PEX10 p.Arg326=
c.978C>G · rs2522247995 · VCV2752346
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
Peroxisome biogenesis disorder, complementation group 7
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 |
|---|---|---|
| Pangolin | Δ0.82 | gain · loss 0.00 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.91 | GERP -0.28, phastCons 0.98 |
| Overall | ||
| CADD | 8.016 | 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
- PEX10
- Protein
- p.Arg326=
- Coding
- c.978C>G
- MANE Select
- NM_002617
- dbSNP
- rs2522247995
- Type
- single nucleotide variant
- Location
- chr1:2405769 (GRCh38)
- Gene constraint
- LOEUF 1.234 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.81
- Residue 326
- a UniProt-annotated variant site (in pbd6b and pbd6a)
Similar variants
- PEX10 p.Arg326Cys Uncertain significance ★★ ⚠ same residue
- PEX10 p.Arg326His Uncertain significance ★★ ⚠ same residue
- PEX10 p.Arg326Ser Uncertain significance ★★ ⚠ same residue
- PEX10 c.113-1G>A Likely pathogenic ★★ same condition
- PEX10 c.776+1G>A Likely pathogenic ★★ same condition
- PEX10 p.Arg125Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX10 p.Met1Ile Pathogenic/Likely pathogenic ★★ same condition
- PEX10 c.776+5G>A 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/pex10-p-arg326 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown