CNGA3 p.Val456=
c.1368G>A · rs369892428 · VCV1137152
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
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 0.2 | GERP -1.9, phastCons 0.85 |
| Overall | ||
| CADD | 5.201 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,880 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000372%
6/1,613,916 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,960 |
| African / African-American | 0.00267% | 37,449 |
| Admixed American | 0.00167% | 59,982 |
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.Val456=
- Coding
- c.1368G>A
- MANE Select
- NM_001298
- dbSNP
- rs369892428
- Type
- single nucleotide variant
- Location
- chr2:98396538 (GRCh38)
- Gene constraint
- LOEUF 1.126 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.33 · 10 PDB
- Residue 456
- an α-helix; the 'c-linker' region
Similar variants
- CNGA3 p.Val456Gly Uncertain significance ★★ ⚠ same residue
- CNGA3 p.Val456fs Pathogenic ★ same residue
- CNGA3 c.216-1G>A Likely pathogenic ★★ same type
- CNGA3 c.396-11C>G Pathogenic/Likely pathogenic ★★ same type
- CNGA3 c.450-1G>A Pathogenic ★★ same type
- CNGA3 p.Ala262Pro Likely pathogenic ★★ ⚠ same type
- CNGA3 p.Ala318Thr Pathogenic ★★ same type
- CNGA3 p.Ala469Thr 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/cnga3-p-val456 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown