TMPRSS15 p.Ser3=
c.9G>A · rs756002643 · VCV2973638
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, 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 | GERP -3.5 |
| Overall | ||
| CADD | 0.454 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,908 alleles
Filtering AF
0.000878%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000717%
Overall
0.00124%
20/1,613,916 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,454 |
| Admixed American | 0.00167% | 59,998 |
| European (non-Finnish) | 0.00144% | 69,410 |
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.Ser3=
- Coding
- c.9G>A
- MANE Select
- NM_002772
- dbSNP
- rs756002643
- Type
- single nucleotide variant
- Location
- chr21:18403614 (GRCh38)
- Gene constraint
- LOEUF 1.12 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.03 · 14 PDB
Similar variants
- TMPRSS15 p.Ser3Trp Uncertain significance ★ ⚠ same residue
- 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
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-ser3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown