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

Gene ID: 157680, updated on 1-Jun-2020

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
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]
Expression
Ubiquitous expression in endometrium (RPKM 3.0), ovary (RPKM 2.8) and 25 other tissues See more
Orthologs

Genomic context

See VPS13B in Genome Data Viewer
Location:
8q22.2
Exon count:
65
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (99013274..99877580)
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 ubiquitin-conjugating enzyme E2 variant 1 pseudogene Neighboring gene Sharpr-MPRA regulatory region 5914 Neighboring gene VPS13B divergent transcript Neighboring gene insulin like growth factor 2 mRNA binding protein 2 pseudogene Neighboring gene MSL complex subunit 3 pseudogene Neighboring gene aconitase 2, mitochondrial pseudogene Neighboring gene microRNA 599 Neighboring gene microRNA 875 Neighboring gene RNA, 7SL, cytoplasmic 350, pseudogene Neighboring gene VISTA enhancer hs909 Neighboring gene leucine zipper and EF-hand containing transmembrane protein 1 pseudogene 3 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

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0532, DKFZp313I0811

Gene Ontology Provided by GOA

Process Evidence Code Pubs
protein transport IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
vacuolar protein sorting-associated protein 13B

NCBI Reference Sequences (RefSeq)

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  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
    ENSP00000347281.1, ENST00000355155.5
    Conserved Domains (1) summary
    pfam12624
    Location:394
    Chorein_N; N-terminal region of Chorein or VPS13
  2. NM_017890.5NP_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
    ENSP00000351346.2, ENST00000358544.6
    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  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
    ENSP00000349685.2, ENST00000357162.6
    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  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
    ENSP00000398472.2, 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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    99013274..99877580
    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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