PDE11A p.Glu20=
c.60G>A · rs147765540 · VCV732821
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.024%, 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 -0.31 | GERP -4, phastCons 0.17 |
| Overall | ||
| CADD | 7.347 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.024%
European (non-Finnish) · 283/1,180,056 alleles
Filtering AF
0.0216%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0207%
Overall
0.018%
291/1,613,790 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.024% | 4,170 |
| Finnishnot grpmax-eligible | 0.00628% | 15,923 |
| African / African-American | 0.004% | 24,984 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
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
- PDE11A
- Protein
- p.Glu20=
- Coding
- c.60G>A
- MANE Select
- NM_016953
- dbSNP
- rs147765540
- Type
- single nucleotide variant
- Location
- chr2:178072378 (GRCh38)
- Gene constraint
- LOEUF 1.118 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.12
Similar variants
- PDE11A p.Lys20Ter Likely benign ★ same residue
- PDE11A p.Ser604Ter Pathogenic/Likely pathogenic ★★ same type
- PDE11A p.Arg329Ter Uncertain significance ★★ same type
- PDE11A p.Arg867Trp Uncertain significance ★★ ⚠ same type
- PDE11A p.Gln374Ter Uncertain significance ★★ same type
- PDE11A p.Pro165Thr Uncertain significance ★★ ⚠ same type
- PDE11A p.Pro893Gln Uncertain significance ★★ ⚠ same type
- PDE11A p.Tyr658Cys 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/pde11a-p-glu20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown