PDE1C p.Ser93=
c.279C>T · rs60578446 · VCV778019
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.45%, 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 1.4 | GERP -0.12, phastCons 1 |
| Overall | ||
| CADD | 7.158 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.45%
African / African-American · 2,591/75,000 alleles
Filtering AF
3.34%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.3%
Overall
0.198%
3,189/1,612,584 alleles · low-frequency
exomes 1,661/1,460,308 · genomes 1,528/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.45% | 29 |
| Admixed American | 0.322% | 311 |
| Remaining individualsnot grpmax-eligible | 0.269% | 372 |
| Middle Eastern | 0.132% | 757 |
| European (non-Finnish) | 0.019% | 5,266 |
| South Asian | 0.00549% | 18,214 |
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.Ser93=
- Coding
- c.279C>T
- MANE Select
- NM_001191057 · reported on NM_001191058
- dbSNP
- rs60578446
- Type
- single nucleotide variant
- Location
- chr7:32169814 (GRCh38)
- Gene constraint
- LOEUF 0.843 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.53
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-ser93 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown