PEX26 p.Ser21=
c.63C>T · rs1487562921 · VCV2130246
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000172%, nfe)
Conditions
2
peroxisome biogenesis disorder 7A (Zellweger)
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 3.6 | GERP 3.5, phastCons 1 |
| Overall | ||
| CADD | 19.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000172%
European (non-Finnish) · 2/1,164,828 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000141%
2/1,422,210 alleles · very rare
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
- PEX26
- Protein
- p.Ser21=
- Coding
- c.63C>T
- MANE Select
- NM_001127649
- dbSNP
- rs1487562921
- Type
- single nucleotide variant
- Location
- chr22:18078439 (GRCh38)
- Gene constraint
- LOEUF 0.893 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.87
Similar variants
- PEX26 c.230+1G>T Pathogenic ★★ same condition
- PEX26 c.667+2T>C Pathogenic/Likely pathogenic ★★ same condition
- PEX26 p.Arg192Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX26 p.Arg98Trp Pathogenic/Likely pathogenic ★★ same condition
- PEX26 p.Gln146Ter Pathogenic ★★ same condition
- PEX26 p.Gly89Arg Pathogenic/Likely pathogenic ★★ ⚠ same condition
- PEX26 p.Trp62Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX26 c.230+3A>G 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/pex26-p-ser21 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown