PEX16 peroxisomal biogenesis factor 16 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PEX16provided by HGNC
Official Full Name: peroxisomal biogenesis factor 16provided by HGNC
Primary source: HGNC:HGNC:8857
See related: Ensembl:ENSG00000121680 MIM:603360; AllianceGenome:HGNC:8857
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: PBD8A; PBD8B
Summary: The protein encoded by this gene is an integral peroxisomal membrane protein. An inactivating nonsense mutation localized to this gene was observed in a patient with Zellweger syndrome of the complementation group CGD/CG9. Expression of this gene product morphologically and biochemically restores the formation of new peroxisomes, suggesting a role in peroxisome organization and biogenesis. Alternative splicing has been observed for this gene and two variants have been described. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 7.9), spleen (RPKM 6.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p11.2

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (45909663..45918822, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (46065593..46074744, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (45931214..45939428, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Knockdown of PEX16 Induces Autophagic Degradation of Peroxisomes.
Title: Knockdown of PEX16 Induces Autophagic Degradation of Peroxisomes.
PEX16 mediates the peroxisomal trafficking of two distinct peroxisomal membrane proteins, PEX3 and PMP34, via the endoplasmic reticulum
Title: PEX16 contributes to peroxisome maintenance by constantly trafficking PEX3 via the ER.
Data show that knockdown of Sec16B but not Sec16A by RNAi affected the morphology of peroxisomes, inhibited the transport of Pex16 from the ER to peroxisomes, and suppressed expression of Pex3.
Title: Sec16B is involved in the endoplasmic reticulum export of the peroxisomal membrane biogenesis factor peroxin 16 (Pex16) in mammalian cells.
An unusual variant peroxisome biogenesis disorder caused by mutations in the PEX16 gene, with a relatively mild clinical phenotype and an unexpected phenotype in fibroblasts, was identified.
Title: Identification of an unusual variant peroxisome biogenesis disorder caused by mutations in the PEX16 gene.
aberrant splicing mutation of the PEX16 gene in patients with Zellweger syndrome
Title: A novel aberrant splicing mutation of the PEX16 gene in two patients with Zellweger syndrome.
PEX16 regulates peroxisome assembly by being cotranslationally inserted into the ER and serving to recruit other peroxisomal membrane proteins to membranes.
Title: The origin and maintenance of mammalian peroxisomes involves a de novo PEX16-dependent pathway from the ER.
Pex16p functions in peroxisome membrane assembly, more likely upstream of Pex3p
Title: The membrane biogenesis peroxin Pex16p. Topogenesis and functional roles in peroxisomal membrane assembly.

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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 MedGen: C1832200 GeneReviews: Zellweger Spectrum Disorder	Compare labs
Peroxisome biogenesis disorder 8A (Zellweger) MedGen: C3553959 OMIM: 614876 GeneReviews: Not available	Compare labs
Peroxisome biogenesis disorder 8B MedGen: C3553960 OMIM: 614877 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error. 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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in ER-dependent peroxisome localization	IDA Inferred from Direct Assay more info	PubMed
involved_in ER-dependent peroxisome organization	IDA Inferred from Direct Assay more info	PubMed
involved_in peroxisome membrane biogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in peroxisome organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in peroxisome organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein import into peroxisome matrix	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein import into peroxisome membrane	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 to membrane docking	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
located_in peroxisomal membrane	HDA more info	PubMed
is_active_in peroxisomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in peroxisomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in peroxisomal membrane	IMP Inferred from Mutant Phenotype 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: peroxisomal biogenesis factor 16

Names: peroxin 16; peroxisomal membrane protein PEX16; peroxisome biogenesis factor 16

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_008460.2 RefSeqGene

Range

5945..14159

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_004813.4 → NP_004804.2 peroxisomal biogenesis factor 16 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) uses an alternate terminal exon. The encoded isoform (1) is shorter than isoform 2 and has a unique C-terminus.

Source sequence(s)

AB016531, AC068385, AF118240, BC000467, BM746616

Consensus CDS

CCDS31472.1

UniProtKB/Swiss-Prot

Q9BWB9, Q9Y5Y5

Related

ENSP00000368024.5, ENST00000378750.10

Conserved Domains (1) summary

pfam08610
Location:10 → 329

Pex16; Peroxisomal membrane protein (Pex16)
NM_057174.3 → NP_476515.2 peroxisomal biogenesis factor 16 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate terminal exon. The resulting protein (isoform 2) is longer and has a unique C-terminus compared to isoform 1.

Source sequence(s)

AC068385

Consensus CDS

CCDS7917.1

Related

ENSP00000241041.3, ENST00000241041.7

Conserved Domains (1) summary

pfam08610
Location:10 → 317

Pex16; Peroxisomal membrane protein (Pex16)