PDE6A p.Ala364=
c.1092G>A · rs774836540 · VCV1142110
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, sas)
Conditions
1
inherited retinal dystrophy
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 -11 | GERP -3.4 |
| Overall | ||
| CADD | 0.432 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
South Asian · 15/91,076 alleles
Filtering AF
0.0101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00811%
Overall
0.00446%
72/1,613,818 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0165% | 6,072 |
| African / African-American | 0.012% | 8,333 |
| Admixed American | 0.005% | 20,002 |
| European (non-Finnish) | 0.00381% | 26,218 |
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
- PDE6A
- Protein
- p.Ala364=
- Coding
- c.1092G>A
- MANE Select
- NM_000440
- dbSNP
- rs774836540
- Type
- single nucleotide variant
- Location
- chr5:149903669 (GRCh38)
- Gene constraint
- LOEUF 0.888 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.80
- Residue 364
- the gaf 2 domain
Similar variants
- PDE6A p.Ala364Val Uncertain significance ★★ ⚠ same residue
- PDE6A p.Ala364Glu Uncertain significance ★ same residue
- PDE6A c.1407+1G>C Pathogenic/Likely pathogenic ★★ same condition
- PDE6A c.1926+1G>A Pathogenic ★★ same condition
- PDE6A c.627+2T>G Pathogenic ★★ same condition
- PDE6A c.998+1G>A Pathogenic ★★ same condition
- PDE6A p.Arg102His Pathogenic/Likely pathogenic ★★ same condition
- PDE6A p.Arg236Ter 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/pde6a-p-ala364 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown