PEX13 p.Pro22=
c.66G>A · rs1264694420 · VCV1450896
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00974%, eas)
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 -0.38 | GERP -0.25, phastCons 0.004 |
| Overall | ||
| CADD | 11.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00974%
East Asian · 4/41,064 alleles
Filtering AF
0.00327%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00193%
Overall
0.000774%
12/1,550,422 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00974% | 10,266 |
| African / African-American | 0.00137% | 73,048 |
| European (non-Finnish) | 0.00061% | 163,830 |
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.Pro22=
- Coding
- c.66G>A
- MANE Select
- NM_002618
- dbSNP
- rs1264694420
- Type
- single nucleotide variant
- Location
- chr2:61017825 (GRCh38)
- Gene constraint
- LOEUF 1.159 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.62 · 3 PDB
- Residue 22
- the 'disordered' region
Similar variants
- PEX13 p.Pro22Ser Uncertain significance ★ ⚠ same residue
- PEX13 p.Pro22Leu 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
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-pro22 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown