TRPC5 p.Ala478=
c.1434G>A · rs151101941 · VCV3029927
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0229%, mid)
Conditions
1
TRPC5-related disorder
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 -0.94 | GERP -2.1, phastCons 0.012 |
| Overall | ||
| CADD | 5.804 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0229%
Middle Eastern · 1/4,373 alleles
Filtering AF
0.00766%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00542%
Overall
0.00645%
78/1,209,517 alleles · ultra-rare
exomes 75/1,098,035 · genomes 3/111,482 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0229% | 4,373 |
| East Asian | 0.0178% | 5,626 |
| European (non-Finnish) | 0.00737% | 13,563 |
| Remaining individualsnot grpmax-eligible | 0.0042% | 23,804 |
| African / African-American | 0.00351% | 28,524 |
| South Asian | 0.00176% | 56,718 |
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
- TRPC5
- Protein
- p.Ala478=
- Coding
- c.1434G>A
- MANE Select
- NM_012471
- dbSNP
- rs151101941
- Type
- single nucleotide variant
- Location
- chrX:111847380 (GRCh38)
- Structure
- AlphaFold pLDDT 73.82 · 30 PDB
- Residue 478
- an α-helix
Disease context
TRPC5-related disorder
Similar variants
- TRPC5 p.Arg222Cys Uncertain significance ★ ⚠ same condition
- TRPC5 p.Gln914Glu Uncertain significance ★ ⚠ same condition
- TRPC5 p.Lys7Gln Uncertain significance ★ ⚠ same condition
- TRPC5 p.Ala912Thr Uncertain significance ⚠ same condition
- TRPC5 p.Arg120Trp Uncertain significance ⚠ same condition
- TRPC5 p.Arg191His Uncertain significance ⚠ same condition
- TRPC5 p.Arg260Trp Uncertain significance ⚠ same condition
- TRPC5 p.Arg324Gln Uncertain significance ⚠ same condition
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/trpc5-p-ala478 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown