PDE6A p.Arg93=
c.279C>T · rs1158661149 · VCV1492730
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, eas)
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 0.63 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 7.494 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
East Asian · 9/44,898 alleles
Filtering AF
0.0104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00779%
Overall
0.000682%
11/1,614,054 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.02% | 4,989 |
| South Asian | 0.0022% | 45,541 |
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
- PDE6A
- Protein
- p.Arg93=
- Coding
- c.279C>T
- MANE Select
- NM_000440
- dbSNP
- rs1158661149
- Type
- single nucleotide variant
- Location
- chr5:149944395 (GRCh38)
- Gene constraint
- LOEUF 0.888 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.80
- Residue 93
- the gaf 1 domain
Similar variants
- PDE6A p.Arg93Cys Uncertain significance ★★ ⚠ same residue
- PDE6A p.Arg93His Uncertain significance ★★ ⚠ same residue
- PDE6A p.Arg93Leu Uncertain significance ★★ ⚠ same residue
- PDE6A c.1065+2T>A Pathogenic/Likely pathogenic ★★ same type
- PDE6A c.1263+1G>T Pathogenic/Likely pathogenic ★★ same type
- PDE6A c.1407+1G>C Pathogenic/Likely pathogenic ★★ same type
- PDE6A c.1620+1G>A Pathogenic ★★ same type
- PDE6A c.1620+2T>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/pde6a-p-arg93 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown