PEX6 p.Pro118=
c.354G>A · VCV4059667
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 1,533,850)
Conditions
1
Zellweger spectrum disorders
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 -1.4 | GERP -3.2 |
| Overall | ||
| CADD | 11.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,533,850). 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
- PEX6
- Protein
- p.Pro118=
- Coding
- c.354G>A
- MANE Select
- NM_000287
- Type
- single nucleotide variant
- Location
- chr6:42978797 (GRCh38)
- Gene constraint
- LOEUF 0.799 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.87
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
- PEX6 p.Pro118Ser Uncertain significance ★ ⚠ same residue
- PEX6 c.1130+1G>A Likely pathogenic ★★ same condition
- PEX6 c.1233+1G>A Likely pathogenic ★★ same condition
- PEX6 c.1962-1G>A Pathogenic/Likely pathogenic ★★ same condition
- PEX6 c.2362+1G>A Likely pathogenic ★★ same condition
- PEX6 c.2589-1G>T Likely pathogenic ★★ same condition
- PEX6 c.2807-2A>G Pathogenic/Likely pathogenic ★★ same condition
- PEX6 c.882+1G>A 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/pex6-p-pro118 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown