PDE6A p.Phe779=
c.2337T>C · rs17110644 · VCV138635
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 11%, amr) — too common for a highly-penetrant pathogenic allele
Conditions
2
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 -2.6 | GERP -5.6 |
| Overall | ||
| CADD | 0.746 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11%
Admixed American · 6,577/60,020 alleles
Filtering AF
10.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.6%
Overall
4.44%
71,577/1,613,712 alleles · common
exomes 63,200/1,461,418 · genomes 8,377/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 11% | 9 |
| African / African-American | 9% | 11 |
| Finnishnot grpmax-eligible | 6.44% | 16 |
| Remaining individualsnot grpmax-eligible | 4.25% | 24 |
| European (non-Finnish) | 4% | 25 |
| South Asian | 3.84% | 26 |
| Middle Eastern | 2.29% | 44 |
| Ashkenazi Jewishnot grpmax-eligible | 1.86% | 54 |
| Amishnot grpmax-eligible | 0.33% | 303 |
| East Asian | 0.187% | 534 |
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.Phe779=
- Coding
- c.2337T>C
- MANE Select
- NM_000440
- dbSNP
- rs17110644
- Type
- single nucleotide variant
- Location
- chr5:149866191 (GRCh38)
- Gene constraint
- LOEUF 0.888 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.80
- Residue 779
- the pdease domain
Similar variants
- PDE6A c.1065+2T>A Pathogenic/Likely pathogenic ★★ same condition
- PDE6A c.1407+1G>C Pathogenic/Likely pathogenic ★★ same condition
- PDE6A c.1620+1G>A Pathogenic ★★ same condition
- PDE6A c.1926+1G>A Pathogenic ★★ same condition
- PDE6A c.1927-1G>C Pathogenic/Likely pathogenic ★★ same condition
- PDE6A c.627+2T>G Pathogenic ★★ same condition
- PDE6A c.998+1G>A Pathogenic ★★ same condition
- PDE6A p.Arg102Cys 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-phe779 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown