PDE5A p.Pro671=
c.2013A>C · rs61729464 · VCV789729
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.29%, 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. | ||
| REVEL | 0.029 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.5 |
| Overall | ||
| CADD | 0.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.29%
African / African-American · 3,960/74,814 alleles
Filtering AF
5.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.1%
Overall
0.29%
4,653/1,607,088 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.29% | 19 |
| Middle Eastern | 0.58% | 173 |
| Admixed American | 0.387% | 258 |
| Remaining individualsnot grpmax-eligible | 0.346% | 289 |
| European (non-Finnish) | 0.0168% | 5,962 |
| South Asian | 0.0155% | 6,471 |
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.Pro671=
- Coding
- c.2013A>C
- MANE Select
- NM_001083
- dbSNP
- rs61729464
- Type
- single nucleotide variant
- Location
- chr4:119511122 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.32 · 50 PDB
- Residue 671
- 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.Ala235Val Uncertain significance ★ ⚠ same type
- PDE5A p.Ala282Val 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-pro671 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown