TAPT1 p.Asp533=
c.1599C>T · rs34007466 · VCV719092
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.4%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.2 | GERP -4.4 |
| Overall | ||
| CADD | 1.007 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.4%
European (non-Finnish) · 16,569/1,179,802 alleles
Filtering AF
1.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.38%
Overall
1.14%
18,371/1,613,744 alleles · low-frequency
exomes 17,322/1,461,624 · genomes 1,049/152,120 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.4% | 71 |
| Remaining individualsnot grpmax-eligible | 0.879% | 114 |
| Finnishnot grpmax-eligible | 0.696% | 144 |
| Amishnot grpmax-eligible | 0.439% | 228 |
| South Asian | 0.435% | 230 |
| Admixed American | 0.332% | 302 |
| African / African-American | 0.213% | 469 |
| Ashkenazi Jewishnot grpmax-eligible | 0.138% | 722 |
| Middle Eastern | 0.099% | 1,010 |
| East Asian | 0.00446% | 22,435 |
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.Asp533=
- Coding
- c.1599C>T
- MANE Select
- NM_153365
- dbSNP
- rs34007466
- Type
- single nucleotide variant
- Location
- chr4:16163413 (GRCh38)
- Gene constraint
- LOEUF 0.698 · pLI 0.13 (gnomAD)
- Structure
- AlphaFold pLDDT 71.98
Similar variants
- TAPT1 p.Asp533Glu 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-asp533 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown