PEX12

protein-coding

peroxisomal biogenesis factor 12, the group of Peroxins

Gene summary

This gene belongs to the peroxin-12 family. Peroxins (PEXs) are proteins that are essential for the assembly of functional peroxisomes. The peroxisome biogenesis disorders (PBDs) are a group of genetically heterogeneous autosomal recessive, lethal diseases characterized by multiple defects in peroxisome function. The peroxisomal biogenesis disorders are a heterogeneous group with at least 14 complementation groups and with more than 1 phenotype being observed in cases falling into particular complementation groups. Although the clinical features of PBD patients vary, cells from all PBD patients exhibit a defect in the import of one or more classes of peroxisomal matrix proteins into the organelle. Defects in this gene are a cause of Zellweger syndrome (ZWS). [provided by RefSeq, Oct 2008]

MANE transcript

NM_000286.3

Inheritance

AR

ClinVar variants

P:134U:195B:159

Top phenotype

Peroxisome biogenesis disorder 3A; Peroxisome biogenesis factor disorder 3B

gnomAD constraint

pLI —, LoF o/e 1.34

Max pathogenic AF

—

Genomic locus

chr17:35,574,795-35,578,863

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~4.1 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

peroxisome biogenesis disorder type 3BDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009959

Submitter: G2P

peroxisome biogenesis disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0019234

Submitter: PanelApp Australia

peroxisome biogenesis disorder 3A (Zellweger)DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013927

Submitter: Myriad Women's Health

peroxisome biogenesis disorderDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019234

Submitter: ClinGen

PEX12 was first reported in relation to autosomal recessive peroxisomal biogenesis disorder in 1997 (Okumoto et al., PMID:9354782). Numerous variants have been reported in humans per ClinVar. Evidence supporting this gene-disease relationship includes case-level data and experimental data. Summary of case-level and experimental data: 16.5 points. Variants (nonsense, missense, and frameshift) in this gene have been reported in at least 16 probands in 5 publications (PMIDS: 9090384, 9792857, 14571262, 9354782, 9632816). More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. The mechanism for disease is expected to be loss of function. This gene-disease association is supported by expression studies, cell culture models, and in vitro functional assays. In summary, PEX12 is definitively associated with autosomal recessive peroxisomal biogenesis disorder. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time.

peroxisome biogenesis disorder 3A (Zellweger)DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013927

Submitter: G2P

Zellweger spectrum disordersSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019609

Submitter: Orphanet

peroxisome biogenesis disorder 3A (Zellweger)STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013927

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Peroxisome biogenesis disorder 3A; Peroxisome biogenesis factor disorder 3BAR

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: 9090384; 9354782; 9632816; 9792857; 14571262; 17041890; 17534573Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PEX12 variants in ClinVar

9 Conditions Cataloged
Peroxisome biogenesis disorder 3A (Zellweger)Total: 460
not providedTotal: 74
Peroxisome biogenesis disorder type 3BTotal: 67
PEX12-related disorderTotal: 67
Inborn genetic diseasesTotal: 51
not specifiedTotal: 28
Peroxisome biogenesis disorderTotal: 27
Peroxisomal biogenesis disorder 3bTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000286.3. 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
2
clinvar
148
clinvar
1
clinvar
151
missense
1
clinvar
4
clinvar
190
clinvar
7
clinvar
1
clinvar
203
nonsense
19
clinvar
18
clinvar
37
start loss
2
clinvar
2
frameshift
43
clinvar
37
clinvar
3
clinvar
83
splice donor/acceptor (+/-2bp)
5
clinvar
5
clinvar
2
clinvar
12
Total68661951572488

Highest pathogenic variant AF is 0.00014373762

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000286.3RefSeqNP_000277.13MANE Select
ENST00000225873.9EnsemblENSP00000225873.33MANE Select
ENST00000585380.1EnsemblENSP00000466280.12Standard
ENST00000586663.2EnsemblENSP00000466894.23Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Peroxisome - Homo sapiens (human)
  • Post-translational protein modification
  • Metabolism of proteins
  • Peroxisomal protein import
  • Protein ubiquitination

Biological Process

  • protein monoubiquitination
  • protein targeting to peroxisome
  • peroxisome organization
  • protein import into peroxisome matrix
  • protein ubiquitination

Molecular Function

  • ubiquitin-protein transferase activity
  • protein binding
  • protein C-terminus binding
  • zinc ion binding

Cellular Component

  • peroxisome
  • peroxisomal membrane
  • integral component of peroxisomal membrane
  • peroxisomal importomer complex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000225873
Coding exons
3
Length
4069
Individuals with no LoFs
124959
Homozygous LoFs
10
Heterozygous LoFs
779
Defined
125748
p
0.00314
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4591611780.9030.000008912314
Missense (PolyPhen)6276.4520.81097999
Synonymous-0.2847067.01.040.00000308748
Loss of Function-1.232014.91.348.62e-7161

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0370.037notable
Latino/Admixed American0.00260.0026notable
Ashkenazi Jewish0.000500.00050rare
East Asian0.000160.00016rare
Finnish00.0absent
European (Non-Finnish)0.000730.00072rare
South Asian0.000460.00046rare
Other0.00160.0016notable

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Required for protein import into peroxisomes. {ECO:0000269|PubMed:9632816}.;
Disease
DISEASE: Peroxisome biogenesis disorder complementation group 3 (PBD-CG3) [MIM:614859]: 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:19105186}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 3A (PBD3A) [MIM:614859]: 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:9090384}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 3B (PBD3B) [MIM:266510]: 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. Note=The disease is caused by mutations affecting the gene represented in this entry. {ECO:0000269|PubMed:10562279, ECO:0000269|PubMed:19105186}.;

Recessive Scores

pRec
0.177

Intolerance Scores

LoFtool
0.491
RVIS EVS
0.53
RVIS percentile EVS
80.73

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.299

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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