PDE6G p.Pro5=
c.15G>A · rs370812916 · VCV1130171
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 -9.1 | GERP -5 |
| Overall | ||
| CADD | 1.826 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,870 alleles
Filtering AF
0.00223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00198%
Overall
0.00236%
38/1,613,476 alleles · very rare
exomes 34/1,461,442 · genomes 4/152,034 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,435 |
| European (non-Finnish) | 0.00305% | 32,777 |
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
- PDE6G
- Protein
- p.Pro5=
- Coding
- c.15G>A
- MANE Select
- NM_002602
- dbSNP
- rs370812916
- Type
- single nucleotide variant
- Location
- chr17:81653291 (GRCh38)
- Gene constraint
- LOEUF 1.446 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.73 · 1 PDB
- Residue 5
- the 'disordered' region
Similar variants
- PDE6G p.Pro5Leu Uncertain significance ★★ ⚠ same residue
- PDE6G p.Pro5Arg Uncertain significance ★ ⚠ same residue
- PDE6G c.146+4A>G Uncertain significance ★★ same type
- PDE6G c.188-14C>A Uncertain significance ★★ same type
- PDE6G p.Ala72Gly Uncertain significance ★★ ⚠ same type
- PDE6G p.Arg11Gln Uncertain significance ★★ ⚠ same type
- PDE6G p.Arg11Trp Uncertain significance ★★ ⚠ same type
- PDE6G p.Arg24Met Uncertain significance ★★ ⚠ 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/pde6g-p-pro5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown