TRPM1 p.Val282=
c.846G>C · rs773186865 · VCV315532
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, eas)
Conditions
1
congenital stationary night blindness 1C
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 1.3 | GERP -0.66, phastCons 0.74 |
| Overall | ||
| CADD | 9.095 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
East Asian · 7/44,890 alleles
Filtering AF
0.00726%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00514%
Overall
0.000496%
8/1,614,046 alleles · ultra-rare
exomes 7/1,461,888 · genomes 1/152,158 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0156% | 6,413 |
| European (non-Finnish) | 8.47e-05% | 1,180,048 |
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
- TRPM1
- Protein
- p.Val282=
- Coding
- c.846G>C
- MANE Select
- NM_001252024
- dbSNP
- rs773186865
- Type
- single nucleotide variant
- Location
- chr15:31063237 (GRCh38)
- Gene constraint
- LOEUF 0.839 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 66.74
Similar variants
- TRPM1 p.Val282Met Conflicting classifications of pathogenicity ★ ⚠ same residue
- TRPM1 c.1089+1G>A Likely pathogenic ★★ same condition
- TRPM1 c.3127+1G>A Pathogenic/Likely pathogenic ★★ same condition
- TRPM1 c.3148+1G>A Pathogenic/Likely pathogenic ★★ same condition
- TRPM1 c.83+1G>A Likely pathogenic ★★ same condition
- TRPM1 p.Ala848Val Pathogenic/Likely pathogenic ★★ same condition
- TRPM1 p.Arg646Cys Pathogenic/Likely pathogenic ★★ same condition
- TRPM1 p.Arg656Ter Pathogenic/Likely pathogenic ★★ same condition
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/trpm1-p-val282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown