PEX6 peroxisomal biogenesis factor 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PEX6provided by HGNC
Official Full Name: peroxisomal biogenesis factor 6provided by HGNC
Primary source: HGNC:HGNC:8859
See related: Ensembl:ENSG00000124587 MIM:601498; AllianceGenome:HGNC:8859
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: PAF2; HMLR2; PAF-2; PBD4A; PDB4B; PXAAA1
Summary: This gene encodes a member of the AAA (ATPases associated with diverse cellular activities) family of ATPases. This member is a predominantly cytoplasmic protein, which plays a direct role in peroxisomal protein import and is required for PTS1 (peroxisomal targeting signal 1, a C-terminal tripeptide of the sequence ser-lys-leu) receptor activity. Mutations in this gene cause peroxisome biogenesis disorders of complementation group 4 and complementation group 6. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
Expression: Ubiquitous expression in prostate (RPKM 9.4), ovary (RPKM 8.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.1

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (42963865..42979181, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (42793003..42808304, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (42931603..42946919, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

[Zellweger syndrome caused by PEX6 gene variation in 2 cases and literature review].
Title: [Zellweger syndrome caused by PEX6 gene variation in 2 cases and literature review].
A homozygous Gly470Ala variant in PEX6 causes severe Zellweger spectrum disorder.
Title: A homozygous Gly470Ala variant in PEX6 causes severe Zellweger spectrum disorder.
The peroxisomal disorder spectrum and Heimler syndrome: Deep phenotyping and review of the literature.
Title: The peroxisomal disorder spectrum and Heimler syndrome: Deep phenotyping and review of the literature.
Exome sequencing identifies PEX6 mutations in three cases diagnosed with Retinitis Pigmentosa and hearing impairment.
Title: Exome sequencing identifies PEX6 mutations in three cases diagnosed with Retinitis Pigmentosa and hearing impairment.
There are no significant differences between PEX1-, PEX6-, and PEX26-associated phenotypes inclinical and genetic spectrum of Heimler syndrome.
Title: Expanding the clinical and genetic spectrum of Heimler syndrome.
This article reviews the abundant records of missense mutations described in Peroxisome biogenesis disorders patients with the aim to classify and rationalize them by mapping them onto a homology model of the human Pex1/Pex6 complex. [review]
Title: Structural Mapping of Missense Mutations in the Pex1/Pex6 Complex.
Mutation in PAX6 gene is associated with Ophthalmic manifestations of Heimler syndrome.
Title: Ophthalmic manifestations of Heimler syndrome due to PEX6 mutations.
This study provides evidence suggesting that monoubiquitinated PEX5 interacts directly with both PEX1 and PEX6 through its ubiquitin moiety and that the PEX5 polypeptide chain is globally unfolded during the ATP-dependent extraction event.
Title: Peroxisomal monoubiquitinated PEX5 interacts with the AAA ATPases PEX1 and PEX6 and is unfolded during its dislocation into the cytosol.
A novel homozygous PEX6 p.Ala94Pro mutation.
Title: Mild Zellweger syndrome due to a novel PEX6 mutation: correlation between clinical phenotype and in silico prediction of variant pathogenicity.
Overexpression models confirmed that the overrepresentation of the pathogenic PEX6 c.2578T variant compared to wild-type PEX6 c.2578C results in a peroxisome biogenesis defect and thus constitutes the cause of disease in the affected individuals.
Title: Allelic Expression Imbalance Promoting a Mutant PEX6 Allele Causes Zellweger Spectrum Disorder.

Submit: New GeneRIF Correction See all GeneRIFs (25)

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
Heimler syndrome 2 MedGen: C4225267 OMIM: 616617 GeneReviews: Not available	not available
Peroxisome biogenesis disorder MedGen: C1832200 GeneReviews: Zellweger Spectrum Disorder	not available
Peroxisome biogenesis disorder 4A (Zellweger) MedGen: C3553936 OMIM: 614862 GeneReviews: Not available	not available
Peroxisome biogenesis disorder 4B MedGen: C3553937 OMIM: 614863 GeneReviews: Not available	not available

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

RH46734 (e-PCR)
- UniSTS:65323

D6S1532E (e-PCR)
- UniSTS:153976

STS-D20352 (e-PCR)
- UniSTS:66451

STS-U56602 (e-PCR)
- UniSTS:38315

SHGC-34360 (e-PCR)
- UniSTS:45742

WI-17066 (e-PCR)
- UniSTS:78010

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP hydrolysis activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-modified protein reader activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in peroxisome organization	IMP Inferred from Mutant Phenotype 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, receptor recycling	IDA Inferred from Direct Assay more info	PubMed
involved_in protein import into peroxisome matrix, translocation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein targeting to peroxisome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein unfolding	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein unfolding	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
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 peroxisome	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor cell cilium	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor outer segment	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: peroxisome biogenesis factor 6

Names: peroxin-6; peroxisomal AAA-type ATPase 1; peroxisomal ATPase PEX6; peroxisomal-type ATPase 1; peroxisome assembly factor 2

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_008370.1 RefSeqGene

Range

5063..20379

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000287.4 → NP_000278.3 peroxisome biogenesis factor 6 isoform 1

See identical proteins and their annotated locations for NP_000278.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).

Source sequence(s)

AL158815, BC033487, BQ773648, DA462214

Consensus CDS

CCDS4877.1

UniProtKB/Swiss-Prot

Q13608, Q5T8W1, Q8WYQ0, Q8WYQ1, Q8WYQ2, Q99476

Related

ENSP00000303511.8, ENST00000304611.13

Conserved Domains (3) summary

COG0464
Location:463 → 967

SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]

pfam00004
Location:743 → 871

AAA; ATPase family associated with various cellular activities (AAA)

pfam09336
Location:918 → 977

Vps4_C; Vps4 C terminal oligomerization domain
NM_001316313.2 → NP_001303242.1 peroxisome biogenesis factor 6 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction in the 5' end compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AB051077, AL158815, BC033487, BQ773648

UniProtKB/Swiss-Prot

Q13608

Conserved Domains (3) summary

COG0464
Location:375 → 879

SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]

pfam00004
Location:655 → 783

AAA; ATPase family associated with various cellular activities (AAA)

pfam09336
Location:830 → 889

Vps4_C; Vps4 C terminal oligomerization domain

RNA

NR_133009.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice junction and lacks two exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB051078, AL158815, BQ773648

Related

ENST00000244546.4

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_000006.12 Reference GRCh38.p14 Primary Assembly

Range

42963865..42979181 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047418872.1 → XP_047274828.1 peroxisome biogenesis factor 6 isoform X2
XM_011514661.3 → XP_011512963.1 peroxisome biogenesis factor 6 isoform X1

Conserved Domains (3) summary

COG0464
Location:435 → 939

SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]

pfam00004
Location:715 → 843

AAA; ATPase family associated with various cellular activities (AAA)

pfam09336
Location:890 → 949

Vps4_C; Vps4 C terminal oligomerization domain
XM_047418873.1 → XP_047274829.1 peroxisome biogenesis factor 6 isoform X3