PDE6B p.Phe797=
c.2391C>T · rs143154045 · VCV1138479
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.044%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.556 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.9 | GERP -4.5 |
| Overall | ||
| CADD | 5.806 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.044%
African / African-American · 33/75,018 alleles
Filtering AF
0.0321%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0281%
Overall
0.00353%
57/1,613,468 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.044% | 2,273 |
| Admixed American | 0.0217% | 4,615 |
| East Asian | 0.00669% | 14,959 |
| Finnishnot grpmax-eligible | 0.00157% | 63,772 |
| European (non-Finnish) | 0.000593% | 168,532 |
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
- PDE6B
- Protein
- p.Phe797=
- Coding
- c.2391C>T
- MANE Select
- NM_000283
- dbSNP
- rs143154045
- Type
- single nucleotide variant
- Location
- chr4:667894 (GRCh38)
- Gene constraint
- LOEUF 1.238 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.72
- Residue 797
- the pdease domain
Similar variants
- PDE6B p.Phe797Leu Uncertain significance ★★ ⚠ same residue
- PDE6B c.1059+2T>G Likely pathogenic ★★ same type
- PDE6B c.1060-1G>T Pathogenic/Likely pathogenic ★★ same type
- PDE6B c.1107+1G>T Likely pathogenic ★★ same type
- PDE6B c.1107+3A>G Pathogenic/Likely pathogenic ★★ same type
- PDE6B c.1468-2A>G Pathogenic/Likely pathogenic ★★ same type
- PDE6B c.1832+1G>T Pathogenic ★★ same type
- PDE6B c.1921-1G>A 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/pde6b-p-phe797 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown