PEX1 p.Gln529=
c.1587A>G · rs2484685600 · VCV3039078
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,383,738)
Conditions
1
PEX1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.28 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP 4.2, phastCons 1 |
| Overall | ||
| CADD | 11.44 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,383,738). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- PEX1
- Protein
- p.Gln529=
- Coding
- c.1587A>G
- MANE Select
- NM_000466
- dbSNP
- rs2484685600
- Type
- single nucleotide variant
- Location
- chr7:92510944 (GRCh38)
- Gene constraint
- LOEUF 0.746 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.19
Disease context
PEX1-related disorder
Similar variants
- PEX1 p.Gln529Ter Likely pathogenic ★ same residue
- PEX1 c.1900+2T>C Pathogenic/Likely pathogenic ★★ same condition
- PEX1 p.Arg581Pro Pathogenic/Likely pathogenic ★★ same condition
- PEX1 p.Arg633Ter Pathogenic ★★ same condition
- PEX1 p.Arg790Ter Pathogenic ★★ same condition
- PEX1 p.Arg795Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX1 p.Gln471Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX1 p.Trp60Ter 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/pex1-p-gln529 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown