TRPM1 p.Ser795=
c.2385G>A · rs539196046 · VCV1644512
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.09%, sas)
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 -10 | GERP -4.1 |
| Overall | ||
| CADD | 0.841 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.09%
South Asian · 82/91,076 alleles
Filtering AF
0.0743%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0685%
Overall
0.00973%
157/1,614,024 alleles · ultra-rare
exomes 144/1,461,806 · genomes 13/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.09% | 1,111 |
| East Asian | 0.0847% | 1,181 |
| Admixed American | 0.025% | 4,002 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,627 |
| Finnishnot grpmax-eligible | 0.00625% | 15,998 |
| European (non-Finnish) | 0.00119% | 84,283 |
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.Ser795=
- Coding
- c.2385G>A
- MANE Select
- NM_001252024
- dbSNP
- rs539196046
- Type
- single nucleotide variant
- Location
- chr15:31038098 (GRCh38)
- Gene constraint
- LOEUF 0.839 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 66.74
- Residue 795
- the 'disordered' region
Similar variants
- TRPM1 c.1089+1G>A Likely pathogenic ★★ same type
- TRPM1 c.2316+1G>A Pathogenic/Likely pathogenic ★★ same type
- TRPM1 c.2317-1G>C Likely pathogenic ★★ same type
- TRPM1 c.2440-2A>G Likely pathogenic ★★ same type
- TRPM1 c.2571+1G>A Likely pathogenic ★★ same type
- TRPM1 c.3127+1G>A Pathogenic/Likely pathogenic ★★ same type
- TRPM1 c.3148+1G>A Pathogenic/Likely pathogenic ★★ same type
- TRPM1 c.3148+1G>T Likely pathogenic ★★ 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/trpm1-p-ser795 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown