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

Gene ID: 157680, updated on 19-Jul-2014
Official Symbol
VPS13Bprovided by HGNC
Official Full Name
vacuolar protein sorting 13 homolog B (yeast)provided by HGNC
Primary source
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]
See VPS13B in Epigenomics, MapViewer
Location:
8q22.2
Exon count:
68
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 8 NC_000008.11 (99011179..99878219)
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 ubiquitin-conjugating enzyme E2 variant 1-like 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 microRNA 599 Neighboring gene microRNA 875 Neighboring gene leucine zipper-EF-hand containing transmembrane protein 1, pseudogene 3 Neighboring gene cytochrome c oxidase subunit VIc Neighboring gene regulator of G-protein signaling 22 Neighboring gene microRNA 1273a Neighboring gene F-box protein 43

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
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
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 

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

mRNA and Protein(s)

  1. NM_015243.2NP_056058.2  vacuolar protein sorting-associated protein 13B isoform 3

    See proteins identical to 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
    Blast Score: 338
    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 proteins identical to 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
    Blast Score: 137
    ATG_C; ATG C terminal domain
    pfam06650
    Location:26322728
    Blast Score: 101
    DUF1162; Protein of unknown function (DUF1162)
    pfam12624
    Location:2101
    Blast Score: 339
    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 proteins identical to 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
    Blast Score: 137
    ATG_C; ATG C terminal domain
    pfam06650
    Location:26072703
    Blast Score: 101
    DUF1162; Protein of unknown function (DUF1162)
    pfam12624
    Location:2101
    Blast Score: 339
    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
    Blast Score: 333
    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 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000008.11 

    Range
    99011179..99878219
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005250801.2XP_005250858.1  

    See proteins identical to XP_005250858.1

    UniProtKB/Swiss-Prot
    Q7Z7G8
    Conserved Domains (3) summary
    pfam09333
    Location:37393826
    Blast Score: 137
    ATG_C; ATG C terminal domain
    pfam06650
    Location:26322728
    Blast Score: 101
    DUF1162; Protein of unknown function (DUF1162)
    pfam12624
    Location:2101
    Blast Score: 339
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  2. XM_006716510.1XP_006716573.1  

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Blast Score: 341
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  3. XM_006716511.1XP_006716574.1  

    Conserved Domains (1) summary
    pfam12624
    Location:2101
    Blast Score: 337
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter
  4. XM_005250800.1XP_005250857.1  

    See proteins identical to XP_005250857.1

    UniProtKB/Swiss-Prot
    Q7Z7G8
    Conserved Domains (3) summary
    pfam09333
    Location:37393826
    Blast Score: 137
    ATG_C; ATG C terminal domain
    pfam06650
    Location:26322728
    Blast Score: 101
    DUF1162; Protein of unknown function (DUF1162)
    pfam12624
    Location:2101
    Blast Score: 339
    Chorein_N; N-terminal region of Chorein, a TM vesicle-mediated sorter

Alternate HuRef

Genomic

  1. AC_000140.1 

    Range
    95228270..96092444
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018919.2 

    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.