PEX2 p.Lys136fs
c.408del · VCV4818158
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Zellweger spectrum disorders
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (4 of 4) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 8.6 | GERP 2.4, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PEX2
- Protein
- p.Lys136fs
- Coding
- c.408del
- MANE Select
- NM_000318
- Type
- Deletion
- Location
- chr8:76983771 (GRCh38)
- Gene constraint
- LOEUF 1.057 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.17
- Residue 136
- a UniProt-annotated variant site (in pbd5a); a UniProt-annotated variant site (in pbd5b and pbd5a)
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
- PEX2 p.Arg94fs Pathogenic/Likely pathogenic ★★ same condition
- PEX2 p.Glu118fs Likely pathogenic ★★ same condition
- PEX2 p.Gly113_Arg114insTer Pathogenic/Likely pathogenic ★★ same condition
- PEX2 p.Leu204fs Pathogenic/Likely pathogenic ★★ same condition
- PEX2 p.Phe263fs Likely pathogenic ★★ same condition
- PEX2 p.Cys283fs Likely pathogenic ★ same condition
- PEX2 p.Gly149fs Likely pathogenic ★ same condition
- PEX2 p.Leu166fs 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/pex2-p-lys136fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown