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    VPS13B vacuolar protein sorting 13 homolog B [ Homo sapiens (human) ]

    Gene ID: 157680, updated on 10-Dec-2024

    Summary

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    Official Symbol
    VPS13Bprovided by HGNC
    Official Full Name
    vacuolar protein sorting 13 homolog Bprovided by HGNC
    Primary source
    HGNC:HGNC:2183
    See related
    Ensembl:ENSG00000132549 MIM:607817; AllianceGenome:HGNC:2183
    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
    CHS1; COH1; BLTP5B
    Summary
    This gene encodes a potential transmembrane protein that may function in vesicle-mediated transport and sorting of proteins within the cell. This protein may play a role in the development and the function of the eye, hematological system, and central nervous system. Mutations in this gene have been associated with Cohen syndrome. Multiple splice variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in endometrium (RPKM 3.0), ovary (RPKM 2.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VPS13B in Genome Data Viewer
    Location:
    8q22.2
    Exon count:
    65
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (99013274..99877580)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (100138009..101002539)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (100025502..100889808)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak7120 silencer Neighboring gene uncharacterized LOC107986872 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19405 Neighboring gene Sharpr-MPRA regulatory region 5914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:100026015-100026516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:100026517-100027016 Neighboring gene VPS13B divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27683 Neighboring gene insulin like growth factor 2 mRNA binding protein 2 pseudogene Neighboring gene uncharacterized LOC124902102 Neighboring gene aconitase 2, mitochondrial pseudogene Neighboring gene MSL3 pseudogene 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:100633076-100633264 Neighboring gene microRNA 599 Neighboring gene microRNA 875 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:100655360-100655944 Neighboring gene uncharacterized LOC124901989 Neighboring gene RNA, 7SL, cytoplasmic 350, pseudogene Neighboring gene VISTA enhancer hs909 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:100782591-100783790 Neighboring gene leucine zipper and EF-hand containing transmembrane protein 1 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:100871617-100872116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:100880771-100881278 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:100883624-100884124 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:100904777-100905425 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:100905426-100906073 Neighboring gene MPRA-validated peak7123 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr8:100947244-100947479 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:100955411-100956610 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:100959374-100959874 Neighboring gene cytochrome c oxidase subunit 6C Neighboring gene small nucleolar RNA, C/D box 77B Neighboring gene regulator of G protein signaling 22

    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. Cohen syndrome-associated protein, COH1, is a novel, giant Golgi matrix protein required for Golgi integrity. Seifert W, et al. J Biol Chem, 2011 Oct 28. PMID 21865173, Free PMC Article
    2. A novel homozygous nonsense mutation of VPS13B associated with previously unreported features of Cohen syndrome. Koehler K, et al. Am J Med Genet A, 2020 Mar. PMID 31825161
    3. Case report: two novel VPS13B mutations in a Chinese family with Cohen syndrome and hyperlinear palms. Zhao S, et al. BMC Med Genet, 2019 Nov 21. PMID 31752730, Free PMC Article
    4. Ophthalmic features of retinitis pigmentosa in Cohen syndrome caused by pathogenic variants in the VPS13B gene. Nasser F, et al. Acta Ophthalmol, 2020 May. PMID 31580008
    5. Mutations in the VPS13B Gene in Iranian Patients with Different Phenotypes of Cohen Syndrome. Alipour N, et al. J Mol Neurosci, 2020 Jan. PMID 31444703

    See all (76) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Sec23IP recruits VPS13B/COH1 to ER exit site-Golgi interface for tubular ERGIC formation.
      Title: Sec23IP recruits VPS13B/COH1 to ER exit site-Golgi interface for tubular ERGIC formation.
    2. Exome sequencing in four families with neurodevelopmental disorders: genotype-phenotype correlation and identification of novel disease-causing variants in VPS13B and RELN.
      Title: Exome sequencing in four families with neurodevelopmental disorders: genotype-phenotype correlation and identification of novel disease-causing variants in VPS13B and RELN.
    3. A Novel Variant in VPS13B Underlying Cohen Syndrome.
      Title: A Novel Variant in VPS13B Underlying Cohen Syndrome.
    4. Disease relevance of rare VPS13B missense variants for neurodevelopmental Cohen syndrome.
      Title: Disease relevance of rare VPS13B missense variants for neurodevelopmental Cohen syndrome.
    5. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation.
      Title: A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation.
    6. A Novel VPS13B Mutation Identified by Whole-Exome Sequencing in Iranian Patients with Cohen Syndrome.
      Title: A Novel VPS13B Mutation Identified by Whole-Exome Sequencing in Iranian Patients with Cohen Syndrome.
    7. Functional Analysis of a Compound Heterozygous Mutation in the VPS13B Gene in a Chinese Pedigree with Cohen Syndrome.
      Title: Functional Analysis of a Compound Heterozygous Mutation in the VPS13B Gene in a Chinese Pedigree with Cohen Syndrome.
    8. Autophagy pathway upregulation in a human iPSC-derived neuronal model of Cohen syndrome with VPS13B missense mutations.
      Title: Autophagy pathway upregulation in a human iPSC-derived neuronal model of Cohen syndrome with VPS13B missense mutations.
    9. An intronic splice site alteration in combination with a large deletion affecting VPS13B (COH1) causes Cohen syndrome.
      Title: An intronic splice site alteration in combination with a large deletion affecting VPS13B (COH1) causes Cohen syndrome.
    10. Cohen Syndrome-Associated Cataract Is Explained by VPS13B Functions in Lens Homeostasis and Is Modified by Additional Genetic Factors.
      Title: Cohen Syndrome-Associated Cataract Is Explained by VPS13B Functions in Lens Homeostasis and Is Modified by Additional Genetic Factors.
    Submit: New GeneRIF Correction See all GeneRIFs (37)

    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
    Cohen syndrome
    MedGen: C0265223 OMIM: 216550 GeneReviews: Cohen Syndrome
    		not available

    EBI GWAS Catalog

    Description
    Genome-wide association study of smoking behaviours among Bangladeshi adults.
    EBI GWAS Catalog
    Multiple loci influencing hippocampal degeneration identified by genome scan.
    EBI GWAS Catalog

    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

    Homology

    Clone Names

    • KIAA0532, DKFZp313I0811

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol-3-phosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in Golgi organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in Golgi reassembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in acrosome assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in adipose tissue development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in central nervous system development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in dentate gyrus development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in head morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in maintenance of lens transparency ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in memory IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in muscle organ development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neuron projection development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in slow endocytic recycling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in social behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in acrosomal membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cis-Golgi network membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum-Golgi intermediate compartment membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum-Golgi intermediate compartment membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in recycling endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in trans-Golgi network membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    intermembrane lipid transfer protein VPS13B
    Names
    bridge-like lipid transfer protein family member 5B
    vacuolar protein sorting-associated protein 13B

    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

    1. NG_007098.2 RefSeqGene

      Range
      5001..869321
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_351

    mRNA and Protein(s)

    1. NM_015243.3 → NP_056058.2  intermembrane lipid transfer protein VPS13B isoform 3

      See identical proteins and their annotated locations for NP_056058.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) includes an alternate exon, which results in an early stop codon, compared to variant 5. The resulting isoform (3) has a shorter and distinct C-terminus, compared to isoform 5.
      Source sequence(s)
      AC105195, AY223817
      UniProtKB/Swiss-Prot
      Q7Z7G8
      Related
      ENST00000682853.1
      Conserved Domains (1) summary
      pfam12624
      Location:3 → 94
      Chorein_N; N-terminal region of Chorein or VPS13

    2. NM_017890.5 → NP_060360.3  intermembrane lipid transfer protein VPS13B isoform 5

      See identical proteins and their annotated locations for NP_060360.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) encodes the longest isoform (5).
      Source sequence(s)
      AC023933, AC026827, AC105195, AC105328, AY223814
      Consensus CDS
      CCDS6280.1
      UniProtKB/Swiss-Prot
      C9JD30, Q709C6, Q709C7, Q7Z7G4, Q7Z7G5, Q7Z7G6, Q7Z7G7, Q7Z7G8, Q8NB77, Q9NWV1, Q9Y4E7
      UniProtKB/TrEMBL
      A0A804HKG9
      Related
      ENSP00000351346.2, ENST00000358544.7
      Conserved Domains (4) summary
      pfam06650
      Location:2632 → 2712
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:3733 → 3839
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:3 → 94
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16909
      Location:3585 → 3731
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    3. NM_152564.5 → NP_689777.3  intermembrane lipid transfer protein VPS13B isoform 1

      See identical proteins and their annotated locations for NP_689777.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks one alternate in-frame exon and includes a different in-frame exon, compared to variant 5. The resulting isoform (1) is shorter and varies within this region of the protein, but has the same C- and N-termini, compared to isoform 5.
      Source sequence(s)
      AC023933, AC105195, AC105328, AY223815
      Consensus CDS
      CCDS6281.1
      UniProtKB/TrEMBL
      A0A804HKG9
      Related
      ENSP00000349685.2, ENST00000357162.7
      Conserved Domains (4) summary
      pfam06650
      Location:2607 → 2687
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:3708 → 3814
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:3 → 94
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16909
      Location:3560 → 3706
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    4. NM_181661.3 → NP_858047.2  intermembrane lipid transfer protein VPS13B isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the coding region, which results in introduction of a stop codon, compared to variant 5. The resulting isoform (4) has a shorter and distinct C-terminus, compared to isoform 5.
      Source sequence(s)
      AC107909, AY223818
      Consensus CDS
      CCDS47903.1
      UniProtKB/TrEMBL
      Q53G09
      Related
      ENSP00000398472.2, ENST00000441350.2
      Conserved Domains (1) summary
      pfam12624
      Location:3 → 94
      Chorein_N; N-terminal region of Chorein or VPS13

    RNA

    1. NR_047582.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) has multiple differences compared to variant 5. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC104986, AC107909, BC144379

    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

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      99013274..99877580
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      100138009..101002539
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_184042.1: Suppressed sequence

      Description
      NM_184042.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z7G8.2 GenPept UniProtKB/Swiss-Prot:Q7Z7G8

    Gene LinkOut

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

    Chemical Information
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