PEX2 p.Gln159=
c.477G>A · rs35218706 · VCV291153
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.489%, afr)
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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.95 | GERP -4, phastCons 0.003 |
| Overall | ||
| CADD | 1.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.489%
African / African-American · 367/75,044 alleles
Filtering AF
0.448%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.432%
Overall
0.0264%
426/1,614,092 alleles · rare
exomes 188/1,461,790 · genomes 238/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.489% | 204 |
| Admixed American | 0.0483% | 2,070 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,718 |
| Middle Eastern | 0.0165% | 6,062 |
| East Asian | 0.00223% | 44,884 |
| European (non-Finnish) | 0.000424% | 236,002 |
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.Gln159=
- Coding
- c.477G>A
- MANE Select
- NM_000318
- dbSNP
- rs35218706
- Type
- single nucleotide variant
- Location
- chr8:76983702 (GRCh38)
- Gene constraint
- LOEUF 1.057 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.17
- Residue 159
- a UniProt-annotated variant site (in pbd5a); a UniProt-annotated variant site (in pbd5b and pbd5a)
Similar variants
- PEX2 p.Gln159Ter 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
- PEX2 p.Glu168Ter 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/pex2-p-gln159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown