TAPT1 p.Ala2=
c.6G>A · rs997581682 · VCV1641648
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.17%, 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 4.7 | GERP 0.42, phastCons 1 |
| Overall | ||
| CADD | 13.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.17%
African / African-American · 100/58,694 alleles
Filtering AF
0.143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.133%
Overall
0.0109%
116/1,064,850 alleles · rare
exomes 67/917,078 · genomes 49/147,772 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.17% | 587 |
| Remaining individualsnot grpmax-eligible | 0.0377% | 2,653 |
| South Asian | 0.00437% | 22,904 |
| European (non-Finnish) | 0.000226% | 441,544 |
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
- TAPT1
- Protein
- p.Ala2=
- Coding
- c.6G>A
- MANE Select
- NM_153365
- dbSNP
- rs997581682
- Type
- single nucleotide variant
- Location
- chr4:16226452 (GRCh38)
- Gene constraint
- LOEUF 0.698 · pLI 0.13 (gnomAD)
- Structure
- AlphaFold pLDDT 71.98
- Residue 2
- a modified residue (n-acetylalanine); the 'disordered' region
Similar variants
- TAPT1 p.Ala2Glu Uncertain significance ★ ⚠ same residue
- TAPT1 p.Ala122Val Uncertain significance ★★ ⚠ same type
- TAPT1 p.Ala472Thr Uncertain significance ★★ ⚠ same type
- TAPT1 p.Gly15Cys Uncertain significance ★★ ⚠ same type
- TAPT1 p.Gly492Ser Uncertain significance ★★ ⚠ same type
- TAPT1 p.Lys90Arg Uncertain significance ★★ ⚠ same type
- TAPT1 p.Met202Val Uncertain significance ★★ ⚠ same type
- TAPT1 p.Met344Ile 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/tapt1-p-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown