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    VSNL1 visinin like 1 [ Homo sapiens (human) ]

    Gene ID: 7447, updated on 27-Dec-2024

    Summary

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    Official Symbol
    VSNL1provided by HGNC
    Official Full Name
    visinin like 1provided by HGNC
    Primary source
    HGNC:HGNC:12722
    See related
    Ensembl:ENSG00000163032 MIM:600817; AllianceGenome:HGNC:12722
    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
    HLP3; VILIP; HPCAL3; HUVISL1; VILIP-1
    Summary
    This gene is a member of the visinin/recoverin subfamily of neuronal calcium sensor proteins. The encoded protein is strongly expressed in granule cells of the cerebellum where it associates with membranes in a calcium-dependent manner and modulates intracellular signaling pathways of the central nervous system by directly or indirectly regulating the activity of adenylyl cyclase. Alternatively spliced transcript variants have been observed, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in brain (RPKM 206.9), esophagus (RPKM 16.5) and 2 other tissues See more
    Orthologs
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    Genomic context

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    See VSNL1 in Genome Data Viewer
    Location:
    2p24.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (17539972..17657018)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (17571738..17688768)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (17721239..17838285)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373448 Neighboring gene nascent polypeptide associated complex subunit alpha pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:17699235-17700434 Neighboring gene RAD51 associated protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15351 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:17724689-17725200 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:17725201-17725712 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:17760843-17761612 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:17771124-17772061 Neighboring gene uncharacterized LOC124908054 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:17825464-17826251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15352 Neighboring gene structural maintenance of chromosomes 6 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:17929152-17929835 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11189 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11190 Neighboring gene uncharacterized LOC105373449 Neighboring gene Sharpr-MPRA regulatory region 14936 Neighboring gene GEN1 Holliday junction 5' flap endonuclease

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. VILIP-1 downregulation in non-small cell lung carcinomas: mechanisms and prediction of survival. Fu J, et al. PLoS One, 2008 Feb 27. PMID 18301774, Free PMC Article
    2. Dimerization of visinin-like protein 1 is regulated by oxidative stress and calcium and is a pathological hallmark of amyotrophic lateral sclerosis. Liebl MP, et al. Free Radic Biol Med, 2014 Jul. PMID 24742816
    3. Serum and cerebrospinal fluid levels of visinin-like protein-1 in acute encephalopathy with biphasic seizures and late reduced diffusion. Hasegawa S, et al. Brain Dev, 2014 Aug. PMID 24075506
    4. CSF levels of the neuronal injury biomarker visinin-like protein-1 in Alzheimer's disease and dementia with Lewy bodies. Luo X, et al. J Neurochem, 2013 Dec. PMID 23800322
    5. CSF VILIP-1 predicts rates of cognitive decline in early Alzheimer disease. Tarawneh R, et al. Neurology, 2012 Mar 6. PMID 22357717, Free PMC Article

    See all (65) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Visinin-like 1, a novel target gene of the Wnt/beta-catenin signaling pathway, is involved in apoptosis resistance in colorectal cancer.
      Title: Visinin-like 1, a novel target gene of the Wnt/β-catenin signaling pathway, is involved in apoptosis resistance in colorectal cancer.
    2. Visinin-like protein 1 levels in blood and CSF as emerging markers for Alzheimer's and other neurodegenerative diseases.
      Title: Visinin-like protein 1 levels in blood and CSF as emerging markers for Alzheimer's and other neurodegenerative diseases.
    3. Predictive value of serum visinin-like protein-1 for early neurologic deterioration and three-month clinical outcome in acute primary basal ganglia hemorrhage: A prospective and observational study.
      Title: Predictive value of serum visinin-like protein-1 for early neurologic deterioration and three-month clinical outcome in acute primary basal ganglia hemorrhage: A prospective and observational study.
    4. VSNL1 Promotes Cell Proliferation, Migration, and Invasion in Colorectal Cancer by Binding with COL10A1.
      Title: VSNL1 Promotes Cell Proliferation, Migration, and Invasion in Colorectal Cancer by Binding with COL10A1.
    5. Transcriptional profiling of medulloblastoma with extensive nodularity (MBEN) reveals two clinically relevant tumor subsets with VSNL1 as potent prognostic marker.
      Title: Transcriptional profiling of medulloblastoma with extensive nodularity (MBEN) reveals two clinically relevant tumor subsets with VSNL1 as potent prognostic marker.
    6. The BDNF level showed a significant ability to discriminate stroke and control patients but did not predict mortality. The VILIP-1 level showed insignificant ability to discriminate stroke patients and again did not predict mortality.
      Title: Clinical usefulness of brain-derived neurotrophic factor and visinin-like protein-1 in early diagnostic tests for acute stroke.
    7. Underexpression of VSNL1 is associated with glioblastoma multiforme.
      Title: Dysregulated miR-671-5p / CDR1-AS / CDR1 / VSNL1 axis is involved in glioblastoma multiforme.
    8. These data indicate that VILIP-1 alone or in combination with other AD CSF biomarkers represent a valuable marker for the early diagnosis of AD, recognition of MCI patients at higher risk to develop dementia, and in differentiating AD from LBD.
      Title: Predictive Value of Cerebrospinal Fluid Visinin-Like Protein-1 Levels for Alzheimer's Disease Early Detection and Differential Diagnosis in Patients with Mild Cognitive Impairment.
    9. These findings suggest a unique role for cerebrospinal fluid Vilip-1 as a biomarker of entorhinal cortex neuron loss in Alzheimer disease
      Title: Altered Levels of Visinin-Like Protein 1 Correspond to Regional Neuronal Loss in Alzheimer Disease and Frontotemporal Lobar Degeneration.
    10. The results suggest that both serum and cerebrospinal fluid levels of VILIP-1 may be one of predictive markers of acute encephalopathy with biphasic seizures.
      Title: Serum and cerebrospinal fluid levels of visinin-like protein-1 in acute encephalopathy with biphasic seizures and late reduced diffusion.
    Submit: New GeneRIF Correction See all GeneRIFs (41)

    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of Alzheimer's disease with psychotic symptoms.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of insulin secretion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of exocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of insulin secretion involved in cellular response to glucose stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    visinin-like protein 1
    Names
    VLP-1
    hippocalcin-like protein 3

    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_001366803.2 → NP_001353732.1  visinin-like protein 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC079839, AC097377
      Consensus CDS
      CCDS1689.1
      UniProtKB/Swiss-Prot
      D6W515, P28677, P29103, P42323, P62760, Q9UM20
      Related
      ENSP00000384719.1, ENST00000406397.1
      Conserved Domains (1) summary
      COG5126
      Location:15 → 181
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    2. NM_001366804.2 → NP_001353733.1  visinin-like protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC079839, AC097377
      Conserved Domains (1) summary
      COG5126
      Location:15 → 124
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    3. NM_001366805.2 → NP_001353734.1  visinin-like protein 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC079839, AC097377
      Conserved Domains (1) summary
      cl08302
      Location:40 → 104
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    4. NM_001366806.2 → NP_001353735.1  visinin-like protein 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC079839, AC097377
      Consensus CDS
      CCDS1689.1
      UniProtKB/Swiss-Prot
      D6W515, P28677, P29103, P42323, P62760, Q9UM20
      Conserved Domains (1) summary
      COG5126
      Location:15 → 181
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    5. NM_003385.5 → NP_003376.2  visinin-like protein 1 isoform 1

      See identical proteins and their annotated locations for NP_003376.2

      Status: REVIEWED

      Source sequence(s)
      AC097377, BC022012, BF055598, BI544338
      Consensus CDS
      CCDS1689.1
      UniProtKB/Swiss-Prot
      D6W515, P28677, P29103, P42323, P62760, Q9UM20
      Related
      ENSP00000295156.4, ENST00000295156.9
      Conserved Domains (1) summary
      COG5126
      Location:15 → 181
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      17539972..17657018
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      17571738..17688768
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P62760.2 GenPept UniProtKB/Swiss-Prot:P62760

    Gene LinkOut

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