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

Gene ID: 157680, updated on 21-May-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:
80
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 8 NC_000008.11 (99013071..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 serine/threonine kinase 3 Neighboring gene collagen alpha-1(I) chain-like Neighboring gene uncharacterized LOC105375666 Neighboring gene ubiquitin-conjugating enzyme E2 variant 1 pseudogene Neighboring gene odd-skipped related transciption factor 2 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 uncharacterized LOC105375664 Neighboring gene microRNA 599 Neighboring gene microRNA 875 Neighboring gene uncharacterized LOC105375663 Neighboring gene leucine zipper and EF-hand containing transmembrane protein 1 pseudogene 3 Neighboring gene cytochrome c oxidase subunit 6C Neighboring gene microRNA 1273a Neighboring gene regulator of G-protein signaling 22

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:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  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 (3) summary
    pfam09333
    Location:37393826
    ATG_C; ATG C terminal domain
    pfam06650
    Location:26322728
    DUF1162; Protein of unknown function (DUF1162)
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  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 (3) summary
    pfam09333
    Location:37143801
    ATG_C; ATG C terminal domain
    pfam06650
    Location:26072703
    DUF1162; Protein of unknown function (DUF1162)
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  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:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter

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 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p2 Primary Assembly

    Range
    99013071..99877586
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005250801.3XP_005250858.1  

    See identical proteins and their annotated locations for XP_005250858.1

    UniProtKB/Swiss-Prot
    Q7Z7G8
    Conserved Domains (3) summary
    pfam09333
    Location:37393826
    ATG_C; ATG C terminal domain
    pfam06650
    Location:26322728
    DUF1162; Protein of unknown function (DUF1162)
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  2. XM_011516849.1XP_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_011516848.1XP_011515150.1  

    UniProtKB/Swiss-Prot
    Q7Z7G8
    Conserved Domains (3) summary
    pfam09333
    Location:37383825
    ATG_C; ATG C terminal domain
    pfam06650
    Location:26312727
    DUF1162; Protein of unknown function (DUF1162)
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  4. XM_011516853.1XP_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
  5. XM_006716510.2XP_006716573.1  

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  6. XM_011516857.1XP_011515159.1  

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  7. XM_011516855.1XP_011515157.1  

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  8. XM_011516856.1XP_011515158.1  

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  9. XM_011516858.1XP_011515160.1  

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  10. XM_011516860.1XP_011515162.1  

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  11. XM_011516859.1XP_011515161.1  

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

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  13. XM_011516862.1XP_011515164.1  

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  14. XM_011516864.1XP_011515166.1  

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  15. XM_011516863.1XP_011515165.1  

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  16. XM_006716511.2XP_006716574.1  

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

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

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  19. XM_005250800.2XP_005250857.1  

    See identical proteins and their annotated locations for XP_005250857.1

    UniProtKB/Swiss-Prot
    Q7Z7G8
    Conserved Domains (3) summary
    pfam09333
    Location:37393826
    ATG_C; ATG C terminal domain
    pfam06650
    Location:26322728
    DUF1162; Protein of unknown function (DUF1162)
    pfam12624
    Location:2101
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  20. XM_011516850.1XP_011515152.1  

    Conserved Domains (2) summary
    pfam09333
    Location:36133700
    ATG_C; ATG C terminal domain
    pfam06650
    Location:25062602
    DUF1162; Protein of unknown function (DUF1162)
  21. XM_011516851.1XP_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)
  22. XM_011516852.1XP_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)
  23. XM_011516854.1XP_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_928303.1 RNA Sequence

  2. XR_928301.1 RNA Sequence

  3. XR_928302.1 RNA Sequence

  4. XR_928304.1 RNA Sequence

    Related
    ENST00000496144, OTTHUMT00000277139

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.