TRPM5 p.Pro455=
c.1365C>T · rs200801959 · VCV723529
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.12%, 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 -0.8 | GERP -3.7 |
| Overall | ||
| CADD | 1.484 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.12%
African / African-American · 834/74,322 alleles
Filtering AF
1.06%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.03%
Overall
0.0615%
967/1,573,560 alleles · low-frequency
exomes 503/1,421,236 · genomes 464/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.12% | 89 |
| Admixed American | 0.094% | 1,064 |
| Remaining individualsnot grpmax-eligible | 0.0671% | 1,490 |
| Middle Eastern | 0.0167% | 5,974 |
| South Asian | 0.0046% | 21,741 |
| European (non-Finnish) | 0.00301% | 33,227 |
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
- TRPM5
- Protein
- p.Pro455=
- Coding
- c.1365C>T
- MANE Select
- NM_014555
- dbSNP
- rs200801959
- Type
- single nucleotide variant
- Location
- chr11:2415235 (GRCh38)
- Gene constraint
- LOEUF 1.345 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.66
Similar variants
- TRPM5 p.Ala574= Benign ★★ same type
- TRPM5 p.Arg500Gln Likely benign ★★ same type
- TRPM5 p.Cys227= Benign ★★ same type
- TRPM5 p.Gly1136Ser Benign ★★ same type
- TRPM5 p.Thr218= Benign ★★ same type
- TRPM5 p.Thr314= Benign/Likely benign ★★ same type
- TRPM5 p.Thr616= Benign ★★ same type
- TRPM5 p.Ala1009Val Uncertain significance ★ ⚠ 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/trpm5-p-pro455 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown