PDE6C p.Lys27fs
c.81del · VCV3775670
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
cone dystrophy 4
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 22 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP -1.8, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PDE6C
- Protein
- p.Lys27fs
- Coding
- c.81del
- MANE Select
- NM_006204
- Type
- Deletion
- Location
- chr10:93612806 (GRCh38)
- Gene constraint
- LOEUF 0.976 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.53 · 7 PDB
- Residue 27
- an α-helix
Disease context
cone dystrophy 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Progressive cone dystrophy (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- Adult
Similar variants
- PDE6C c.2367+1_2367+5del Pathogenic/Likely pathogenic ★★ same condition
- PDE6C p.Gln685fs Pathogenic/Likely pathogenic ★★ same condition
- PDE6C p.Val268fs Pathogenic/Likely pathogenic ★★ same condition
- PDE6C c.480+1del Pathogenic same condition
- PDE6C c.1004+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PDE6C c.2283+1G>T Pathogenic/Likely pathogenic ★★ same condition
- PDE6C c.939+5G>A Pathogenic/Likely pathogenic ★★ same condition
- PDE6C p.Arg238Ter 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/pde6c-p-lys27fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown