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PEX10 peroxisomal biogenesis factor 10 [ Homo sapiens (human) ]

Gene ID: 5192, updated on 5-Mar-2024

Summary

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Official Symbol
PEX10provided by HGNC
Official Full Name
peroxisomal biogenesis factor 10provided by HGNC
Primary source
HGNC:HGNC:8851
See related
Ensembl:ENSG00000157911 MIM:602859; AllianceGenome:HGNC:8851
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NALD; PBD6A; PBD6B; RNF69
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]
Expression
Ubiquitous expression in prostate (RPKM 12.5), fat (RPKM 12.4) and 25 other tissues See more
Orthologs
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Genomic context

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See PEX10 in Genome Data Viewer
Location:
1p36.32
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (2403974..2413827, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (1843564..1853417, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (2335413..2345266, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2246747-2247500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2253541-2254148 Neighboring gene MORN repeat containing 1 Neighboring gene small nuclear ribonucleoprotein polypeptide N pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:2306674-2306868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 54 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 55 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 56 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 114 Neighboring gene Sharpr-MPRA regulatory region 13804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2340121-2340621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2342650-2343230 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:2343231-2343811 to GRCh37_chr1:2344393-2344972 Neighboring gene retention in endoplasmic reticulum sorting receptor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:2361610-2361787 Neighboring gene phospholipase C eta 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2377030-2377864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2378700-2379534 Neighboring gene Sharpr-MPRA regulatory region 13638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2383066-2383714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2383715-2384362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2423421-2423982 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:2430511-2431710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2454755-2455542 Neighboring gene pantothenate kinase 4 (inactive)

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Expanding the spectrum of PEX10-related peroxisomal biogenesis disorders: slowly progressive recessive ataxia. Renaud M, et al. J Neurol, 2016 Aug. PMID 27230853
  2. [Abnormal expression of PEX10 gene may be related to epilepsy associated with 1p36 copy number variations]. Zhang Y, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2015 Feb. PMID 25636090
  3. Mutations in PEX10 are a cause of autosomal recessive ataxia. Régal L, et al. Ann Neurol, 2010 Aug. PMID 20695019
  4. Genetic heterogeneity in Japanese patients with peroxisome biogenesis disorders and evidence for a founder haplotype for the most common mutation in PEX10 gene. Shimozawa N, et al. Adv Exp Med Biol, 2003. PMID 14713216
  5. Phenotype-genotype relationships in PEX10-deficient peroxisome biogenesis disorder patients. Warren DS, et al. Hum Mutat, 2000. PMID 10862081

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Effect and in silico characterization of genetic variants associated with severe spermatogenic disorders in a large Iberian cohort.
    Title: Effect and in silico characterization of genetic variants associated with severe spermatogenic disorders in a large Iberian cohort.
  2. Collectively, the rs2477686 in PEX10 , rs6080550 in SIRPA-SIRPG, and rs10842262 in SOX5 gene may indeed be the genetic risk factors for nonobstructive azoospermia (NOA), which requires further investigation using larger independent sets of samples in different ethnic populations.
    Title: PEX10, SIRPA-SIRPG, and SOX5 gene polymorphisms are strongly associated with nonobstructive azoospermia susceptibility.
  3. This study demonstrated that two mutations in PEX10 were found in the three peroxisomal biogenesis disorders patients: c.827G>T (novel) causing the missense change p.Cys276Phe and c.932G>A causing the missense change p.Arg311Gln.
    Title: Expanding the spectrum of PEX10-related peroxisomal biogenesis disorders: slowly progressive recessive ataxia.
  4. abnormal expression of PEX10 gene resulting from copy number variations of 1p36 region may be associated with the epilepsy phenotype
    Title: [Abnormal expression of PEX10 gene may be related to epilepsy associated with 1p36 copy number variations].
  5. child and an adult of normal intelligence with progressive ataxia, axonal motor neuropathy, decreased vibration sense and cerebellar atrophy; 2 mutations in PEX10 found in child, c.992G>A and c.764_765insA, and in the adult, c.2T>C and c.790C>T
    Title: Mutations in PEX10 are a cause of autosomal recessive ataxia.
  6. the relative fraction of disease-causing alleles that occur in the coding and splice junction sequences of PEX10 gene.
    Title: Identification of novel mutations and sequence variation in the Zellweger syndrome spectrum of peroxisome biogenesis disorders.
  7. Genetic heterogeneity in Japanese patients with peroxisome biogenesis disorders and evidence for a founder haplotype for the most common mutation in PEX10 gene.
    Title: Genetic heterogeneity in Japanese patients with peroxisome biogenesis disorders and evidence for a founder haplotype for the most common mutation in PEX10 gene.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Peroxisome biogenesis disorder 6A (Zellweger)
MedGen: C3553947 OMIM: 614870 GeneReviews: Not available
Compare labs
Peroxisome biogenesis disorder 6B
MedGen: C3553948 OMIM: 614871 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
A genome-wide association study in Chinese men identifies three risk loci for non-obstructive azoospermia.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC1998

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cellular response to reactive oxygen species IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in peroxisome organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in protein import into peroxisome matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein import into peroxisome matrix IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein import into peroxisome matrix, receptor recycling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein import into peroxisome matrix, substrate release ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in protein polyubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein quality control for misfolded or incompletely synthesized proteins ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Component Evidence Code Pubs
is_active_in peroxisomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in peroxisomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in peroxisomal membrane TAS
Traceable Author Statement
more info
  
located_in peroxisome IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
peroxisome biogenesis factor 10
Names
RING finger protein 69
peroxin 10
peroxisome assembly protein 10
NP_001361354.1
NP_001361355.1
NP_001361356.1
NP_002608.1
NP_722540.1
XP_011539878.1
XP_047278495.1
XP_054192986.1
XP_054192987.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008342.1 RefSeqGene

    Range
    5008..13598
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001374425.1 → NP_001361354.1  peroxisome biogenesis factor 10 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL513477
    UniProtKB/TrEMBL
    Q6FGN0
    Conserved Domains (2) summary
    cd16527
    Location:292 → 330
    RING-HC_PEX10; RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins
    pfam04757
    Location:18 → 262
    Pex2_Pex12; Pex2 / Pex12 amino terminal region

  2. NM_001374426.1 → NP_001361355.1  peroxisome biogenesis factor 10 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL513477
    Conserved Domains (2) summary
    cd16527
    Location:148 → 186
    RING-HC_PEX10; RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins
    pfam04757
    Location:2 → 118
    Pex2_Pex12; Pex2 / Pex12 amino terminal region

  3. NM_001374427.1 → NP_001361356.1  peroxisome biogenesis factor 10 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL513477
    Conserved Domains (2) summary
    cd16527
    Location:129 → 167
    RING-HC_PEX10; RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins
    pfam04757
    Location:2 → 99
    Pex2_Pex12; Pex2 / Pex12 amino terminal region

  4. NM_002617.4 → NP_002608.1  peroxisome biogenesis factor 10 isoform 2

    See identical proteins and their annotated locations for NP_002608.1

    Status: REVIEWED

    Source sequence(s)
    AL513477
    Consensus CDS
    CCDS44045.1
    UniProtKB/Swiss-Prot
    B3KWD8, O60683, Q5T095, Q9BW90
    UniProtKB/TrEMBL
    Q6FGN0
    Related
    ENSP00000407922.2, ENST00000447513.7
    Conserved Domains (2) summary
    cd00162
    Location:273 → 314
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam04757
    Location:18 → 243
    Pex2_Pex12; Pex2 / Pex12 amino terminal region

  5. NM_153818.2 → NP_722540.1  peroxisome biogenesis factor 10 isoform 1

    See identical proteins and their annotated locations for NP_722540.1

    Status: REVIEWED

    Source sequence(s)
    AL513477
    Consensus CDS
    CCDS41.1
    UniProtKB/TrEMBL
    Q6FGN0
    Related
    ENSP00000288774.3, ENST00000288774.8
    Conserved Domains (2) summary
    cd00162
    Location:293 → 334
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam04757
    Location:18 → 263
    Pex2_Pex12; Pex2 / Pex12 amino terminal region

RNA

  1. NR_164636.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL513477

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    2403974..2413827 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422539.1 → XP_047278495.1  peroxisome biogenesis factor 10 isoform X1

    UniProtKB/TrEMBL
    D6RA89
    Related
    ENSP00000423051.1, ENST00000510434.1

  2. XM_011541576.3 → XP_011539878.1  peroxisome biogenesis factor 10 isoform X2

    Conserved Domains (1) summary
    pfam04757
    Location:18 → 199
    Pex2_Pex12; Pex2 / Pex12 amino terminal region

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    1843564..1853417 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337011.1 → XP_054192986.1  peroxisome biogenesis factor 10 isoform X1

    UniProtKB/TrEMBL
    D6RA89

  2. XM_054337012.1 → XP_054192987.1  peroxisome biogenesis factor 10 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60683.1 GenPept UniProtKB/Swiss-Prot:O60683

Gene LinkOut

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