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

Gene ID: 157680, updated on 5-Mar-2024

Summary

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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
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. A Novel Variant in VPS13B Underlying Cohen Syndrome. Hussain A, et al. Biomed Res Int, 2023. PMID 37090188, Free PMC Article
  2. Disease relevance of rare VPS13B missense variants for neurodevelopmental Cohen syndrome. Zorn M, et al. Sci Rep, 2022 Jun 11. PMID 35690661, Free PMC Article
  3. A Novel VPS13B Mutation Identified by Whole-Exome Sequencing in Iranian Patients with Cohen Syndrome. Karimzadeh MR, et al. J Mol Neurosci, 2021 Dec. PMID 34041686
  4. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation. Bonfante B, et al. Sci Adv, 2021 Feb. PMID 33547071, Free PMC Article
  5. Functional Analysis of a Compound Heterozygous Mutation in the VPS13B Gene in a Chinese Pedigree with Cohen Syndrome. Lou G, et al. J Mol Neurosci, 2021 May. PMID 33025479

See all (72) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A Novel Variant in VPS13B Underlying Cohen Syndrome.
    Title: A Novel Variant in VPS13B Underlying Cohen Syndrome.
  2. Disease relevance of rare VPS13B missense variants for neurodevelopmental Cohen syndrome.
    Title: Disease relevance of rare VPS13B missense variants for neurodevelopmental Cohen syndrome.
  3. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation.
    Title: A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation.
  4. A Novel VPS13B Mutation Identified by Whole-Exome Sequencing in Iranian Patients with Cohen Syndrome.
    Title: A Novel VPS13B Mutation Identified by Whole-Exome Sequencing in Iranian Patients with Cohen Syndrome.
  5. Functional Analysis of a Compound Heterozygous Mutation in the VPS13B Gene in a Chinese Pedigree with Cohen Syndrome.
    Title: Functional Analysis of a Compound Heterozygous Mutation in the VPS13B Gene in a Chinese Pedigree with Cohen Syndrome.
  6. Autophagy pathway upregulation in a human iPSC-derived neuronal model of Cohen syndrome with VPS13B missense mutations.
    Title: Autophagy pathway upregulation in a human iPSC-derived neuronal model of Cohen syndrome with VPS13B missense mutations.
  7. An intronic splice site alteration in combination with a large deletion affecting VPS13B (COH1) causes Cohen syndrome.
    Title: An intronic splice site alteration in combination with a large deletion affecting VPS13B (COH1) causes Cohen syndrome.
  8. Cohen Syndrome-Associated Cataract Is Explained by VPS13B Functions in Lens Homeostasis and Is Modified by Additional Genetic Factors.
    Title: Cohen Syndrome-Associated Cataract Is Explained by VPS13B Functions in Lens Homeostasis and Is Modified by Additional Genetic Factors.
  9. Ophthalmic features of retinitis pigmentosa in Cohen syndrome caused by pathogenic variants in the VPS13B gene.
    Title: Ophthalmic features of retinitis pigmentosa in Cohen syndrome caused by pathogenic variants in the VPS13B gene.
  10. A novel homozygous nonsense mutation of VPS13B associated with previously unreported features of Cohen syndrome.
    Title: A novel homozygous nonsense mutation of VPS13B associated with previously unreported features of Cohen syndrome.
Submit: New GeneRIF Correction See all GeneRIFs (35)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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

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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)

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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_015243.3 → NP_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:3 → 94
    Chorein_N; N-terminal region of Chorein or VPS13

  2. NM_017890.5 → NP_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:2632 → 2712
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:3733 → 3839
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:3 → 94
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16909
    Location:3585 → 3731
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

  3. NM_152564.5 → NP_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:2607 → 2687
    SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
    pfam09333
    Location:3708 → 3814
    ATG_C; Autophagy-related protein C terminal domain
    pfam12624
    Location:3 → 94
    Chorein_N; N-terminal region of Chorein or VPS13
    pfam16909
    Location:3560 → 3706
    VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

  4. NM_181661.3 → NP_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:3 → 94
    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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z7G8.2 GenPept UniProtKB/Swiss-Prot:Q7Z7G8

Gene LinkOut

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