PEX1 p.Ser254fs
c.760dup · rs1554375511 · VCV557794
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
ultra-rare (gnomAD MAF 7.222e-07)
Conditions
1
peroxisome biogenesis disorder 1A (Zellweger)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 24 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 10 | GERP 2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
dbSNP / gnomAD
Global frequency
7.22e-05%
via dbSNP · ultra-rare
No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.
Variant & gene context
- Gene
- PEX1
- Protein
- p.Ser254fs
- Coding
- c.760dup
- MANE Select
- NM_000466
- dbSNP
- rs1554375511
- Type
- Duplication
- Location
- chr7:92517754 (GRCh38)
- Gene constraint
- LOEUF 0.746 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.19
Similar variants
- PEX1 p.His951fs Pathogenic/Likely pathogenic ★★ same condition
- PEX1 p.Ile700fs Pathogenic ★★ same condition
- PEX1 p.Leu1177fs Pathogenic/Likely pathogenic ★★ same condition
- PEX1 p.Lys614fs Pathogenic ★★ same condition
- PEX1 p.Pro934fs Pathogenic/Likely pathogenic ★★ same condition
- PEX1 p.Thr181fs Pathogenic/Likely pathogenic ★★ same condition
- PEX1 p.Thr643fs Pathogenic ★★ same condition
- PEX1 p.Trp653_Met654insThrValTrp 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/pex1-p-ser254fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown