TRPM2 p.Val873=
c.2619C>T · rs149066607 · VCV778912
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.94%, 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 -9.4 | GERP -2.9 |
| Overall | ||
| CADD | 0.126 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.94%
African / African-American · 1,456/75,034 alleles
Filtering AF
1.86%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.82%
Overall
0.188%
3,027/1,613,376 alleles · low-frequency
exomes 2,040/1,461,078 · genomes 987/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.94% | 52 |
| Middle Eastern | 1.27% | 79 |
| Remaining individualsnot grpmax-eligible | 0.282% | 355 |
| Admixed American | 0.247% | 405 |
| South Asian | 0.224% | 446 |
| European (non-Finnish) | 0.0778% | 1,285 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0676% | 1,480 |
| Finnishnot grpmax-eligible | 0.041% | 2,436 |
| East Asian | 0.00446% | 22,446 |
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
- TRPM2
- Protein
- p.Val873=
- Coding
- c.2619C>T
- MANE Select
- NM_003307
- dbSNP
- rs149066607
- Type
- single nucleotide variant
- Location
- chr21:44405222 (GRCh38)
- Gene constraint
- LOEUF 1.047 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.51 · 15 PDB
- Residue 873
- an α-helix
Similar variants
- TRPM2 p.Val873Ile Benign ★ same residue
- TRPM2 c.1932+141G>A Benign ★★ same type
- TRPM2 c.1933-10T>C Benign ★★ same type
- TRPM2 c.2322-35T>C Benign ★★ same type
- TRPM2 c.2538+14C>T Benign ★★ same type
- TRPM2 c.2962+96A>G Benign ★★ same type
- TRPM2 c.3146+68T>C Benign ★★ same type
- TRPM2 c.3147-20T>C Benign ★★ 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/trpm2-p-val873 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown