APOL1 p.Pro297=
c.891G>A · rs148496792 · VCV2705834
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0667%, 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 -12 | GERP -2.3 |
| Overall | ||
| CADD | 2.322 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0667%
Admixed American · 40/59,976 alleles
Filtering AF
0.0503%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0446%
Overall
0.00502%
81/1,613,640 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0667% | 1,499 |
| South Asian | 0.0176% | 5,689 |
| East Asian | 0.00668% | 14,963 |
| African / African-American | 0.004% | 24,971 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,478 |
| European (non-Finnish) | 0.00153% | 65,545 |
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
- APOL1
- Protein
- p.Pro297=
- Coding
- c.891G>A
- MANE Select
- NM_003661
- dbSNP
- rs148496792
- Type
- single nucleotide variant
- Location
- chr22:36265727 (GRCh38)
- Gene constraint
- LOEUF 1.68 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.94 · 5 PDB
- Residue 297
- the 'disordered' region
Similar variants
- APOL1 p.Pro297Leu Uncertain significance ★ ⚠ same residue
- APOL1 p.Ala108Glu Uncertain significance ★★ ⚠ same type
- APOL1 p.Ala394Gly Uncertain significance ★★ ⚠ same type
- APOL1 p.Arg112Cys Uncertain significance ★★ ⚠ same type
- APOL1 p.Asp46Gly Uncertain significance ★★ ⚠ same type
- APOL1 p.Gln396Ter Uncertain significance ★★ same type
- APOL1 p.Glu110Asp Uncertain significance ★★ ⚠ same type
- APOL1 p.Glu323Gln 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/apol1-p-pro297 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown