Ala268=
c.804G>A · rs138269979 · VCV2653094
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.625%, 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 -11 | GERP -3.5 |
| Overall | ||
| CADD | 0.165 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.625%
European (non-Finnish) · 7,378/1,180,016 alleles
Filtering AF
0.613%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.608%
Overall
0.501%
8,085/1,614,120 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.625% | 160 |
| Remaining individualsnot grpmax-eligible | 0.414% | 241 |
| South Asian | 0.2% | 500 |
| Admixed American | 0.158% | 632 |
| Finnishnot grpmax-eligible | 0.119% | 843 |
| African / African-American | 0.105% | 950 |
| Middle Eastern | 0.066% | 1,516 |
| East Asian | 0.0178% | 5,609 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0135% | 7,401 |
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
- APOL6
- Protein
- p.Ala268=
- Coding
- c.804G>A
- MANE Select
- NM_030641
- dbSNP
- rs138269979
- Type
- single nucleotide variant
- Location
- chr22:35659368 (GRCh38)
- Gene constraint
- LOEUF 1.656 · pLI 0.16 (gnomAD)
- Structure
- AlphaFold pLDDT 54.86
Similar variants
- APOL6 p.Ala161Val Uncertain significance ★ ⚠ same type
- APOL6 p.Ala166Pro Uncertain significance ★ ⚠ same type
- APOL6 p.Ala181Asp Uncertain significance ★ ⚠ same type
- APOL6 p.Ala200Val Uncertain significance ★ ⚠ same type
- APOL6 p.Ala263Thr Uncertain significance ★ ⚠ same type
- APOL6 p.Ala275Asp Uncertain significance ★ ⚠ same type
- APOL6 p.Ala300Ser Uncertain significance ★ ⚠ same type
- APOL6 p.Ala5Val 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/apol6-p-ala268 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown