AKAP13 p.Pro80=
c.240C>T · VCV3280727
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
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 -4.3 |
| Overall | ||
| CADD | 4.114 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,890 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.00105%
17/1,613,956 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,482 |
| South Asian | 0.00549% | 18,213 |
| European (non-Finnish) | 0.000508% | 196,669 |
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
- AKAP13
- Protein
- p.Pro80=
- Coding
- c.240C>T
- MANE Select
- NM_007200
- Type
- single nucleotide variant
- Location
- chr15:85533642 (GRCh38)
- Gene constraint
- LOEUF 0.362 · pLI 1.00 (gnomAD)
Similar variants
- AKAP13 p.Ala2026= Benign/Likely benign ★★ same type
- AKAP13 p.Arg2678Trp Benign ★★ same type
- AKAP13 p.Glu1175= Benign/Likely benign ★★ same type
- AKAP13 p.Glu334Lys Benign ★★ same type
- AKAP13 p.Ile1260= Benign ★★ same type
- AKAP13 p.Leu2461= Benign ★★ same type
- AKAP13 p.Leu915= Benign ★★ same type
- AKAP13 p.Lys410= 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/akap13-p-pro80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown