TAPT1 p.Ser384=
c.1152C>T · VCV4698326
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00174%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.21 | acceptor loss, 44 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.2 | GERP 0.16, phastCons 1 |
| Overall | ||
| CADD | 11.98 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00174%
Admixed American · 1/57,408 alleles
Filtering AF
0.00062%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000478%
Overall
0.001%
16/1,593,454 alleles · very rare
exomes 15/1,441,370 · genomes 1/152,084 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00174% | 57,408 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,654 |
| African / African-American | 0.00134% | 74,364 |
| European (non-Finnish) | 0.00111% | 89,953 |
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.Ser384=
- Coding
- c.1152C>T
- MANE Select
- NM_153365
- Type
- single nucleotide variant
- Location
- chr4:16174685 (GRCh38)
- Gene constraint
- LOEUF 0.698 · pLI 0.13 (gnomAD)
- Structure
- AlphaFold pLDDT 71.98
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-ser384 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown