PDE4D p.Ser97=
c.291G>C · rs1383145221 · VCV2022425
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000179%, nfe)
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 -4.1 | GERP -1.5 |
| Overall | ||
| CADD | 8.413 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000179%
European (non-Finnish) · 2/1,115,950 alleles
Filtering AF
3e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000149%
2/1,338,900 alleles · very rare
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
- PDE4D
- Protein
- p.Ser97=
- Coding
- c.291G>C
- MANE Select
- NM_001104631
- dbSNP
- rs1383145221
- Type
- single nucleotide variant
- Location
- chr5:59893332 (GRCh38)
- Gene constraint
- LOEUF 0.403 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.01 · 122 PDB
- Residue 97
- the 'disordered' region
Similar variants
- PDE4D p.Ile678Thr Pathogenic ★★ same type
- PDE4D p.Pro225Leu Pathogenic ★★ same type
- PDE4D c.*4886A>C Uncertain significance ★★ same type
- PDE4D p.Arg133Trp Uncertain significance ★★ ⚠ same type
- PDE4D p.Arg151Gly Uncertain significance ★★ ⚠ same type
- PDE4D p.Arg249Gln Uncertain significance ★★ ⚠ same type
- PDE4D p.Arg727Trp Uncertain significance ★★ ⚠ same type
- PDE4D p.Asn264Ser 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/pde4d-p-ser97 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown