PDE6C p.Leu653=
c.1959A>G · rs373041297 · VCV2133523
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000512%, nfe)
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 0.59 | GERP -4.1, phastCons 0.92 |
| Overall | ||
| CADD | 7.652 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000512%
European (non-Finnish) · 6/1,170,740 alleles
Filtering AF
0.000184%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000121%
Overall
0.000374%
6/1,603,706 alleles · very rare
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
- PDE6C
- Protein
- p.Leu653=
- Coding
- c.1959A>G
- MANE Select
- NM_006204
- dbSNP
- rs373041297
- Type
- single nucleotide variant
- Location
- chr10:93655783 (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 653
- a UniProt-annotated variant site (in achm5); the pdease domain
Similar variants
- PDE6C p.Leu653Pro Likely pathogenic ★★ same residue
- PDE6C c.1004+1G>A Pathogenic/Likely pathogenic ★★ same type
- PDE6C c.1269+1G>A Pathogenic/Likely pathogenic ★★ same type
- PDE6C c.2283+1G>T Pathogenic/Likely pathogenic ★★ same type
- PDE6C c.481-1G>A Likely pathogenic ★★ same type
- PDE6C c.939+2T>G Pathogenic/Likely pathogenic ★★ same type
- PDE6C c.939+5G>A Pathogenic/Likely pathogenic ★★ same type
- PDE6C p.Arg104Trp Pathogenic/Likely pathogenic ★★ 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/pde6c-p-leu653 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown