PDE3B p.Asn910=
c.2730T>C · rs113803419 · VCV709845
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, afr)
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 -1.1 | GERP -0.42, phastCons 0.003 |
| Overall | ||
| CADD | 4.805 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
African / African-American · 934/74,780 alleles
Filtering AF
1.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.16%
Overall
0.0779%
1,250/1,604,948 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.25% | 80 |
| Middle Eastern | 0.232% | 430 |
| Remaining individualsnot grpmax-eligible | 0.184% | 545 |
| Admixed American | 0.111% | 898 |
| South Asian | 0.0134% | 7,487 |
| European (non-Finnish) | 0.00928% | 10,773 |
| East Asian | 0.00224% | 44,578 |
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
- PDE3B
- Protein
- p.Asn910=
- Coding
- c.2730T>C
- MANE Select
- NM_000922
- dbSNP
- rs113803419
- Type
- single nucleotide variant
- Location
- chr11:14861210 (GRCh38)
- Gene constraint
- LOEUF 0.955 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.10 · 4 PDB
- Residue 910
- an α-helix; the pdease domain
Similar variants
- CYP2R1 p.Gly450Arg Uncertain significance ★★ ⚠ same type
- CYP2R1 p.Gly91Asp Uncertain significance ★★ ⚠ same type
- CYP2R1 p.His381Arg Uncertain significance ★★ ⚠ same type
- CYP2R1 p.Ile332Thr Uncertain significance ★★ ⚠ same type
- CYP2R1 p.Met284Ile Uncertain significance ★★ ⚠ same type
- CYP2R1 p.Pro36Leu Uncertain significance ★★ ⚠ same type
- CYP2R1 p.Tyr431His Uncertain significance ★★ ⚠ same type
- PDE3B p.Thr137Ala 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/pde3b-p-asn910 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown