PDE1A c.1516+17841A>G
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 11.4%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +17841 | deep intronic (+17841 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP -3.2 |
| Non-coding constraint | Z -1.02 | 1 kb window · o/e 1.08 · regional · uncalibrated |
| Overall | ||
| CADD | 0.988 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.4%
African / African-American · 7,461/65,360 alleles
Filtering AF
11.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 11.1%
Overall
0.668%
8,547/1,279,596 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 11.4% | 9 |
| Admixed American | 1.06% | 94 |
| Remaining individualsnot grpmax-eligible | 0.871% | 115 |
| Middle Eastern | 0.608% | 165 |
| European (non-Finnish) | 0.0349% | 2,865 |
| South Asian | 0.00947% | 10,563 |
| East Asian | 0.00297% | 33,626 |
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
- PDE1A
- Coding
- c.1516+17841A>G
- MANE Select
- NM_001363871
- dbSNP
- rs78879279
- Type
- single nucleotide variant
- Location
- chr2:182168051 (GRCh38)
- Gene constraint
- LOEUF 0.854 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.12
Similar variants
- PDE1A c.1004+24G>T Benign ★★ same type
- PDE1A c.101+113C>T Benign ★★ same type
- PDE1A c.1207+48G>C Benign ★★ same type
- PDE1A c.1207+62A>T Benign ★★ same type
- PDE1A c.1208-106T>C Benign ★★ same type
- PDE1A c.168-1739A>C Benign ★★ same type
- PDE1A c.168-1806A>G Benign ★★ same type
- PDE1A c.54-101T>C 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/pde1a-c-1516-plus-17841a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown