PEX13

protein-coding

peroxisomal biogenesis factor 13, the group of Peroxins

Gene summary

This gene encodes a peroxisomal membrane protein that binds the type 1 peroxisomal targeting signal receptor via a SH3 domain located in the cytoplasm. Mutations and deficiencies in peroxisomal protein importing and peroxisome assembly lead to peroxisomal biogenesis disorders, an example of which is Zellweger syndrome. [provided by RefSeq, Oct 2008]

MANE transcript

NM_002618.4

Inheritance

AR

ClinVar variants

P:47U:274B:173

Top phenotype

Peroxisome biogenesis disorder 11A (Zellweger syndrome); Peroxisome biogenesis disorder 11B

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr2:61,017,225-61,051,990

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~34.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

peroxisome biogenesis disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0019234

Submitter: PanelApp Australia

peroxisome biogenesis disorder 11A (Zellweger)STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013949

Submitter: Labcorp Genetics (formerly Invitae)

peroxisome biogenesis disorderDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019234

Submitter: ClinGen

The relationship between PEX13 and peroxisome biogenesis disorder (types 11A and 11B included), an autosomal recessive disorder, was evaluated using the ClinGen Clinical Validity Framework as of August, 2019. PEX13 encodes a peroxisome membrane protein involved in PTS1 and PTS2 import. Peroxisomal biogenesis disorders are caused by defects in various stages of peroxisomal protein import and/or peroxisome biogenesis, involving at least 14 PEX genes. PEX13 belongs to complementation group H or group 13, and mutations in the gene result in cells devoid of peroxisomes (Waterham and Ebberink 2012, PMID 22871920). PEX13 was first reported in relation to autosomal recessive Peroxisome biogenesis disorder in 1999. (Shimozawa et al, 1999; PMID: 10332040, Liu et al, 1999; PMID: 10441568). At least 9 nonsense, splice site, frameshift, deletion/duplication and missense variants have been reported in humans. Evidence supporting this gene-disease relationship includes case-level data and experimental data. Summary of Case Level Data (11 points): Variants in this gene have been reported in at least 9 probands in 5 publications (PMIDs: 10332040, 21031596, 17041890, 10441568, 19449432). The mechanism for disease is expected to be homozygous loss of function. Summary of experimental data (5 points): This gene-disease association is supported by in vitro functional assays and animal models. PEX13 interacts with PEX19 and PEX14 (PMID: 12096124, 15798189). Mouse models of PEX13 recapitulate the human disease (PMIDs: 12897163, 29187321) and functional experiments show impaired PTS1 and PTS2 import in PEX13-deficient cells (PMIDs: 21669930, 8858165). In summary, PEX13 is definitively associated with autosomal recessive peroxisome biogenesis disorder. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the Peroxisomal Disorders GCEP on October 4, 2019.

Zellweger spectrum disordersSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019609

Submitter: Orphanet

peroxisome biogenesis disorder 11BDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013950

Submitter: G2P

peroxisome biogenesis disorder 11A (Zellweger)DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013949

Submitter: G2P

Clinical Genomic Database (CGD)

Peroxisome biogenesis disorder 11A (Zellweger syndrome); Peroxisome biogenesis disorder 11BAR

Manifestation: Biochemical; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Renal

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 9480815; 10441568; 10332040; 17041890; 19449432Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PEX13 variants in ClinVar

8 Conditions Cataloged
Peroxisome biogenesis disorder 11A (Zellweger)Total: 475
not providedTotal: 89
PEX13-related disorderTotal: 79
Inborn genetic diseasesTotal: 71
not specifiedTotal: 44
Peroxisome biogenesis disorder 11BTotal: 15
Peroxisome biogenesis disorderTotal: 6
Peroxisome biogenesis disorder 4A (Zellweger)Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002618.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
159
clinvar
162
missense
1
clinvar
3
clinvar
267
clinvar
13
clinvar
1
clinvar
285
nonsense
12
clinvar
6
clinvar
2
clinvar
20
start loss
1
clinvar
1
frameshift
17
clinvar
4
clinvar
21
splice donor/acceptor (+/-2bp)
4
clinvar
1
clinvar
5
Total30172741721494

Highest pathogenic variant AF is 0.00008432519

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002618.4RefSeqNP_002609.14MANE Select
ENST00000295030.6EnsemblENSP00000295030.44MANE Select
ENST00000401576.1EnsemblENSP00000384738.12Standard
ENST00000401576.2EnsemblENSP00000384738.12Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
pex13Danio rerio

Structure: hepatocyte

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Peroxisome - Homo sapiens (human)
  • Beta Oxidation of Very Long Chain Fatty Acids
  • Oxidation of Branched Chain Fatty Acids
  • Adrenoleukodystrophy, X-linked
  • Carnitine-acylcarnitine translocase deficiency

Biological Process

  • fatty acid alpha-oxidation
  • neuron migration
  • suckling behavior
  • protein targeting to peroxisome
  • locomotory behavior

Molecular Function

  • protein binding

Cellular Component

  • peroxisome
  • peroxisomal membrane
  • integral component of peroxisomal membrane
  • membrane
  • intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000295030
Coding exons
4
Length
34766
Individuals with no LoFs
125728
Homozygous LoFs
0
Heterozygous LoFs
18
Defined
125746
p
0.0000716
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.2972302181.060.00001132606
Missense (PolyPhen)6267.0830.92422867
Synonymous-0.5748376.61.080.00000362840
Loss of Function1.53915.50.5828.38e-7184

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish00.0absent
East Asian0.000160.00016rare
Finnish00.0absent
European (Non-Finnish)0.0000440.000044rare
South Asian0.000130.00013rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Component of the peroxisomal translocation machinery with PEX14 and PEX17. Functions as a docking factor for the predominantly cytoplasmic PTS1 receptor (PAS10/PEX5). Involved in the import of PTS1 and PTS2 proteins.;
Disease
DISEASE: Peroxisome biogenesis disorder complementation group 13 (PBD-CG13) [MIM:614883]: A peroxisomal disorder arising from a failure of protein import into the peroxisomal membrane or matrix. The peroxisome biogenesis disorders (PBD group) are genetically heterogeneous with at least 14 distinct genetic groups as concluded from complementation studies. Include disorders are: Zellweger syndrome (ZWS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD), and classical rhizomelic chondrodysplasia punctata (RCDP). ZWS, NALD and IRD are distinct from RCDP and constitute a clinical continuum of overlapping phenotypes known as the Zellweger spectrum (PBD-ZSS). {ECO:0000269|PubMed:10332040, ECO:0000269|PubMed:19449432}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 11A (PBD11A) [MIM:614883]: A fatal peroxisome biogenesis disorder belonging to the Zellweger disease spectrum and clinically characterized by severe neurologic dysfunction with profound psychomotor retardation, severe hypotonia and neonatal seizures, craniofacial abnormalities, liver dysfunction, and biochemically by the absence of peroxisomes. Additional features include cardiovascular and skeletal defects, renal cysts, ocular abnormalities, and hearing impairment. Most severely affected individuals with the classic form of the disease (classic Zellweger syndrome) die within the first year of life. {ECO:0000269|PubMed:10332040, ECO:0000269|PubMed:19449432}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 11B (PBD11B) [MIM:614885]: A peroxisome biogenesis disorder that includes neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease (IRD), two milder manifestations of the Zellweger disease spectrum. The clinical course of patients with the NALD and IRD presentation is variable and may include developmental delay, hypotonia, liver dysfunction, sensorineural hearing loss, retinal dystrophy and vision impairment. Children with the NALD presentation may reach their teens, while patients with the IRD presentation may reach adulthood. The clinical conditions are often slowly progressive in particular with respect to loss of hearing and vision. The biochemical abnormalities include accumulation of phytanic acid, very long chain fatty acids (VLCFA), di- and trihydroxycholestanoic acid and pipecolic acid. {ECO:0000269|PubMed:10332040, ECO:0000269|PubMed:10441568}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.216

Intolerance Scores

LoFtool
0.511
RVIS EVS
0.37
RVIS percentile EVS
75.29

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
K
Indispensability pred.
E
Indispensability score
0.955

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.