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

    Gene ID: 63894, updated on 3-Apr-2024

    Summary

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    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

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    See VIPAS39 in Genome Data Viewer
    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_000014.9Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr14:77846838-77847018 Neighboring gene sterile alpha motif domain containing 15 Neighboring gene HNF1 motif-containing MPRA enhancer 277 Neighboring gene NADP dependent oxidoreductase domain containing 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:77923742-77924264 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:77924265-77924787 Neighboring gene activator of HSP90 ATPase activity 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_36801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77950905-77951405 Neighboring gene isthmin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77957001-77957502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:77957503-77958002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5974

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Novel VIPAS39 mutation in a syndromic patient with arthrogryposis, renal tubular dysfunction and intrahepatic cholestasis. Aflatounian M, et al. Eur J Med Genet, 2016 Apr. PMID 26808426
    2. Design and validation of a metabolic disorder resequencing microarray (BRUM1). Bruce CK, et al. Hum Mutat, 2010 Jul. PMID 20578233
    3. Mechanism of platelet α-granule biogenesis: study of cargo transport and the VPS33B-VPS16B complex in a model system. Ambrosio AL, et al. Blood Adv, 2019 Sep 10. PMID 31501156, Free PMC Article
    4. Genetic profiling of children with advanced cholestatic liver disease. Shagrani M, et al. Clin Genet, 2017 Jul. PMID 28039895
    5. The CHEVI tethering complex: facilitating special deliveries. Rogerson C, et al. J Pathol, 2016 Nov. PMID 27555442

    See all (54) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    Submit: New GeneRIF Correction

    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12707

    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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    NEW Try the new Transcript table

    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

    1. NG_023421.2 RefSeqGene

      Range
      5040..35966
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1019

    mRNA and Protein(s)

    1. 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

    2. 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

    3. 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

    4. 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

    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

    6. NM_001400325.1 → NP_001387254.1  spermatogenesis-defective protein 39 homolog isoform 2

      Status: REVIEWED

      Source sequence(s)
      AF111168
      Consensus CDS
      CCDS53905.1

    7. 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

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

      Status: REVIEWED

      Source sequence(s)
      AF111168

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

      Status: REVIEWED

      Source sequence(s)
      AF111168

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

      Status: REVIEWED

      Source sequence(s)
      AF111168

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

      Status: REVIEWED

      Source sequence(s)
      AF111168

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

      Status: REVIEWED

      Source sequence(s)
      AF111168

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

      Status: REVIEWED

      Source sequence(s)
      AF111168

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

      Status: REVIEWED

      Source sequence(s)
      AF111168

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

      Status: REVIEWED

      Source sequence(s)
      AF111168

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

      Status: REVIEWED

      Source sequence(s)
      AF111168

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

      Status: REVIEWED

      Source sequence(s)
      AF111168

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

      Status: REVIEWED

      Source sequence(s)
      AF111168

    19. 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

    RNA

    1. NR_174476.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AF111168

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      77426675..77457601 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017021581.3 → XP_016877070.1  spermatogenesis-defective protein 39 homolog isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      71636055..71666984 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376556.1 → XP_054232531.1  spermatogenesis-defective protein 39 homolog isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H9C1.1 GenPept UniProtKB/Swiss-Prot:Q9H9C1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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