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    VAT1L vesicle amine transport 1 like [ Homo sapiens (human) ]

    Gene ID: 57687, updated on 2-Nov-2024

    Summary

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    Official Symbol
    VAT1Lprovided by HGNC
    Official Full Name
    vesicle amine transport 1 likeprovided by HGNC
    Primary source
    HGNC:HGNC:29315
    See related
    Ensembl:ENSG00000171724 MIM:620202; AllianceGenome:HGNC:29315
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable oxidoreductase activity and zinc ion binding activity. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in adrenal (RPKM 44.1), brain (RPKM 16.6) and 3 other tissues See more
    Orthologs
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    Genomic context

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    See VAT1L in Genome Data Viewer
    Location:
    16q23.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (77788564..77980107)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (83844682..84036081)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (77822461..78014004)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2131 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45434 Neighboring gene Sharpr-MPRA regulatory region 41 Neighboring gene uncharacterized LOC107984878 Neighboring gene nudix hydrolase 7 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:77866929-77867894 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:77867895-77868858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:77885719-77886220 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:77911218-77912417 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:77928177-77928677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:77952963-77953462 Neighboring gene peptidylprolyl isomerase A pseudogene 50 Neighboring gene uncharacterized LOC105371351 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11154 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78000722-78001339 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78001340-78001958 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:78003196-78003813 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45488 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:78025071-78026270 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78026297-78026990 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78026991-78027683 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:78028377-78029069 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:78029289-78030488 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45524 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7735 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45548 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45593 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45596 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45605 Neighboring gene C-type lectin domain family 3 member A Neighboring gene keratin 8 pseudogene 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 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. Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects. Dastani Z, et al. Eur J Hum Genet, 2010 Mar. PMID 19844255, Free PMC Article
    2. Genome-wide association study of the rate of cognitive decline in Alzheimer's disease. Sherva R, et al. Alzheimers Dement, 2014 Jan. PMID 23535033, Free PMC Article
    3. A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. Wang KS, et al. Schizophr Res, 2010 Dec. PMID 20889312
    4. Interaction between the scaffold proteins CBP by IQGAP1 provides an interface between gene expression and cytoskeletal activity. Kosol S, et al. Sci Rep, 2020 Apr 1. PMID 32238831, Free PMC Article
    5. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Aug 31. PMID 10997877

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
    EBI GWAS Catalog
    Genome-wide association study of the rate of cognitive decline in Alzheimer's disease.
    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

    • KIAA1576

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    synaptic vesicle membrane protein VAT-1 homolog-like
    Names
    vesicle amine transport protein 1 homolog (T. californica)-like
    vesicle amine transport protein 1 homolog-like (T. californica)

    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.

    mRNA and Protein(s)

    1. NM_020927.3 → NP_065978.1  synaptic vesicle membrane protein VAT-1 homolog-like

      See identical proteins and their annotated locations for NP_065978.1

      Status: VALIDATED

      Source sequence(s)
      AA609348, AC010650, AK290153, BC033537, HY132852
      Consensus CDS
      CCDS32492.1
      UniProtKB/Swiss-Prot
      Q8IYW8, Q9HCJ6
      UniProtKB/TrEMBL
      A8K288
      Related
      ENSP00000303129.2, ENST00000302536.3
      Conserved Domains (1) summary
      cd08275
      Location:43 → 380
      MDR3; Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      77788564..77980107
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      83844682..84036081
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HCJ6.2 GenPept UniProtKB/Swiss-Prot:Q9HCJ6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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