GNAT2
Chr 1G protein subunit alpha transducin 2
Also known as: ACHM4, GNATC, HG1D
GNAT2 encodes the alpha subunit of cone transducin, a G protein that couples rhodopsin to cGMP-phosphodiesterase in the phototransduction cascade of cone photoreceptors. Biallelic mutations cause achromatopsia 4, a congenital disorder characterized by complete color blindness, reduced visual acuity, and photophobia affecting cone function from birth. The gene shows very low constraint against loss-of-function variants (pLI near 0), suggesting the phenotype follows autosomal recessive inheritance.
Primary Disease Associations & Inheritance
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
283 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 15 | 2 | 22 | 0 | 39 |
Likely Pathogenic | 6 | 2 | 4 | 0 | 12 |
VUS | 0 | 96 | 22 | 5 | 123 |
Likely Benign | 0 | 3 | 34 | 48 | 85 |
Benign | 0 | 1 | 2 | 1 | 4 |
Conflicting | — | 14 | |||
| Total | 21 | 104 | 84 | 54 | 277 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
GNAT2 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools