TAPT1 p.Pro10=
c.30G>A · rs1207149173 · VCV1485144
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0017%, 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 0.34 | GERP -0.64, phastCons 0.96 |
| Overall | ||
| CADD | 13.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0017%
African / African-American · 1/58,838 alleles
Filtering AF
0.000386%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000279%
Overall
0.000834%
9/1,079,714 alleles · very rare
exomes 6/932,392 · genomes 3/147,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0017% | 58,838 |
| European (non-Finnish) | 0.000897% | 111,540 |
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.Pro10=
- Coding
- c.30G>A
- MANE Select
- NM_153365
- dbSNP
- rs1207149173
- Type
- single nucleotide variant
- Location
- chr4:16226428 (GRCh38)
- Gene constraint
- LOEUF 0.698 · pLI 0.13 (gnomAD)
- Structure
- AlphaFold pLDDT 71.98
- Residue 10
- the 'disordered' region
Similar variants
- 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
- TAPT1 p.Ser490Ala 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-pro10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown