PEX2 p.Ile104=
c.312C>A · rs1242924229 · VCV1667717
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Conditions
1
peroxisome biogenesis disorder 5A (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 -0.4 | GERP -4.9, phastCons 0.013 |
| Overall | ||
| CADD | 1.987 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,870 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000186%
3/1,614,074 alleles · very rare
exomes 3/1,461,860 · genomes 0/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,435 |
| European (non-Finnish) | 8.47e-05% | 1,179,997 |
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
- PEX2
- Protein
- p.Ile104=
- Coding
- c.312C>A
- MANE Select
- NM_000318
- dbSNP
- rs1242924229
- Type
- single nucleotide variant
- Location
- chr8:76983867 (GRCh38)
- Gene constraint
- LOEUF 1.057 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.17
- Residue 104
- a UniProt-annotated variant site (in pbd5a)
Similar variants
- PEX2 p.Ile104Met Uncertain significance ★ ⚠ same residue
- PEX2 p.Ile104fs Pathogenic/Likely pathogenic ★★ same residue
- PEX2 c.-17-2A>G Pathogenic/Likely pathogenic ★★ same condition
- PEX2 p.Arg119Ter Pathogenic ★★ same condition
- PEX2 p.Arg125Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX2 p.Gln31Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX2 p.Gln78Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX2 p.Gln96Ter 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/pex2-p-ile104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown