PDE6D p.Phe134=
c.402T>C · rs1414752195 · VCV764748
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 |
|---|---|---|
| Pangolin | Δ0.21 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.3 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 9.852 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PDE6D
- Protein
- p.Phe134=
- Coding
- c.402T>C
- MANE Select
- NM_002601
- dbSNP
- rs1414752195
- Type
- single nucleotide variant
- Location
- chr2:231733003 (GRCh38)
- Gene constraint
- LOEUF 1.027 · pLI 0.23 (gnomAD)
- Structure
- AlphaFold pLDDT 96.40 · 40 PDB
- Residue 134
- a β-strand
Similar variants
- PDE6D p.Arg23Trp Uncertain significance ★★ ⚠ same type
- PDE6D p.Arg75His Uncertain significance ★★ ⚠ same type
- PDE6D c.140-3C>T Likely benign ★★ same type
- PDE6D c.371+8A>C Benign/Likely benign ★★ same type
- PDE6D c.50+11G>C Likely benign ★★ same type
- PDE6D p.Ala58= Likely benign ★★ same type
- PDE6D p.Arg13= Likely benign ★★ same type
- PDE6D p.Asp136Asn Likely benign ★★ 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/pde6d-p-phe134 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown