TRPM1 p.Pro879=
c.2637G>A · rs776938008 · VCV1128531
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, 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 -0.17 | GERP -5.5, phastCons 0.048 |
| Overall | ||
| CADD | 6.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
African / African-American · 11/74,932 alleles
Filtering AF
0.00815%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00633%
Overall
0.00273%
44/1,613,998 alleles · ultra-rare
exomes 35/1,461,788 · genomes 9/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0147% | 6,812 |
| South Asian | 0.00439% | 22,773 |
| East Asian | 0.00223% | 44,896 |
| European (non-Finnish) | 0.0022% | 45,383 |
| Admixed American | 0.00167% | 60,002 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
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.Pro879=
- Coding
- c.2637G>A
- MANE Select
- NM_001252024
- dbSNP
- rs776938008
- Type
- single nucleotide variant
- Location
- chr15:31035609 (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.Pro879Leu Uncertain significance ★★ ⚠ same residue
- 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
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-pro879 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown