PDE4A p.Ser760=
c.2280G>C · rs201995124 · VCV723426
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 -2.6 | GERP -1.9 |
| Overall | ||
| CADD | 0.179 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,896 alleles
Filtering AF
0.000803%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00065%
Overall
0.00105%
17/1,614,072 alleles · very rare
exomes 14/1,461,890 · genomes 3/152,182 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,896 |
| European (non-Finnish) | 0.00136% | 73,752 |
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
- PDE4A
- Protein
- p.Ser760=
- Coding
- c.2280G>C
- MANE Select
- NM_001111307
- dbSNP
- rs201995124
- Type
- single nucleotide variant
- Location
- chr19:10467240 (GRCh38)
- Gene constraint
- LOEUF 0.434 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.87 · 5 PDB
Similar variants
- PDE4A p.Ala590= Benign ★★ same type
- PDE4A p.Arg20= Benign ★★ same type
- PDE4A p.Arg608= Benign ★★ same type
- PDE4A p.Glu732Gly Benign ★★ same type
- PDE4A p.Pro331Ser Benign/Likely benign ★★ same type
- PDE4A p.Ser279= Benign ★★ same type
- PDE4A c.620+2T>C Uncertain significance ★ same type
- PDE4A p.Ala428Thr Uncertain significance ★ ⚠ 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/pde4a-p-ser760 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown