PDE3A p.His1078=
c.3234C>T · rs1423318062 · VCV1999705
Uncertain significance
Single submitter
Classification
Uncertain significance
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/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.33 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.35 | gain · loss 0.02 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 15.25 | 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
- PDE3A
- Protein
- p.His1078=
- Coding
- c.3234C>T
- MANE Select
- NM_000921
- dbSNP
- rs1423318062
- Type
- single nucleotide variant
- Location
- chr12:20680079 (GRCh38)
- Gene constraint
- LOEUF 0.763 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.11 · 9 PDB
- Residue 1078
- the 'interaction with slfn12' region; the pdease domain; an α-helix
Similar variants
- PDE3A p.Arg268Lys Uncertain significance ★★ ⚠ same type
- PDE3A p.Arg424His Uncertain significance ★★ ⚠ same type
- PDE3A p.Glu648Val Uncertain significance ★★ ⚠ same type
- PDE3A p.Pro430Leu Uncertain significance ★★ ⚠ same type
- PDE3A p.Ser325Pro Uncertain significance ★★ ⚠ same type
- PDE3A p.Ser633Ile Uncertain significance ★★ ⚠ same type
- PDE3A p.Thr383Lys Uncertain significance ★★ ⚠ same type
- PDE3A p.Thr609Ser 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/pde3a-p-his1078 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown