TRPC5 p.Arg643=
c.1929G>A · rs777503770 · VCV3057707
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00771%, nfe)
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 0.6 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 6.952 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00771%
European (non-Finnish) · 69/894,628 alleles
Filtering AF
0.0062%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00568%
Overall
0.00596%
72/1,208,162 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00771% | 12,966 |
| Finnishnot grpmax-eligible | 0.00215% | 46,584 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,515 |
| African / African-American | 0.00175% | 57,058 |
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.Arg643=
- Coding
- c.1929G>A
- MANE Select
- NM_012471
- dbSNP
- rs777503770
- Type
- single nucleotide variant
- Location
- chrX:111782106 (GRCh38)
- Structure
- AlphaFold pLDDT 73.82 · 30 PDB
- Residue 643
- 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-arg643 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown