TRPV5 p.Pro11=
c.33C>T · rs377258108 · VCV64571
Uncertain significance
No assertion criteria
Classification
Uncertain significance
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0542%, nfe)
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 1.3 | GERP 1.2, phastCons 0.99 |
| Overall | ||
| CADD | 5.005 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0542%
European (non-Finnish) · 640/1,179,990 alleles
Filtering AF
0.0508%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0493%
Overall
0.0423%
682/1,614,042 alleles · ultra-rare
exomes 647/1,461,796 · genomes 35/152,246 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0542% | 1,844 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,976 |
| Finnishnot grpmax-eligible | 0.0109% | 9,148 |
| African / African-American | 0.008% | 12,500 |
| South Asian | 0.00549% | 18,212 |
| Admixed American | 0.005% | 20,005 |
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
- TRPV5
- Protein
- p.Pro11=
- Coding
- c.33C>T
- MANE Select
- NM_019841
- dbSNP
- rs377258108
- Type
- single nucleotide variant
- Location
- chr7:142933427 (GRCh38)
- Gene constraint
- LOEUF 1.007 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.87 · 1 PDB
Similar variants
- TRPV5 p.Arg263Trp Benign ★★ ⚠ same type
- TRPV5 p.Leu23Pro Benign ★★ same type
- TRPV5 p.Ala102Thr Uncertain significance ★ ⚠ same type
- TRPV5 p.Ala114Thr Uncertain significance ★ ⚠ same type
- TRPV5 p.Ala191Thr Uncertain significance ★ ⚠ same type
- TRPV5 p.Ala247Val Uncertain significance ★ ⚠ same type
- TRPV5 p.Ala376Ser Uncertain significance ★ ⚠ same type
- TRPV5 p.Ala507Val 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/trpv5-p-pro11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown