PDE6C p.Thr460=
c.1380C>A · rs3737228 · VCV1574119
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00834%, amr)
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 0.51 | GERP -0.81, phastCons 0.66 |
| Overall | ||
| CADD | 6.522 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00834%
Admixed American · 5/59,974 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00286%
Overall
0.00353%
57/1,613,576 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00834% | 11,995 |
| European (non-Finnish) | 0.00415% | 24,077 |
| East Asian | 0.00223% | 44,852 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,474 |
| African / African-American | 0.00134% | 74,880 |
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.Thr460=
- Coding
- c.1380C>A
- MANE Select
- NM_006204
- dbSNP
- rs3737228
- Type
- single nucleotide variant
- Location
- chr10:93635607 (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 460
- a UniProt-annotated variant site (in achm5); an α-helix
Similar variants
- PDE6C p.Thr460Ile Uncertain significance ★★ ⚠ same residue
- PDE6C p.Thr460Met Uncertain significance ★ 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
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-thr460 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown