U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

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

    Gene ID: 157680, updated on 1-Mar-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See VPS13B in Genome Data Viewer
    Location:
    8q22.2
    Exon count:
    65
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (99013274..99877580)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (100138009..101002539)
    105.20220307 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Cohen syndrome
    MedGen: C0265223 OMIM: 216550 GeneReviews: Cohen Syndrome
    Compare labs

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 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 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 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 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 early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    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
     

    General protein information

    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)

    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_007098.2 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_015243.3NP_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:394
      Chorein_N; N-terminal region of Chorein or VPS13
    2. NM_017890.5NP_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:26322712
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:37333839
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:394
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16909
      Location:35853731
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    3. NM_152564.5NP_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:26072687
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:37083814
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:394
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16909
      Location:35603706
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    4. NM_181661.3NP_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:394
      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_2023_10

    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.