PDE6D p.Val59=
c.177G>A · VCV4748637
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Conditions
1
Joubert syndrome 22
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 0.16 | GERP -0.99, phastCons 0.95 |
| Overall | ||
| CADD | 5.786 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,848 alleles
Overall
6.2e-05%
1/1,613,374 alleles · very rare
exomes 1/1,461,038 · genomes 0/152,336 · 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
- PDE6D
- Protein
- p.Val59=
- Coding
- c.177G>A
- MANE Select
- NM_002601
- Type
- single nucleotide variant
- Location
- chr2:231738101 (GRCh38)
- Gene constraint
- LOEUF 1.027 · pLI 0.23 (gnomAD)
- Structure
- AlphaFold pLDDT 96.40 · 40 PDB
- Residue 59
- a β-strand
Similar variants
- PDE6D p.Arg23Trp Uncertain significance ★★ ⚠ same condition
- PDE6D p.Arg75His Uncertain significance ★★ ⚠ same condition
- PDE6D c.140-3C>T Likely benign ★★ same condition
- PDE6D c.371+8A>C Benign/Likely benign ★★ same condition
- PDE6D c.50+11G>C Likely benign ★★ same condition
- PDE6D p.Ala58= Likely benign ★★ same condition
- PDE6D p.Arg13= Likely benign ★★ same condition
- PDE6D p.Asp136Asn Likely benign ★★ 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/pde6d-p-val59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown