PEX13

peroxisomal biogenesis factor 13, the group of Peroxins

Basic information

Region (hg38): 2:61017225-61051990

Links

ENSG00000162928 ∙ NCBI:5194 ∙ OMIM:601789 ∙ HGNC:8855 ∙ Uniprot:Q92968 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Zellweger spectrum disorders (Supportive), mode of inheritance: AR
• peroxisome biogenesis disorder 11A (Zellweger) (Strong), mode of inheritance: AR
• peroxisome biogenesis disorder (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Peroxisome biogenesis disorder 11A (Zellweger syndrome); Peroxisome biogenesis disorder 11B	AR	General	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	Biochemical; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Renal	9480815; 10441568; 10332040; 17041890; 19449432

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PEX13 gene.

• Peroxisome biogenesis disorder 11A (Zellweger) (24 variants)
• Peroxisome biogenesis disorder (3 variants)
• PEX13-related disorder (2 variants)
• Peroxisome biogenesis disorder 11B (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEX13 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	124		127
missense			235	2	1	238
nonsense	11	3	1			15
start loss			1			1
frameshift	13	1				14
inframe indel						0
splice donor/acceptor (+/-2bp)	1	3				4
splice region			3	13		16
non coding			62	31	12	105
Total	25	7	302	157	13

Highest pathogenic variant AF is 0.0000263

Variants in PEX13

This is a list of pathogenic ClinVar variants found in the PEX13 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-61017528-A-C			Benign (Aug 07, 2018)
2-61017692-C-T		Peroxisome biogenesis disorder 1A (Zellweger)	Uncertain significance (Jun 14, 2016)
2-61017748-G-A		Peroxisome biogenesis disorder 11A (Zellweger)	Uncertain significance (Jan 12, 2018)
2-61017753-G-A		not specified • Peroxisome biogenesis disorder 11A (Zellweger)	Conflicting classifications of pathogenicity (Jan 13, 2018)
2-61017754-G-C		not specified • Peroxisome biogenesis disorder 11A (Zellweger) • PEX13-related disorder	Likely benign (Nov 01, 2024)
2-61017760-A-G		Peroxisome biogenesis disorder 11A (Zellweger)	Uncertain significance (Feb 10, 2022)
2-61017765-G-C		Peroxisome biogenesis disorder 11A (Zellweger)	Likely benign (Dec 03, 2022)
2-61017765-G-T		Peroxisome biogenesis disorder 11A (Zellweger)	Likely benign (May 27, 2023)
2-61017767-C-G		Peroxisome biogenesis disorder 11A (Zellweger)	Uncertain significance (Oct 09, 2021)
2-61017768-C-G		Peroxisome biogenesis disorder 11A (Zellweger)	Likely benign (Jun 27, 2022)
2-61017768-C-T		Peroxisome biogenesis disorder 11A (Zellweger)	Conflicting classifications of pathogenicity (Jan 31, 2024)
2-61017770-A-C		Peroxisome biogenesis disorder 11A (Zellweger) • Inborn genetic diseases • PEX13-related disorder	Uncertain significance (Feb 23, 2023)
2-61017771-G-A		Peroxisome biogenesis disorder 11A (Zellweger)	Likely benign (Aug 04, 2023)
2-61017773-C-T		Peroxisome biogenesis disorder 11A (Zellweger) • Inborn genetic diseases	Uncertain significance (Aug 31, 2022)
2-61017777-A-G		Peroxisome biogenesis disorder 11A (Zellweger)	Conflicting classifications of pathogenicity (Jan 11, 2024)
2-61017777-A-T		Peroxisome biogenesis disorder 11A (Zellweger)	Likely benign (Dec 30, 2022)
2-61017777-A-AC		Peroxisome biogenesis disorder 11A (Zellweger)	Pathogenic (Apr 30, 2023)
2-61017780-TC-T		Peroxisome biogenesis disorder 11A (Zellweger)	Pathogenic (Aug 22, 2023)
2-61017782-C-T		Peroxisome biogenesis disorder 11A (Zellweger)	Uncertain significance (May 04, 2022)
2-61017783-C-A		Peroxisome biogenesis disorder 11A (Zellweger)	Conflicting classifications of pathogenicity (Jan 15, 2024)
2-61017785-C-A		Peroxisome biogenesis disorder 11A (Zellweger)	Uncertain significance (Feb 14, 2022)
2-61017785-C-G		Peroxisome biogenesis disorder 11A (Zellweger) • Inborn genetic diseases	Uncertain significance (Jun 21, 2023)
2-61017786-C-G		Peroxisome biogenesis disorder 11A (Zellweger)	Likely benign (Nov 02, 2023)
2-61017786-C-T		Peroxisome biogenesis disorder 11A (Zellweger)	Likely benign (Nov 16, 2022)
2-61017788-A-G		Peroxisome biogenesis disorder 11A (Zellweger)	Uncertain significance (Oct 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PEX13	protein_coding	protein_coding	ENST00000295030	4	34766

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000590	0.901	125728	0	18	125746	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.297	230	218	1.06	0.0000113	2606
Missense in Polyphen		62	67.083	0.92422		867
Synonymous	-0.574	83	76.6	1.08	0.00000362	840
Loss of Function	1.53	9	15.5	0.582	8.38e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000440
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

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.
• Pathway: 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;Post-translational protein modification;Metabolism of proteins;Peroxisomal protein import;Protein ubiquitination;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Recessive Scores

• pRec: 0.216

Intolerance Scores

• loftool: 0.511
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.207
• hipred: Y
• hipred_score: 0.756
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pex13
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system phenotype; skeleton phenotype; renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: pex13
• Affected structure: hepatocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: fatty acid alpha-oxidation;neuron migration;suckling behavior;protein targeting to peroxisome;locomotory behavior;protein import into peroxisome matrix, docking;protein ubiquitination;cerebral cortex cell migration;microtubule-based peroxisome localization
• Cellular component: peroxisome;peroxisomal membrane;integral component of peroxisomal membrane;membrane;intracellular membrane-bounded organelle;peroxisomal importomer complex
• Molecular function: protein binding