PEX1 p.Arg995=
c.2985G>A · rs2484636645 · VCV2106162
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Zellweger spectrum disorders
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 3.1, phastCons 1 |
| Overall | ||
| CADD | 17.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PEX1
- Protein
- p.Arg995=
- Coding
- c.2985G>A
- MANE Select
- NM_000466
- dbSNP
- rs2484636645
- Type
- single nucleotide variant
- Location
- chr7:92494338 (GRCh38)
- Gene constraint
- LOEUF 0.746 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.19
- Residue 995
- a UniProt-annotated variant site (in pbd1a)
Disease context
Zellweger spectrum disorders — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Zellweger syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Neonatal
Similar variants
- PEX1 c.1239+1G>T Pathogenic ★★ same condition
- PEX1 c.130-1G>T Pathogenic/Likely pathogenic ★★ same condition
- PEX1 c.130-2A>G Pathogenic/Likely pathogenic ★★ same condition
- PEX1 c.130-2A>T Pathogenic/Likely pathogenic ★★ same condition
- PEX1 c.1483+1G>A Pathogenic ★★ same condition
- PEX1 c.1587+1G>A Likely pathogenic ★★ same condition
- PEX1 c.1670+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PEX1 c.1670+1G>T 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-arg995 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown