VPS33B VPS33B late endosome and lysosome associated [Homo sapiens (human)] - Gene

Summary

Official Symbol: VPS33Bprovided by HGNC
Official Full Name: VPS33B late endosome and lysosome associatedprovided by HGNC
Primary source: HGNC:HGNC:12712
See related: Ensembl:ENSG00000184056 MIM:608552; AllianceGenome:HGNC:12712
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: KDIDAR; PFIC12
Summary: Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene is a member of the Sec-1 domain family, and encodes the human ortholog of rat Vps33b which is homologous to the yeast class C Vps33 protein. The mammalian class C vacuolar protein sorting proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Mutations in this gene are associated with arthrogryposis-renal dysfunction-cholestasis syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
Expression: Ubiquitous expression in brain (RPKM 5.8), testis (RPKM 4.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q26.1

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (90998416..91022621, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (88757999..88782209, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (91541646..91565851, complement)

Chromosome 15 - NC_000015.10 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?

The Sec1-Munc18 protein VPS33B forms a uniquely bidirectional complex with VPS16B.
Title: The Sec1-Munc18 protein VPS33B forms a uniquely bidirectional complex with VPS16B.
Mucopolysaccharidosis-Plus Syndrome: Report on a Polish Patient with a Novel VPS33A Variant with Comparison with Other Described Patients.
Title: Mucopolysaccharidosis-Plus Syndrome: Report on a Polish Patient with a Novel VPS33A Variant with Comparison with Other Described Patients.
Syntaxin 12 and COMMD3 are new factors that function with VPS33B in the biogenesis of platelet alpha-granules.
Title: Syntaxin 12 and COMMD3 are new factors that function with VPS33B in the biogenesis of platelet α-granules.
VPS33B interacts with NESG1 to suppress cell growth and cisplatin chemoresistance in ovarian cancer.
Title: VPS33B interacts with NESG1 to suppress cell growth and cisplatin chemoresistance in ovarian cancer.
Mechanism of platelet alpha-granule biogenesis: study of cargo transport and the VPS33B-VPS16B complex in a model system.
Title: Mechanism of platelet α-granule biogenesis: study of cargo transport and the VPS33B-VPS16B complex in a model system.
VPS33B is negatively regulated by LMP-1 and nicotine and thus suppresses the proliferation of nasopharyngeal carcinoma (NPC) cells by interacting with NESG1 to regulate EGFR/PI3K/AKT/c-Myc/P53/miR-133a-3p signaling in NPC cells.
Title: VPS33B interacts with NESG1 to modulate EGFR/PI3K/AKT/c-Myc/P53/miR-133a-3p signaling and induce 5-fluorouracil sensitivity in nasopharyngeal carcinoma.
Results found VPS33B variation c.1726T>C, p.Cys576Arg to be associated with the attenuated phenotype of arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome.
Title: Novel missense mutation in VPS33B is associated with isolated low gamma-glutamyltransferase cholestasis: Attenuated, incomplete phenotype of arthrogryposis, renal dysfunction, and cholestasis syndrome.
NESG1 also activated VPS33B expression via the RAS/ERK/c-Jun pathway.
Title: VPS33B negatively modulated by nicotine functions as a tumor suppressor in colorectal cancer.
Down-regulation of Vps33b expression is a critical step for inflammation-driven hepatocellular carcinoma, and Vps33b serves as an important tumor suppressor in hepatocarcinogenesis.
Title: Vacuolar Protein Sorting 33B Is a Tumor Suppressor in Hepatocarcinogenesis.
ARKID syndrome is caused by VPS33B mutation.
Title: Autosomal Recessive Keratoderma-Ichthyosis-Deafness (ARKID) Syndrome Is Caused by VPS33B Mutations Affecting Rab Protein Interaction and Collagen Modification.

Submit: New GeneRIF Correction See all GeneRIFs (26)

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
Arthrogryposis, renal dysfunction, and cholestasis 1 MedGen: C1859722 OMIM: 208085 GeneReviews: Not available	Compare labs
Cholestasis, progressive familial intrahepatic, 12 MedGen: C5774311 OMIM: 620010 GeneReviews: Not available	Compare labs
Keratoderma-ichthyosis-deafness syndrome, autosomal recessive MedGen: C5774200 OMIM: 620009 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility. 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

RH44068 (e-PCR)
- UniSTS:36691

WI-22047 (e-PCR)
- UniSTS:43108

Gene Ontology Provided by GOA

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

Process	Evidence Code	Pubs
NOT involved_in autophagosome maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in collagen fibril organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within collagen metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endosome organization	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in endosome to lysosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular transport	NAS Non-traceable Author Statement more info	PubMed
involved_in lysosome localization	IDA Inferred from Direct Assay more info	PubMed
involved_in megakaryocyte development	IEA Inferred from Electronic Annotation more info
involved_in melanosome localization	IDA Inferred from Direct Assay more info	PubMed
involved_in membrane fusion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within peptidyl-lysine hydroxylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phagosome-lysosome fusion	NAS Non-traceable Author Statement more info	PubMed
involved_in platelet alpha granule organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of platelet aggregation	IEA Inferred from Electronic Annotation more info
involved_in skin morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within vesicle-mediated transport	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of CORVET complex	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
NOT part_of HOPS complex	IDA Inferred from Direct Assay more info	PubMed
part_of HOPS complex	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	TAS Traceable Author Statement more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
is_active_in lysosome	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in platelet alpha granule	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome	IEA Inferred from Electronic Annotation more info
part_of vesicle tethering complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 33B

Names: vacuolar protein sorting 33 homolog B; vacuolar protein sorting 33-like protein B

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_012162.1 RefSeqGene

Range

4983..29188

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_884

mRNA and Protein(s)

NM_001289148.1 → NP_001276077.1 vacuolar protein sorting-associated protein 33B isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

AK074863, AK293688, CB048637, DC397488

Consensus CDS

CCDS73783.1

UniProtKB/TrEMBL

B7Z1N4, F5H008

Related

ENSP00000444053.1, ENST00000535906.1

Conserved Domains (1) summary

pfam00995
Location:32 → 578

Sec1; Sec1 family
NM_001289149.1 → NP_001276078.1 vacuolar protein sorting-associated protein 33B isoform 3

See identical proteins and their annotated locations for NP_001276078.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in its 5' UTR and uses a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AK074863, CB048637, DC397488

UniProtKB/TrEMBL

B7Z6M7

Conserved Domains (1) summary

pfam00995
Location:10 → 514

Sec1; Sec1 family
NM_018668.5 → NP_061138.3 vacuolar protein sorting-associated protein 33B isoform 1

See identical proteins and their annotated locations for NP_061138.3

Status: REVIEWED

Description

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

Source sequence(s)

AF201694, AF308803, DC397488

Consensus CDS

CCDS10369.1

UniProtKB/Swiss-Prot

B3KQF6, Q96K14, Q9H267, Q9NRP6, Q9NSF3

UniProtKB/TrEMBL

A0A0S2Z577, B7Z1N4

Related

ENSP00000327650.4, ENST00000333371.8

Conserved Domains (1) summary

pfam00995
Location:37 → 605

Sec1; Sec1 family

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_000015.10 Reference GRCh38.p14 Primary Assembly

Range

90998416..91022621 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005254887.2 → XP_005254944.1 vacuolar protein sorting-associated protein 33B isoform X1

See identical proteins and their annotated locations for XP_005254944.1

UniProtKB/TrEMBL

B7Z6M7

Conserved Domains (1) summary

pfam00995
Location:10 → 514

Sec1; Sec1 family
XM_047432383.1 → XP_047288339.1 vacuolar protein sorting-associated protein 33B isoform X1
XM_011521449.3 → XP_011519751.1 vacuolar protein sorting-associated protein 33B isoform X2

UniProtKB/TrEMBL

B7Z6M7

Conserved Domains (1) summary

pfam00995
Location:23 → 497

Sec1; Sec1 family
XM_047432384.1 → XP_047288340.1 vacuolar protein sorting-associated protein 33B isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060939.1 Alternate T2T-CHM13v2.0

Range

88757999..88782209 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054377722.1 → XP_054233697.1 vacuolar protein sorting-associated protein 33B isoform X1
XM_054377721.1 → XP_054233696.1 vacuolar protein sorting-associated protein 33B isoform X1
XM_054377723.1 → XP_054233698.1 vacuolar protein sorting-associated protein 33B isoform X2
XM_054377724.1 → XP_054233699.1 vacuolar protein sorting-associated protein 33B isoform X3