PEX13 p.Ile333=
c.999T>C · rs750110664 · VCV1642991
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, 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 1.4 | GERP -0.71, phastCons 1 |
| Overall | ||
| CADD | 11.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
East Asian · 5/44,898 alleles
Filtering AF
0.00434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.00031%
5/1,614,008 alleles · ultra-rare
exomes 4/1,461,826 · genomes 1/152,182 · 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
- PEX13
- Protein
- p.Ile333=
- Coding
- c.999T>C
- MANE Select
- NM_002618
- dbSNP
- rs750110664
- Type
- single nucleotide variant
- Location
- chr2:61048557 (GRCh38)
- Gene constraint
- LOEUF 1.159 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.62 · 3 PDB
- Residue 333
- a β-strand; the sh3 domain
Similar variants
- 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
- PEX13 p.Ala302Gly 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-ile333 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown