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

Summary

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: mouse all
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Genomic context

Location:: 1p36.32

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (2403974..2413827, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (1843564..1853417, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (2335413..2345266, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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].
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.
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.
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.

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PEX10_1028 (e-PCR)
- UniSTS:277580

PEX10_V285 (e-PCR)
- UniSTS:277580

SHGC-74114 (e-PCR)
- UniSTS:1967

SHGC-30638 (e-PCR)
- UniSTS:38847

G43268 (e-PCR)
- UniSTS:94912

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
enables zinc ion binding	NAS Non-traceable Author Statement more info	PubMed

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	IMP Inferred from Mutant Phenotype 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
located_in peroxisomal membrane	HDA more info	PubMed
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	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

EC 2.3.2.27

NP_001361355.1

EC 2.3.2.27

NP_001361356.1

EC 2.3.2.27

NP_002608.1

EC 2.3.2.27

NP_722540.1

EC 2.3.2.27

XP_011539878.1

EC 2.3.2.27

XP_047278495.1

EC 2.3.2.27

XP_054192986.1

EC 2.3.2.27

XP_054192987.1

EC 2.3.2.27

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

NG_008342.1 RefSeqGene

Range

5008..13598

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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

NR_164636.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL513477

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

2403974..2413827 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

D6RA89

Related

ENSP00000423051.1, ENST00000510434.1
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

NC_060925.1 Alternate T2T-CHM13v2.0

Range

1843564..1853417 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

D6RA89
XM_054337012.1 → XP_054192987.1 peroxisome biogenesis factor 10 isoform X2