CNGA1 p.Pro493=
c.1479C>T · rs186845150 · VCV2043912
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0107%, afr)
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 0.51 | GERP -1.9, phastCons 0.99 |
| Overall | ||
| CADD | 6.724 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0107%
African / African-American · 8/74,960 alleles
Filtering AF
0.00528%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.000558%
9/1,613,996 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0107% | 9,370 |
| South Asian | 0.0011% | 91,074 |
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
- CNGA1
- Protein
- p.Pro493=
- Coding
- c.1479C>T
- MANE Select
- NM_001379270
- dbSNP
- rs186845150
- Type
- single nucleotide variant
- Location
- chr4:47937003 (GRCh38)
- Gene constraint
- LOEUF 0.779 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.88 · 19 PDB
- Residue 493
- the 'cyclic nucleotide-binding domain' region; a β-strand
Similar variants
- CNGA1 c.107+1G>A Likely pathogenic ★★ same type
- CNGA1 c.107+2T>G Likely pathogenic ★★ same type
- CNGA1 c.545+2T>A Likely pathogenic ★★ same type
- CNGA1 c.545+2T>C Likely pathogenic ★★ same type
- CNGA1 c.546-1G>C Pathogenic/Likely pathogenic ★★ same type
- CNGA1 p.Arg214Ter Pathogenic ★★ same type
- CNGA1 p.Arg28Ter Pathogenic ★★ same type
- CNGA1 p.Arg420Ter 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/cnga1-p-pro493 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown