TAOK2 p.Ala487=
c.1461G>A · rs753050453 · VCV1619827
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00864%, nfe)
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 -0.45 | GERP -3.5, phastCons 0.031 |
| Overall | ||
| CADD | 9.675 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00864%
European (non-Finnish) · 99/1,145,768 alleles
Filtering AF
0.00723%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00671%
Overall
0.00678%
105/1,548,428 alleles · very rare
exomes 97/1,396,182 · genomes 8/152,246 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00864% | 11,573 |
| South Asian | 0.00372% | 26,861 |
| Remaining individualsnot grpmax-eligible | 0.00336% | 29,771 |
| East Asian | 0.00226% | 44,230 |
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
- TAOK2
- Protein
- p.Ala487=
- Coding
- c.1461G>A
- MANE Select
- NM_016151
- dbSNP
- rs753050453
- Type
- single nucleotide variant
- Location
- chr16:29985251 (GRCh38)
- Gene constraint
- LOEUF 0.459 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 67.17
Similar variants
- TAOK2 p.Ala487Glu Uncertain significance ★ ⚠ same residue
- TAOK2 p.Ala1057Val Uncertain significance ★★ ⚠ same type
- TAOK2 p.Ala1062Val Uncertain significance ★★ ⚠ same type
- TAOK2 p.Ala1148Thr Uncertain significance ★★ ⚠ same type
- TAOK2 p.Ala444Val Uncertain significance ★★ ⚠ same type
- TAOK2 p.Ala733Val Uncertain significance ★★ ⚠ same type
- TAOK2 p.Ala747Val Uncertain significance ★★ ⚠ same type
- TAOK2 p.Ala761Val 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/taok2-p-ala487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown