TRPM1 p.Phe968=
c.2904T>C · rs773212571 · VCV1643328
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00653%, 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 0.29 | GERP -0.7, phastCons 0.44 |
| Overall | ||
| CADD | 8.966 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00653%
European (non-Finnish) · 77/1,180,048 alleles
Filtering AF
0.0053%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0049%
Overall
0.0052%
84/1,614,086 alleles · very rare
exomes 79/1,461,892 · genomes 5/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00653% | 15,325 |
| Admixed American | 0.005% | 20,003 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| East Asian | 0.00223% | 44,906 |
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.Phe968=
- Coding
- c.2904T>C
- MANE Select
- NM_001252024
- dbSNP
- rs773212571
- Type
- single nucleotide variant
- Location
- chr15:31032737 (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 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-phe968 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown