PDE10A p.Pro949=
c.2847C>T · rs145110839 · VCV2905333
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, 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 -3.7 | GERP -3.2 |
| Overall | ||
| CADD | 6.866 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,850 alleles
Filtering AF
0.00231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00202%
Overall
0.0026%
42/1,613,764 alleles · very rare
exomes 38/1,461,732 · genomes 4/152,032 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,713 |
| European (non-Finnish) | 0.00314% | 31,890 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
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.Pro949=
- Coding
- c.2847C>T
- MANE Select
- NM_001385079
- dbSNP
- rs145110839
- Type
- single nucleotide variant
- Location
- chr6:165343439 (GRCh38)
- Gene constraint
- LOEUF 0.427 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.05 · 359 PDB
- Residue 949
- the pdease domain; an α-helix
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-pro949 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown