Is PEX13 p.Arg50fs (c.148del) pathogenic?

PEX13 p.Arg50fs (c.148del) is classified Pathogenic in PEX13 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-27). Absent from gnomAD; Associated with peroxisome biogenesis disorder 11A (Zellweger).

What condition is associated with PEX13 p.Arg50fs (c.148del)?

PEX13 p.Arg50fs (c.148del) is associated with peroxisome biogenesis disorder 11A (Zellweger) (ClinVar).

How common is PEX13 p.Arg50fs (c.148del) in the general population?

PEX13 p.Arg50fs (c.148del) is absent from gnomAD (gnomAD).

PEX13 p.Arg50fs

c.148del · rs2467507433 · VCV1993651

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

peroxisome biogenesis disorder 11A (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 2 of 4
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP 0.81, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: PEX13
Protein: p.Arg50fs
Coding: c.148del
MANE Select: NM_002618
dbSNP: rs2467507433
Type: Deletion
Location: chr2:61031474 (GRCh38)
Gene constraint: LOEUF 1.159 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.62 · 3 PDB
Residue 50: the 'disordered' region

Full PEX13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

peroxisome biogenesis disorder 11A (Zellweger) — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX13 p.Gly36fs Likely pathogenic ★ same condition
PEX13 p.His167fs Pathogenic ★ same condition
PEX13 p.Ile291fs Pathogenic ★ same condition
PEX13 p.Leu254fs Pathogenic ★ same condition
PEX13 p.Lys10fs Pathogenic ★ same condition
PEX13 p.Met198fs Pathogenic ★ same condition
PEX13 p.Phe71fs Pathogenic ★ same condition
PEX13 p.Pro54fs 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/pex13-p-arg50fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown