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VSNL1 visinin like 1 [ Homo sapiens (human) ]

Gene ID: 7447, updated on 5-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (17539972..17657018)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (17571738..17688768)
105.20220307 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: 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. Visinin-like 1, a novel target gene of the Wnt/β-catenin signaling pathway, is involved in apoptosis resistance in colorectal cancer. Tage H, et al. Cancer Med, 2023 Jun. PMID 37096864, Free PMC Article
  2. Visinin-like protein 1 levels in blood and CSF as emerging markers for Alzheimer's and other neurodegenerative diseases. Halbgebauer S, et al. Alzheimers Res Ther, 2022 Nov 22. PMID 36419075, Free PMC Article
  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. Yan XJ, et al. Clin Chim Acta, 2022 Jun 1. PMID 35292254
  4. Transcriptional profiling of medulloblastoma with extensive nodularity (MBEN) reveals two clinically relevant tumor subsets with VSNL1 as potent prognostic marker. Korshunov A, et al. Acta Neuropathol, 2020 Mar. PMID 31781912
  5. 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. Babić Leko M, et al. J Alzheimers Dis, 2016. PMID 26836160

See all (63) 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)

Genotypes

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
  
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_2023_10

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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