TRPM6 p.Leu1237=
c.3711C>T · VCV4806807
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -0.22 | GERP -1.1, phastCons 0.007 |
| Overall | ||
| CADD | 1.736 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- TRPM6
- Protein
- p.Leu1237=
- Coding
- c.3711C>T
- MANE Select
- NM_017662
- Type
- single nucleotide variant
- Location
- chr9:74762960 (GRCh38)
- Gene constraint
- LOEUF 0.494 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 65.03
Similar variants
- TRPM6 c.1308+7T>G Pathogenic ★★ same type
- TRPM6 c.841+1G>A Pathogenic ★★ same type
- TRPM6 p.Arg1772Ter Pathogenic ★★ same type
- TRPM6 p.Arg340Ter Pathogenic/Likely pathogenic ★★ same type
- TRPM6 p.Arg56Ter Pathogenic/Likely pathogenic ★★ same type
- TRPM6 p.Cys1429Ter Pathogenic/Likely pathogenic ★★ same type
- TRPM6 p.Gln1212Ter Likely pathogenic ★★ same type
- TRPM6 p.Tyr574Ter 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/trpm6-p-leu1237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown