PDE5A p.Arg794=
c.2380A>C · rs144204269 · VCV719486
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.581%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.367 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 13.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.581%
African / African-American · 435/74,868 alleles
Filtering AF
0.536%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.518%
Overall
0.0355%
570/1,605,460 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.581% | 172 |
| Admixed American | 0.149% | 673 |
| Remaining individualsnot grpmax-eligible | 0.0466% | 2,145 |
| Middle Eastern | 0.0166% | 6,040 |
| European (non-Finnish) | 0.00136% | 73,289 |
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
- PDE5A
- Protein
- p.Arg794=
- Coding
- c.2380A>C
- MANE Select
- NM_001083
- dbSNP
- rs144204269
- Type
- single nucleotide variant
- Location
- chr4:119502607 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.32 · 50 PDB
- Residue 794
- the pdease domain; an α-helix
Similar variants
- PDE5A c.2190-4G>A Benign/Likely benign ★★ same type
- PDE5A p.Arg740Lys Likely benign ★★ same type
- PDE5A p.Glu119Val Benign/Likely benign ★★ same type
- PDE5A p.Glu475= Benign/Likely benign ★★ same type
- PDE5A p.Glu808= Benign ★★ same type
- PDE5A p.Lys480Gln Benign ★★ same type
- PDE5A p.Pro671= Benign ★★ same type
- PDE5A p.Ala235Val 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/pde5a-p-arg794 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown