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

    Gene ID: 157680, updated on 17-Sep-2016
    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 HPRD:06379; MIM:607817; Vega:OTTHUMG00000140383
    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
    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]
    Orthologs
    Location:
    8q22.2
    Exon count:
    77
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 8 NC_000008.11 (99007014..99877586)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (100025299..100890447)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986872 Neighboring gene uncharacterized LOC105375666 Neighboring gene ubiquitin-conjugating enzyme E2 variant 1 pseudogene Neighboring gene insulin like growth factor 2 mRNA binding protein 2 pseudogene Neighboring gene male-specific lethal 3 homolog (Drosophila) pseudogene Neighboring gene aconitase 2, mitochondrial pseudogene Neighboring gene microRNA 599 Neighboring gene microRNA 875 Neighboring gene RNA, 7SL, cytoplasmic 350, pseudogene Neighboring gene leucine zipper and EF-hand containing transmembrane protein 1 pseudogene 3 Neighboring gene cytochrome c oxidase subunit 6C Neighboring gene regulator of G-protein signaling 22 Neighboring gene microRNA 1273a

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

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

    NHGRI GWAS Catalog

    Description
    Genome-wide association study of smoking behaviours among Bangladeshi adults.
    NHGRI GWA Catalog
    Multiple loci influencing hippocampal degeneration identified by genome scan.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • KIAA0532, DKFZp313I0811

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    vacuolar protein sorting-associated protein 13B

    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_015243.2NP_056058.2  vacuolar protein sorting-associated protein 13B 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
      Consensus CDS
      CCDS6283.1
      UniProtKB/Swiss-Prot
      Q7Z7G8
      Related
      ENSP00000347281, OTTHUMP00000179148, ENST00000355155, OTTHUMT00000277140
      Conserved Domains (1) summary
      pfam12624
      Location:394
      Chorein_N; N-terminal region of Chorein or VPS13
    2. NM_017890.4NP_060360.3  vacuolar protein sorting-associated protein 13B 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
      Q7Z7G8
      Related
      ENSP00000351346, OTTHUMP00000179147, ENST00000358544, OTTHUMT00000277138
      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_152564.4NP_689777.3  vacuolar protein sorting-associated protein 13B 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/Swiss-Prot
      Q7Z7G8
      Related
      ENSP00000349685, OTTHUMP00000179146, ENST00000357162, OTTHUMT00000277137
      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_181661.2NP_858047.2  vacuolar protein sorting-associated protein 13B 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/Swiss-Prot
      Q7Z7G8
      Related
      ENSP00000398472, OTTHUMP00000227256, ENST00000441350, OTTHUMT00000379820
      Conserved Domains (1) summary
      pfam12624
      Location:394
      Chorein_N; N-terminal region of Chorein or VPS13

    RNA

    1. NR_047582.1 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: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p7 Primary Assembly

      Range
      99007014..99877586
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005250801.4XP_005250858.1  

      See identical proteins and their annotated locations for XP_005250858.1

      UniProtKB/Swiss-Prot
      Q7Z7G8
      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
    2. XM_011516849.2XP_011515151.1  

      Conserved Domains (3) summary
      pfam09333
      Location:37133800
      ATG_C; ATG C terminal domain
      pfam06650
      Location:26062702
      DUF1162; Protein of unknown function (DUF1162)
      pfam12624
      Location:2101
      Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
    3. XM_011516848.2XP_011515150.1  

      UniProtKB/Swiss-Prot
      Q7Z7G8
      Conserved Domains (4) summary
      pfam06650
      Location:26312711
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam09333
      Location:37323838
      ATG_C; Autophagy-related protein C terminal domain
      pfam12624
      Location:394
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16909
      Location:35843730
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    4. XM_017013109.1XP_016868598.1  

    5. XM_011516853.2XP_011515155.1  

      Conserved Domains (2) summary
      pfam06650
      Location:26322706
      DUF1162; Protein of unknown function (DUF1162)
      pfam12624
      Location:2101
      Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
    6. XM_006716510.3XP_006716573.1  

      Conserved Domains (1) summary
      pfam12624
      Location:394
      Chorein_N; N-terminal region of Chorein or VPS13
    7. XM_011516859.2XP_011515161.1  

      Conserved Domains (1) summary
      pfam12624
      Location:2101
      Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
    8. XM_011516861.1XP_011515163.1  

      Conserved Domains (1) summary
      pfam12624
      Location:2101
      Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
    9. XM_011516865.1XP_011515167.1  

      Conserved Domains (1) summary
      pfam12624
      Location:2101
      Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
    10. XM_011516866.2XP_011515168.1  

      Conserved Domains (1) summary
      pfam12624
      Location:2101
      Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
    11. XM_005250800.3XP_005250857.1  

      See identical proteins and their annotated locations for XP_005250857.1

      UniProtKB/Swiss-Prot
      Q7Z7G8
      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
    12. XM_011516850.2XP_011515152.1  

      Conserved Domains (2) summary
      pfam09333
      Location:36133700
      ATG_C; ATG C terminal domain
      pfam06650
      Location:25062602
      DUF1162; Protein of unknown function (DUF1162)
    13. XM_017013110.1XP_016868599.1  

    14. XM_011516851.2XP_011515153.1  

      See identical proteins and their annotated locations for XP_011515153.1

      Conserved Domains (2) summary
      pfam09333
      Location:27012788
      ATG_C; ATG C terminal domain
      pfam06650
      Location:15941690
      DUF1162; Protein of unknown function (DUF1162)
    15. XM_011516852.2XP_011515154.1  

      See identical proteins and their annotated locations for XP_011515154.1

      Conserved Domains (2) summary
      pfam09333
      Location:27012788
      ATG_C; ATG C terminal domain
      pfam06650
      Location:15941690
      DUF1162; Protein of unknown function (DUF1162)
    16. XM_017013111.1XP_016868600.1  

    17. XM_017013112.1XP_016868601.1  

    18. XM_011516854.2XP_011515156.1  

      Conserved Domains (2) summary
      pfam09333
      Location:23322419
      ATG_C; ATG C terminal domain
      pfam06650
      Location:12251321
      DUF1162; Protein of unknown function (DUF1162)

    RNA

    1. XR_001745482.1 RNA Sequence

    2. XR_928302.2 RNA Sequence

    3. XR_928301.1 RNA Sequence

    4. XR_928304.1 RNA Sequence

      Related
      ENST00000496144, OTTHUMT00000277139
    5. XR_001745483.1 RNA Sequence

    6. XR_001745480.1 RNA Sequence

    7. XR_001745481.1 RNA Sequence

    8. XR_001745484.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018919.2 Alternate CHM1_1.1

      Range
      100066127..100930595
      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.
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