TMPRSS15 p.Phe327=
c.981T>C · VCV3689613
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00224%, eas)
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 4.3 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 12.56 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00224%
East Asian · 1/44,682 alleles
Overall
6.2e-05%
1/1,611,698 alleles · very rare
exomes 1/1,459,670 · genomes 0/152,028 · joint denominator
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
- TMPRSS15
- Protein
- p.Phe327=
- Coding
- c.981T>C
- MANE Select
- NM_002772
- Type
- single nucleotide variant
- Location
- chr21:18353763 (GRCh38)
- Gene constraint
- LOEUF 1.12 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.03 · 14 PDB
- Residue 327
- the cub 1 domain
Similar variants
- TMPRSS15 c.1922-1G>A Likely pathogenic ★★ same type
- TMPRSS15 c.2033-1G>A Likely pathogenic ★★ same type
- TMPRSS15 c.2486+1G>A Likely pathogenic ★★ same type
- TMPRSS15 p.Arg871Ter Pathogenic/Likely pathogenic ★★ same type
- TMPRSS15 p.Ser712Ter Pathogenic ★★ same type
- TMPRSS15 p.Ala491Thr Uncertain significance ★★ ⚠ same type
- TMPRSS15 p.Ala744Val Uncertain significance ★★ ⚠ same type
- TMPRSS15 p.Arg1000His 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/tmprss15-p-phe327 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown