CNGB3 p.Asp460=
c.1380T>C · VCV3672401
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
achromatopsia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -1.3, phastCons 0.12 |
| Overall | ||
| CADD | 2.688 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CNGB3
- Protein
- p.Asp460=
- Coding
- c.1380T>C
- MANE Select
- NM_019098
- Type
- single nucleotide variant
- Location
- chr8:86629019 (GRCh38)
- Gene constraint
- LOEUF 1.044 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.87 · 9 PDB
- Residue 460
- the 'c-linker' region; an α-helix
Disease context
achromatopsia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Achromatopsia (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Worldwide)
Similar variants
- CNGB3 p.Asp460Asn Uncertain significance ★ ⚠ same residue
- CNGB3 c.1055+1G>C Pathogenic/Likely pathogenic ★★ same condition
- CNGB3 c.1055+2T>G Likely pathogenic ★★ same condition
- CNGB3 c.130-1G>T Pathogenic/Likely pathogenic ★★ same condition
- CNGB3 c.1578+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CNGB3 c.1578+1G>T Pathogenic ★★ same condition
- CNGB3 c.1579-1G>A Pathogenic ★★ same condition
- CNGB3 c.1579-2A>G Pathogenic/Likely pathogenic ★★ same condition
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/cngb3-p-asp460 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown