TMPRSS15 p.Val855=
c.2565C>T · rs755464044 · VCV2779646
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00246%, 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 0.14 | GERP -4.8, phastCons 0.69 |
| Overall | ||
| CADD | 0.387 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00246%
European (non-Finnish) · 29/1,179,982 alleles
Filtering AF
0.00172%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00149%
Overall
0.00198%
32/1,613,814 alleles · very rare
exomes 31/1,461,802 · genomes 1/152,012 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00246% | 40,689 |
| Admixed American | 0.00167% | 59,992 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| Finnishnot grpmax-eligible | 0.00156% | 63,970 |
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.Val855=
- Coding
- c.2565C>T
- MANE Select
- NM_002772
- dbSNP
- rs755464044
- Type
- single nucleotide variant
- Location
- chr21:18281143 (GRCh38)
- Gene constraint
- LOEUF 1.12 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.03 · 14 PDB
- Residue 855
- the peptidase s1 domain; a β-strand
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-val855 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown