PDE1C p.Val236=
c.708T>C · rs61736721 · VCV3033520
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.512%, 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 -0.22 | GERP -3.9, phastCons 0.013 |
| Overall | ||
| CADD | 0.809 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.512%
African / African-American · 384/75,046 alleles
Filtering AF
0.469%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.453%
Overall
0.0317%
511/1,614,054 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.512% | 195 |
| Remaining individualsnot grpmax-eligible | 0.0624% | 1,603 |
| Admixed American | 0.0516% | 1,936 |
| Middle Eastern | 0.033% | 3,029 |
| European (non-Finnish) | 0.00458% | 21,850 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,600 |
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
- PDE1C
- Protein
- p.Val236=
- Coding
- c.708T>C
- MANE Select
- NM_001191057
- dbSNP
- rs61736721
- Type
- single nucleotide variant
- Location
- chr7:31864984 (GRCh38)
- Gene constraint
- LOEUF 0.843 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.53
- Residue 236
- the pdease domain
Similar variants
- PDE1C p.Arg45Gln Uncertain significance ★★ ⚠ same type
- PDE1C p.His619Tyr Uncertain significance ★★ ⚠ same type
- PPP1R17 p.Asp21Glu Uncertain significance ★★ ⚠ same type
- PPP1R17 p.Gln8Arg Uncertain significance ★★ ⚠ same type
- PDE1C c.1203+28A>G Benign ★★ same type
- PDE1C p.Ala594= Benign ★★ same type
- PDE1C p.Arg635His Likely benign ★★ same type
- PDE1C p.Arg660His Benign ★★ 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/pde1c-p-val236 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown