CNGA3 p.Thr147=
c.441G>T · rs754767905 · VCV1607570
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -5.1 | GERP -2.9 |
| Overall | ||
| CADD | 0.047 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.000442%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000274%
4/1,461,872 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| African / African-American | 0.00267% | 37,512 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,512 |
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.Thr147=
- Coding
- c.441G>T
- MANE Select
- NM_001298
- dbSNP
- rs754767905
- Type
- single nucleotide variant
- Location
- chr2:98383433 (GRCh38)
- Gene constraint
- LOEUF 1.126 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.33 · 10 PDB
- Residue 147
- the 'disordered' region
Similar variants
- CNGA3 p.Thr147Arg Conflicting classifications of pathogenicity ★ ⚠ 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
- CNGA3 p.Arg129Ter 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-thr147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown