peroxisome biogenesis disorder 11B

Summary

peroxisome biogenesis disorder 11B (MONDO:0013950) is a disease caused by PEX13 (GenCC Definitive), with 1 cohort gene.

At a glance

• Causal gene: PEX13 (GenCC Definitive)
• Cohort genes: 1
• ClinVar variants: 12

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	peroxisome biogenesis disorder 11B
Mondo ID	MONDO:0013950
OMIM	614885
DOID	DOID:0081439
UMLS	C3554001
MedGen	766915
GARD	0015875
Is cancer (heuristic)	no

Also known as: PBD11B · peroxisome biogenesis disorder 11B · peroxisome biogenesis disorder type 11B

Data availability: 12 ClinVar variants · 1 GenCC gene-disease record.

Disease family

Classification path: disease › human disease › disease by developmental or physiological process › metabolic disease › developmental anomaly of metabolic origin › Zellweger spectrum disorders › peroxisome biogenesis disorder due to PEX13 defect › peroxisome biogenesis disorder 11B

Related subtypes (1): peroxisome biogenesis disorder 11A (Zellweger)

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

12 retrieved; paginated sample, class counts are floors:

4 uncertain significance, 3 conflicting classifications of pathogenicity, 3 likely pathogenic, 2 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
1411346	NM_002618.4(PEX13):c.367G>T (p.Glu123Ter)	PEX13	Pathogenic	criteria provided, multiple submitters, no conflicts
375270	NM_002618.4(PEX13):c.937T>G (p.Trp313Gly)	PEX13	Pathogenic	no assertion criteria provided
3586794	NM_002618.4(PEX13):c.35G>A (p.Trp12Ter)	PEX13	Likely pathogenic	criteria provided, single submitter
3586795	NM_002618.4(PEX13):c.744C>A (p.Tyr248Ter)	PEX13	Likely pathogenic	criteria provided, single submitter
7704	NM_002618.4(PEX13):c.977T>C (p.Ile326Thr)	PEX13	Likely pathogenic	criteria provided, multiple submitters, no conflicts
196352	NM_002618.4(PEX13):c.893T>C (p.Met298Thr)	PEX13	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
287094	NM_002618.4(PEX13):c.880C>T (p.Arg294Trp)	PEX13	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
999729	NM_002618.4(PEX13):c.589C>T (p.Arg197Trp)	PEX13	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1366013	NM_002618.4(PEX13):c.595T>A (p.Leu199Ile)	PEX13	Uncertain significance	criteria provided, multiple submitters, no conflicts
499526	NM_002618.4(PEX13):c.677G>A (p.Arg226Gln)	PEX13	Uncertain significance	criteria provided, multiple submitters, no conflicts
500639	NM_002618.4(PEX13):c.89T>C (p.Phe30Ser)	PEX13	Uncertain significance	criteria provided, multiple submitters, no conflicts
938182	NM_002618.4(PEX13):c.278A>G (p.Tyr93Cys)	PEX13	Uncertain significance	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 3 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

Gene	Classification	Inheritance	Disease	Records
PEX13	Definitive	Autosomal recessive	peroxisome biogenesis disorder 11A (Zellweger)	5

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
PEX13	Orphanet:44	Neonatal adrenoleukodystrophy
PEX13	Orphanet:772	Infantile Refsum disease
PEX13	Orphanet:912	Zellweger syndrome

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
PEX13	HGNC:8855	ENSG00000162928	Q92968	Peroxisomal membrane protein PEX13	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
PEX13	Peroxisomal membrane protein PEX13	Component of the PEX13-PEX14 docking complex, a translocon channel that specifically mediates the import of peroxisomal cargo proteins bound to PEX5 receptor.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 0 · Druggable fraction: 0.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

Family	Genes	Fold	FDR
Scaffold/PPI	1	17.3×	0.058

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
PEX13	Scaffold/PPI	no		SH3_domain, Peroxin-13_N, Pex13

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
oocyte	1
secondary oocyte	1
sperm	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
PEX13	264	ubiquitous	marker	secondary oocyte, sperm, oocyte

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
PEX13	1,127

Structural data

PDB: 1 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
PEX13	Q92968	3

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 3. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Class I peroxisomal membrane protein import	1	519.1×	0.006	PEX13
E3 ubiquitin ligases ubiquitinate target proteins	1	193.6×	0.006	PEX13
Peroxisomal protein import	1	173.0×	0.006	PEX13

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
microtubule-based peroxisome localization	1	8426.0×	7e-04	PEX13
protein import into peroxisome matrix, docking	1	4213.0×	7e-04	PEX13
protein import into peroxisome matrix, translocation	1	4213.0×	7e-04	PEX13
fatty acid alpha-oxidation	1	2407.4×	9e-04	PEX13
suckling behavior	1	1685.2×	1e-03	PEX13
cerebral cortex cell migration	1	1532.0×	1e-03	PEX13
cellular response to reactive oxygen species	1	411.0×	0.003	PEX13
locomotory behavior	1	179.3×	0.006	PEX13
neuron migration	1	133.8×	0.007	PEX13

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1

Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
PEX13	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	PEX13

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
PEX13	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.