AKAP1 p.Pro475=
c.1425G>A · rs73991772 · VCV777892
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.35%, 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 -0.32 | GERP -3.8 |
| Overall | ||
| CADD | 3.298 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.35%
African / African-American · 1,761/75,044 alleles
Filtering AF
2.26%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.22%
Overall
0.93%
15,007/1,613,822 alleles · low-frequency
exomes 13,235/1,461,488 · genomes 1,772/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.35% | 43 |
| Middle Eastern | 1.72% | 58 |
| Ashkenazi Jewishnot grpmax-eligible | 1.28% | 78 |
| Remaining individualsnot grpmax-eligible | 1.13% | 89 |
| European (non-Finnish) | 0.93% | 107 |
| Admixed American | 0.791% | 126 |
| South Asian | 0.546% | 183 |
| Finnishnot grpmax-eligible | 0.173% | 577 |
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.Pro475=
- Coding
- c.1425G>A
- MANE Select
- NM_003488
- dbSNP
- rs73991772
- Type
- single nucleotide variant
- Location
- chr17:57106889 (GRCh38)
- Gene constraint
- LOEUF 0.526 · pLI 0.67 (gnomAD)
- Structure
- AlphaFold pLDDT 57.02
Similar variants
- AKAP1 p.Pro475Leu Likely benign ★ same residue
- AKAP1 c.1976-6A>G Benign ★★ same type
- AKAP1 p.Ala218Thr Benign ★★ same type
- AKAP1 p.Gly323Ser 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-pro475 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown