PEX5 p.Pro45=
c.135G>C · rs761885230 · VCV287000
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00169%, afr)
Conditions
1
peroxisome biogenesis disorder 2B
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 -2.1 | GERP -2.3 |
| Overall | ||
| CADD | 1.858 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00169%
African / African-American · 1/59,310 alleles
Overall
6.44e-05%
1/1,552,818 alleles · very rare
exomes 1/1,457,414 · genomes 0/95,404 · joint denominator
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
- PEX5
- Protein
- p.Pro45=
- Coding
- c.135G>C
- MANE Select
- NM_001351132
- dbSNP
- rs761885230
- Type
- single nucleotide variant
- Location
- chr12:7190512 (GRCh38)
- Gene constraint
- LOEUF 0.768 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.28 · 11 PDB
- Residue 45
- the 'disordered' region
Similar variants
- PEX5 p.Pro45Leu Uncertain significance ★ ⚠ same residue
- PEX5 p.Pro45Ser Uncertain significance ★ ⚠ same residue
- PEX5 c.449-2A>G Pathogenic/Likely pathogenic ★★ same condition
- PEX5 c.552-1G>A Pathogenic/Likely pathogenic ★★ same condition
- PEX5 c.847-2A>G Likely pathogenic ★★ same condition
- PEX5 c.967-1G>A Likely pathogenic ★★ same condition
- PEX5 p.Arg237Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX5 p.Arg276Ter Pathogenic/Likely pathogenic ★★ same condition
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/pex5-p-pro45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown