CNGA3 p.Ile159=
c.477C>T · rs150944260 · VCV1098031
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.141%, sas)
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 -8.1 | GERP -3.4 |
| Overall | ||
| CADD | 0.095 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.141%
South Asian · 128/91,056 alleles
Filtering AF
0.121%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.113%
Overall
0.0111%
179/1,613,868 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.141% | 711 |
| African / African-American | 0.028% | 3,574 |
| Middle Eastern | 0.0173% | 5,796 |
| East Asian | 0.00891% | 11,219 |
| Admixed American | 0.00833% | 12,007 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,498 |
| European (non-Finnish) | 0.00127% | 78,668 |
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.Ile159=
- Coding
- c.477C>T
- MANE Select
- NM_001298
- dbSNP
- rs150944260
- Type
- single nucleotide variant
- Location
- chr2:98389685 (GRCh38)
- Gene constraint
- LOEUF 1.126 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.33 · 10 PDB
Similar variants
- 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
- CNGA3 p.Arg129Ter Pathogenic ★★ same type
- CNGA3 p.Arg221Ter 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-ile159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown