VIPAS39 VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog [Homo sapiens (human)] - Gene

Summary

Official Symbol: VIPAS39provided by HGNC
Official Full Name: VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homologprovided by HGNC
Primary source: HGNC:HGNC:20347
See related: Ensembl:ENSG00000151445 MIM:613401; AllianceGenome:HGNC:20347
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: SPE39; VIPAR; SPE-39; VPS16B; hSPE-39; C14orf133
Summary: Involved in endosome to lysosome transport and intracellular protein transport. Acts upstream of or within collagen metabolic process and peptidyl-lysine hydroxylation. Located in Golgi apparatus and endosome. Implicated in arthrogryposis, renal dysfunction, and cholestasis 2. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in testis (RPKM 8.8), ovary (RPKM 6.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q24.3

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (77426675..77457601, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (71636055..71666984, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (77893018..77923944, complement)

Chromosome 14 - NC_000014.9 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.
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.
The Rab-binding module of FERARI (factors for endosome recycling and Rab interactions) consists of Rab11FIP5 and rabenosyn-5, while the SNARE-interacting module comprises VPS45 and VIPAS39.
Title: FERARI is required for Rab11-dependent endocytic recycling.
A likely causal mutation was identified in the majority (61%), spanning many genes including ones that have only rarely been reported to cause cholestatic liver disease, e.g. TJP2 and VIPAS39
Title: Genetic profiling of children with advanced cholestatic liver disease.
Genetic studies showed a homozygous mutation in the VIPAS39 gene. Making the definite diagnosis of the syndrome is important, while increased risk of mutation in other siblings highlights the importance of prenatal diagnosis.
Title: Novel VIPAS39 mutation in a syndromic patient with arthrogryposis, renal tubular dysfunction and intrahepatic cholestasis.
Our data suggest that the ARC syndrome may result through impaired VIPAS39/SPE-39 and Vps33b-dependent endosomal maturation or fusion.
Title: Vps33b pathogenic mutations preferentially affect VIPAS39/SPE-39-positive endosomes.
VPS16B, similar to its binding partner VPS33B, is essential for megakaryocyte and platelet alpha-granule biogenesis.
Title: The VPS33B-binding protein VPS16B is required in megakaryocyte and platelet α-granule biogenesis.
SPE-39 has an inhibitory effect due to tyrosine phosphorylation and ubiquitination on the function of Vps33B in the EGF-stimulated cells
Title: Inhibitory effect of SPE-39 due to tyrosine phosphorylation and ubiquitination on the function of Vps33B in the EGF-stimulated cells.
SPE-39 homologues are present in RAB5-, RAB7-, and RAB11-positive endosomes where they play a conserved role in lysosomal delivery and probably function via their interaction with the core HOPS complex.
Title: SPE-39 family proteins interact with the HOPS complex and function in lysosomal delivery.

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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
Arthrogryposis, renal dysfunction, and cholestasis 2 MedGen: C3150672 OMIM: 613404 GeneReviews: Not available	Compare labs

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

RH77763 (e-PCR)
- UniSTS:4485

G35916 (e-PCR)
- UniSTS:29349

G44715 (e-PCR)
- UniSTS:95190

RH11279 (e-PCR)
- UniSTS:86490

G35725 (e-PCR)
- UniSTS:44002

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	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
NOT involved_in autophagosome maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
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
NOT involved_in endosome to lysosome transport	IMP Inferred from Mutant Phenotype more info	PubMed
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 protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular transport	NAS Non-traceable Author Statement 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 post-translational protein modification	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
involved_in vacuolar transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
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
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome	IDA Inferred from Direct Assay more info	PubMed
part_of vesicle tethering complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: spermatogenesis-defective protein 39 homolog

Names: VPS33B-interacting protein involved in polarity and apical protein restriction

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_023421.2 RefSeqGene

Range

5040..35966

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1019

mRNA and Protein(s)

NM_001193314.2 → NP_001180243.1 spermatogenesis-defective protein 39 homolog isoform 1

See identical proteins and their annotated locations for NP_001180243.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).

Source sequence(s)

AF111168

Consensus CDS

CCDS9862.1

UniProtKB/Swiss-Prot

B4DPI6, O95434, Q9H7E1, Q9H9C1, Q9H9I9

UniProtKB/TrEMBL

Q53H75, Q6IA61

Related

ENSP00000452181.1, ENST00000553888.5

Conserved Domains (1) summary

pfam09787
Location:26 → 471

Golgin_A5; Golgin subfamily A member 5
NM_001193315.2 → NP_001180244.1 spermatogenesis-defective protein 39 homolog isoform 1

See identical proteins and their annotated locations for NP_001180244.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).

Source sequence(s)

AF111168, AK022769, AW629161

Consensus CDS

CCDS9862.1

UniProtKB/Swiss-Prot

B4DPI6, O95434, Q9H7E1, Q9H9C1, Q9H9I9

UniProtKB/TrEMBL

Q53H75, Q6IA61

Related

ENSP00000452191.1, ENST00000557658.6

Conserved Domains (1) summary

pfam09787
Location:26 → 471

Golgin_A5; Golgin subfamily A member 5
NM_001193316.2 → NP_001180245.1 spermatogenesis-defective protein 39 homolog isoform 2

See identical proteins and their annotated locations for NP_001180245.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.

Source sequence(s)

AF111168

Consensus CDS

CCDS53905.1

UniProtKB/TrEMBL

Q53H75

Related

ENSP00000404815.2, ENST00000448935.6

Conserved Domains (1) summary

pfam09787
Location:26 → 422

Golgin_A5; Golgin subfamily A member 5
NM_001193317.2 → NP_001180246.1 spermatogenesis-defective protein 39 homolog isoform 1

See identical proteins and their annotated locations for NP_001180246.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).

Source sequence(s)

AF111168

Consensus CDS

CCDS9862.1

UniProtKB/Swiss-Prot

B4DPI6, O95434, Q9H7E1, Q9H9C1, Q9H9I9

UniProtKB/TrEMBL

Q53H75, Q6IA61

Related

ENSP00000451857.1, ENST00000556412.4

Conserved Domains (1) summary

pfam09787
Location:26 → 471

Golgin_A5; Golgin subfamily A member 5
NM_001400324.1 → NP_001387253.1 spermatogenesis-defective protein 39 homolog isoform 2

Status: REVIEWED

Source sequence(s)

AF111168

Consensus CDS

CCDS53905.1

Related

ENSP00000313098.5, ENST00000327028.8
NM_001400325.1 → NP_001387254.1 spermatogenesis-defective protein 39 homolog isoform 2

Status: REVIEWED

Source sequence(s)

AF111168

Consensus CDS

CCDS53905.1
NM_001400326.1 → NP_001387255.1 spermatogenesis-defective protein 39 homolog isoform 1

Status: REVIEWED

Source sequence(s)

AF111168

Consensus CDS

CCDS9862.1

UniProtKB/Swiss-Prot

B4DPI6, O95434, Q9H7E1, Q9H9C1, Q9H9I9

UniProtKB/TrEMBL

Q6IA61
NM_001400327.1 → NP_001387256.1 spermatogenesis-defective protein 39 homolog isoform 4

Status: REVIEWED

Source sequence(s)

AF111168
NM_001400330.1 → NP_001387259.1 spermatogenesis-defective protein 39 homolog isoform 5

Status: REVIEWED

Source sequence(s)

AF111168
NM_001400331.1 → NP_001387260.1 spermatogenesis-defective protein 39 homolog isoform 5

Status: REVIEWED

Source sequence(s)

AF111168
NM_001400332.1 → NP_001387261.1 spermatogenesis-defective protein 39 homolog isoform 5

Status: REVIEWED

Source sequence(s)

AF111168
NM_001400333.1 → NP_001387262.1 spermatogenesis-defective protein 39 homolog isoform 6

Status: REVIEWED

Source sequence(s)

AF111168
NM_001400334.1 → NP_001387263.1 spermatogenesis-defective protein 39 homolog isoform 6

Status: REVIEWED

Source sequence(s)

AF111168
NM_001400335.1 → NP_001387264.1 spermatogenesis-defective protein 39 homolog isoform 7

Status: REVIEWED

Source sequence(s)

AF111168
NM_001400336.1 → NP_001387265.1 spermatogenesis-defective protein 39 homolog isoform 8

Status: REVIEWED

Source sequence(s)

AF111168
NM_001400337.1 → NP_001387266.1 spermatogenesis-defective protein 39 homolog isoform 9

Status: REVIEWED

Source sequence(s)

AF111168
NM_001400338.1 → NP_001387267.1 spermatogenesis-defective protein 39 homolog isoform 10

Status: REVIEWED

Source sequence(s)

AF111168
NM_001400339.1 → NP_001387268.1 spermatogenesis-defective protein 39 homolog isoform 11

Status: REVIEWED

Source sequence(s)

AF111168
NM_022067.4 → NP_071350.2 spermatogenesis-defective protein 39 homolog isoform 1

See identical proteins and their annotated locations for NP_071350.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein (isoform 1).

Source sequence(s)

AF111168

Consensus CDS

CCDS9862.1

UniProtKB/Swiss-Prot

B4DPI6, O95434, Q9H7E1, Q9H9C1, Q9H9I9

UniProtKB/TrEMBL

Q53H75, Q6IA61

Related

ENSP00000339122.2, ENST00000343765.6

Conserved Domains (1) summary

pfam09787
Location:26 → 471

Golgin_A5; Golgin subfamily A member 5