PEX10

protein-coding

peroxisomal biogenesis factor 10, the group of Peroxins|Ring finger proteins

Gene summary

This gene encodes a protein involved in import of peroxisomal matrix proteins. This protein localizes to the peroxisomal membrane. Mutations in this gene result in phenotypes within the Zellweger spectrum of peroxisomal biogenesis disorders, ranging from neonatal adrenoleukodystrophy to Zellweger syndrome. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002617.4

Inheritance

AR

ClinVar variants

P:168U:266B:236

Top phenotype

Peroxisome biogenesis disorder 6A (Zellweger syndrome); Peroxisome biogenesis disorder 6B

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr1:2,403,964-2,413,797

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~9.8 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

peroxisome biogenesis disorderDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019234

Submitter: ClinGen

PEX10 was first reported in relation to autosomal recessive peroxisomal biogenesis disorder in 1998 (Okumoto et al., PMID: 9700193). 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: 17.5 points. Variants (nonsense, missense, and frameshift) in this gene have been reported in at least 11 probands in 4 publications (PMIDS: 17041890, 9700193, 20695019, 19127411, 9683594, 10862081). 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 homozygous loss of function. This gene-disease association is supported by expression studies, animal models, and in vitro functional assays. In summary, PEX10 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 disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0019234

Submitter: PanelApp Australia

peroxisome biogenesis disorder 6BMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0013937

Submitter: Ambry Genetics

peroxisome biogenesis disorder 6A (Zellweger)DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013936

Submitter: Myriad Women's Health

Zellweger spectrum disordersSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019609

Submitter: Orphanet

peroxisome biogenesis disorder due to PEX10 defectDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0100264

Submitter: Natera

peroxisome biogenesis disorder 6BDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013937

Submitter: G2P

peroxisome biogenesis disorder 6A (Zellweger)STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013936

Submitter: Ambry Genetics

autosomal recessive ataxia due to PEX10 deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0016614

Submitter: Orphanet

peroxisome biogenesis disorder 6A (Zellweger)DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013936

Submitter: G2P

peroxisome biogenesis disorder 6BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013937

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Peroxisome biogenesis disorder 6A (Zellweger syndrome); Peroxisome biogenesis disorder 6BAR

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: 9700193; 9683594; 12794690; 10862081; 17041890; 19127411; 20695019Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PEX10 variants in ClinVar

10 Conditions Cataloged
Peroxisome biogenesis disorder, complementation group 7Total: 674
Zellweger spectrum disordersTotal: 146
Peroxisome biogenesis disorder 6A (Zellweger)Total: 131
not providedTotal: 125
PEX10-related disorderTotal: 101
not specifiedTotal: 78
Inborn genetic diseasesTotal: 71
Peroxisome biogenesis disorder 6BTotal: 64

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002617.4. 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
6
clinvar
221
clinvar
1
clinvar
228
missense
2
clinvar
9
clinvar
256
clinvar
13
clinvar
1
clinvar
281
nonsense
13
clinvar
17
clinvar
1
clinvar
31
start loss
3
clinvar
4
clinvar
7
frameshift
54
clinvar
46
clinvar
1
clinvar
101
splice donor/acceptor (+/-2bp)
1
clinvar
19
clinvar
2
clinvar
22
Total73952662342670

Highest pathogenic variant AF is 0.00013969238

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002617.4RefSeqNP_002608.16MANE Select
ENST00000447513.7EnsemblENSP00000407922.26MANE Select
NM_001374425.1RefSeqNP_001361354.16Standard
NM_001374426.1RefSeqNP_001361355.14Standard

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

Molecular Function

  • protein binding
  • zinc ion binding

Cellular Component

  • peroxisome
  • peroxisomal membrane
  • integral component of peroxisomal membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000288774
Coding exons
6
Length
9001
Individuals with no LoFs
125680
Homozygous LoFs
0
Heterozygous LoFs
49
Defined
125729
p
0.000195
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.2942292171.060.00001522142
Missense (PolyPhen)6069.3730.86489762
Synonymous0.01169696.10.9990.00000624759
Loss of Function1.99816.80.4779.93e-7157

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00012rare
Latino/Admixed American0.000350.00026rare
Ashkenazi Jewish0.000100.000099rare
East Asian0.000290.00027rare
Finnish00.0absent
European (Non-Finnish)0.000230.00023rare
South Asian0.000200.00020rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Somewhat implicated in the biogenesis of peroxisomes.;
Disease
DISEASE: Peroxisome biogenesis disorder complementation group 7 (PBD-CG7) [MIM:614870]: 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 6A (PBD6A) [MIM:614870]: 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:9700193}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 6B (PBD6B) [MIM:614871]: 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:9683594}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.165

Intolerance Scores

LoFtool
0.234
RVIS EVS
-0.27
RVIS percentile EVS
34.82

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.876

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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