TRPC6 p.Tyr658=
c.1974C>T · VCV4779960
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 7.949 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,648 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,613,500 alleles · very rare
exomes 2/1,461,262 · genomes 0/152,238 · joint denominator
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
- TRPC6
- Protein
- p.Tyr658=
- Coding
- c.1974C>T
- MANE Select
- NM_004621
- Type
- single nucleotide variant
- Location
- chr11:101473544 (GRCh38)
- Gene constraint
- LOEUF 0.708 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.98 · 6 PDB
Similar variants
- TRPC6 p.Tyr658Asn Uncertain significance ★ ⚠ same residue
- TRPC6 p.Arg175Gln Likely pathogenic ★★ ⚠ same type
- TRPC6 p.Arg175Trp Pathogenic/Likely pathogenic ★★ same type
- TRPC6 p.Arg895Cys Pathogenic ★★ same type
- TRPC6 p.Arg895Leu Pathogenic ★★ same type
- TRPC6 p.Gln869Ter Pathogenic/Likely pathogenic ★★ same type
- TRPC6 p.Gln889Lys Pathogenic/Likely pathogenic ★★ ⚠ same type
- TRPC6 p.Glu897Lys 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/trpc6-p-tyr658 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown