PDE10A p.Pro12=
c.36C>A · VCV4823532
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00149%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.8 | GERP -0.2, phastCons 1 |
| Overall | ||
| CADD | 12.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00149%
European (non-Finnish) · 1/66,986 alleles
Overall
0.000669%
1/149,492 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
- PDE10A
- Protein
- p.Pro12=
- Coding
- c.36C>A
- MANE Select
- NM_001385079
- Type
- single nucleotide variant
- Location
- chr6:165662776 (GRCh38)
- Gene constraint
- LOEUF 0.427 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.05 · 359 PDB
- Residue 12
- the 'disordered' region
Similar variants
- PDE10A p.Phe566Leu Likely pathogenic ★★ same type
- PDE10A p.Phe600Cys Pathogenic/Likely pathogenic ★★ same type
- PDE10A p.Phe600Leu Pathogenic ★★ same type
- PDE10A p.Ala1052Ser Uncertain significance ★★ ⚠ same type
- PDE10A p.Asn502Ser Uncertain significance ★★ ⚠ same type
- PDE10A p.Asn559Ser Uncertain significance ★★ ⚠ same type
- PDE10A p.Asp307Glu Uncertain significance ★★ same type
- PDE10A p.Cys284Gly 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/pde10a-p-pro12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown