APOL1 p.Arg303=
c.909C>T · rs141788376 · VCV2081832
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.313%, 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 -10 | GERP -3.4 |
| Overall | ||
| CADD | 0.379 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.313%
African / African-American · 235/75,038 alleles
Filtering AF
0.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.268%
Overall
0.0199%
321/1,614,086 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.313% | 319 |
| Admixed American | 0.0367% | 2,728 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,472 |
| European (non-Finnish) | 0.00331% | 30,256 |
| South Asian | 0.00329% | 30,353 |
| Finnishnot grpmax-eligible | 0.00312% | 32,012 |
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.Arg303=
- Coding
- c.909C>T
- MANE Select
- NM_003661
- dbSNP
- rs141788376
- Type
- single nucleotide variant
- Location
- chr22:36265745 (GRCh38)
- Gene constraint
- LOEUF 1.68 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.94 · 5 PDB
- Residue 303
- the 'disordered' region
Similar variants
- APOL1 p.Arg303Cys Uncertain significance ★ ⚠ same residue
- APOL1 p.Arg303His 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
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-arg303 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown