PEX13 p.Pro18=
c.54G>A · rs1002699754 · VCV595682
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 0.00589%, amr)
Conditions
1
peroxisome biogenesis disorder 11A (Zellweger)
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 -0.77 | GERP -2.7, phastCons 0.001 |
| Overall | ||
| CADD | 7.649 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00589%
Admixed American · 3/50,972 alleles
Filtering AF
0.00156%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000833%
Overall
0.000258%
4/1,550,448 alleles · very rare
exomes 2/1,398,234 · genomes 2/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00589% | 16,991 |
| European (non-Finnish) | 8.72e-05% | 1,146,846 |
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
- PEX13
- Protein
- p.Pro18=
- Coding
- c.54G>A
- MANE Select
- NM_002618
- dbSNP
- rs1002699754
- Type
- single nucleotide variant
- Location
- chr2:61017813 (GRCh38)
- Gene constraint
- LOEUF 1.159 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.62 · 3 PDB
- Residue 18
- the 'disordered' region
Similar variants
- PEX13 p.Pro18Leu Uncertain significance ★ ⚠ same residue
- PEX13 p.Arg16Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX13 p.Arg170Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX13 p.Arg226Ter Pathogenic ★★ same condition
- PEX13 p.Gln131Ter Pathogenic ★★ same condition
- PEX13 p.Glu123Ter Pathogenic ★★ same condition
- PEX13 p.Tyr155Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX13 c.913+3A>G Uncertain significance ★★ 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/pex13-p-pro18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown