PDE5A p.Thr357=
c.1071T>A · rs202018090 · VCV2655055
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, nfe)
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 -4.2 | GERP -3.7 |
| Overall | ||
| CADD | 1.265 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
European (non-Finnish) · 194/1,174,712 alleles
Filtering AF
0.0146%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0139%
Overall
0.0132%
212/1,601,030 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0165% | 6,055 |
| Remaining individualsnot grpmax-eligible | 0.0145% | 6,878 |
| Finnishnot grpmax-eligible | 0.011% | 9,127 |
| African / African-American | 0.0027% | 36,982 |
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.Thr357=
- Coding
- c.1071T>A
- MANE Select
- NM_001083
- dbSNP
- rs202018090
- Type
- single nucleotide variant
- Location
- chr4:119562893 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.32 · 50 PDB
- Residue 357
- the gaf 2 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-thr357 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown