AKAP1 p.Pro59=
c.177C>T · rs146969737 · VCV2647950
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.535%, 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 -2.3 | GERP -2.3 |
| Overall | ||
| CADD | 2.239 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.535%
African / African-American · 401/75,000 alleles
Filtering AF
0.491%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.474%
Overall
0.0499%
805/1,614,108 alleles · rare
exomes 509/1,461,870 · genomes 296/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.535% | 187 |
| East Asian | 0.25% | 401 |
| Middle Eastern | 0.132% | 758 |
| Remaining individualsnot grpmax-eligible | 0.0928% | 1,078 |
| Finnishnot grpmax-eligible | 0.0828% | 1,208 |
| Admixed American | 0.0666% | 1,501 |
| South Asian | 0.0253% | 3,960 |
| European (non-Finnish) | 0.00932% | 10,727 |
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
- AKAP1
- Protein
- p.Pro59=
- Coding
- c.177C>T
- MANE Select
- NM_003488
- dbSNP
- rs146969737
- Type
- single nucleotide variant
- Location
- chr17:57105641 (GRCh38)
- Gene constraint
- LOEUF 0.526 · pLI 0.67 (gnomAD)
- Structure
- AlphaFold pLDDT 57.02
Similar variants
- AKAP1 c.1976-6A>G Benign ★★ same type
- AKAP1 p.Ala218Thr Benign ★★ same type
- AKAP1 p.Gly323Ser Benign ★★ same type
- AKAP1 p.Pro475= Benign ★★ same type
- AKAP1 p.Pro818= Benign ★★ same type
- AKAP1 p.Ser330Gly Benign ★★ same type
- AKAP1 p.Ser388= Benign ★★ same type
- AKAP1 p.Thr521Ile Likely benign ★★ 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/akap1-p-pro59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown