PDE6G p.Pro69=
c.207T>C · rs201370215 · VCV1658047
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 -16 | GERP -5.2 |
| Overall | ||
| CADD | 0.021 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,076 alleles
Overall
6.2e-05%
1/1,613,726 alleles · very rare
exomes 1/1,461,456 · genomes 0/152,270 · joint denominator
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.Pro69=
- Coding
- c.207T>C
- MANE Select
- NM_002602
- dbSNP
- rs201370215
- Type
- single nucleotide variant
- Location
- chr17:81651131 (GRCh38)
- Gene constraint
- LOEUF 1.446 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.73 · 1 PDB
Similar variants
- PDE6G p.Pro69His Uncertain significance ★ ⚠ same residue
- PDE6G p.Pro69fs Conflicting classifications of pathogenicity ★ 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-pro69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown