TRPM1 p.Phe1002=
c.3006C>T · rs554342777 · VCV1131629
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0173%, 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 -2.2 | GERP -5.5 |
| Overall | ||
| CADD | 1.372 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0173%
African / African-American · 13/75,048 alleles
Filtering AF
0.0102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00811%
Overall
0.00242%
39/1,614,184 alleles · ultra-rare
exomes 36/1,461,886 · genomes 3/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0173% | 5,773 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,946 |
| South Asian | 0.00659% | 15,179 |
| East Asian | 0.00223% | 44,892 |
| Admixed American | 0.00167% | 60,028 |
| European (non-Finnish) | 0.000763% | 131,112 |
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.Phe1002=
- Coding
- c.3006C>T
- MANE Select
- NM_001252024
- dbSNP
- rs554342777
- Type
- single nucleotide variant
- Location
- chr15:31031104 (GRCh38)
- Gene constraint
- LOEUF 0.839 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 66.74
- Residue 1002
- a UniProt-annotated variant site (in csnb1c)
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-phe1002 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown