CNGA3 p.Ala645=
c.1935A>G · VCV3356098
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000424%, nfe)
Conditions
1
CNGA3-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 -11 | GERP -3.7 |
| Overall | ||
| CADD | 0.396 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,180,026 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000342%
5/1,461,872 alleles · very rare
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
- CNGA3
- Protein
- p.Ala645=
- Coding
- c.1935A>G
- MANE Select
- NM_001298
- Type
- single nucleotide variant
- Location
- chr2:98397105 (GRCh38)
- Gene constraint
- LOEUF 1.126 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.33 · 10 PDB
- Residue 645
- an α-helix
Disease context
CNGA3-related disorder
Similar variants
- CNGA3 c.450-1G>A Pathogenic ★★ same condition
- CNGA3 p.Ala318Thr Pathogenic ★★ same condition
- CNGA3 p.Ala469Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CNGA3 p.Arg223Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CNGA3 p.Arg274Ser Pathogenic ★★ same condition
- CNGA3 p.Arg277Cys Pathogenic/Likely pathogenic ★★ same condition
- CNGA3 p.Arg277His Pathogenic ★★ ⚠ same condition
- CNGA3 p.Arg283Gln Pathogenic ★★ ⚠ 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/cnga3-p-ala645 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown