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    VNN2 vanin 2 [ Homo sapiens (human) ]

    Gene ID: 8875, updated on 5-Mar-2024

    Summary

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    Official Symbol
    VNN2provided by HGNC
    Official Full Name
    vanin 2provided by HGNC
    Primary source
    HGNC:HGNC:12706
    See related
    Ensembl:ENSG00000112303 MIM:603571; AllianceGenome:HGNC:12706
    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
    FOAP-4; GPI-80
    Summary
    This gene product is a member of the Vanin family of proteins that share extensive sequence similarity with each other, and also with biotinidase. The family includes secreted and membrane-associated proteins, a few of which have been reported to participate in hematopoietic cell trafficking. No biotinidase activity has been demonstrated for any of the vanin proteins, however, they possess pantetheinase activity, which may play a role in oxidative-stress response. The encoded protein is a GPI-anchored cell surface molecule that plays a role in transendothelial migration of neutrophils. This gene lies in close proximity to, and in same transcriptional orientation as two other vanin genes on chromosome 6q23-q24. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, May 2011]
    Expression
    Biased expression in spleen (RPKM 12.9), lymph node (RPKM 11.0) and 11 other tissues See more
    Orthologs
    all
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    Genomic context

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    See VNN2 in Genome Data Viewer
    Location:
    6q23.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (132743870..132763455, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (133938837..133958444, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (133065009..133084594, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene vanin 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_89876 Neighboring gene cyclin G1 pseudogene 1 Neighboring gene vanin 3, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:133069914-133071113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25075 Neighboring gene RNA binding motif protein 11 pseudogene 1 Neighboring gene solute carrier family 18 member B1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:133118062-133118562

    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. The hematopoietic stem cell marker VNN2 is associated with chemoresistance in pediatric B-cell precursor ALL. Bornhauser B, et al. Blood Adv, 2020 Sep 8. PMID 32853382, Free PMC Article
    2. GPI-80 as a Useful Index for Myeloid Cell Heterogeneity and a Potential Prognostic Biomarker for Metastatic Renal Cell Carcinoma. Kato T, et al. Tohoku J Exp Med, 2019 Nov. PMID 31776298
    3. The pattern of GPI-80 expression is a useful marker for unusual myeloid maturation in peripheral blood. Takeda Y, et al. Clin Exp Immunol, 2016 Dec. PMID 27569996, Free PMC Article
    4. GPI-80 defines self-renewal ability in hematopoietic stem cells during human development. Prashad SL, et al. Cell Stem Cell, 2015 Jan 8. PMID 25465114, Free PMC Article
    5. Structural divergence of GPI-80 in activated human neutrophils. Nitto T, et al. Biochem Biophys Res Commun, 2007 Jul 27. PMID 17543284

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. GPI-80 Augments NF-kappaB Activation in Tumor Cells.
      Title: GPI-80 Augments NF-κB Activation in Tumor Cells.
    2. The hematopoietic stem cell marker VNN2 is associated with chemoresistance in pediatric B-cell precursor ALL.
      Title: The hematopoietic stem cell marker VNN2 is associated with chemoresistance in pediatric B-cell precursor ALL.
    3. the expression of GPI-80 on myeloid cells, a useful index for the heterogeneity of Myeloid-derived suppressor cells, serves as a potential prognostic biomarker for Metastatic Renal Cell Carcinoma.
      Title: GPI-80 as a Useful Index for Myeloid Cell Heterogeneity and a Potential Prognostic Biomarker for Metastatic Renal Cell Carcinoma.
    4. Low VNN2 expression is associated with invasion of osteosarcoma.
      Title: MicroRNA‑106a regulates the proliferation and invasion of human osteosarcoma cells by targeting VNN2.
    5. the GPI-80 CV in the CD16(hi) population was correlated inversely with the proliferative ability of T cells and the GPI-80 MFI of the CD33(hi) population was correlated with reactive oxygen species production. These results led us to propose that the pattern of GPI-80 expression in these populations is a simple and useful marker for unusual differentiation, which is related to MDSC functions.
      Title: The pattern of GPI-80 expression is a useful marker for unusual myeloid maturation in peripheral blood.
    6. GPI-80 defines a subpopulation of human fetal liver hematopoietic stem/progenitor cells (HSPCs) with self-renewal ability.
      Title: GPI-80 defines self-renewal ability in hematopoietic stem cells during human development.
    7. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Use of expression data and the CGEMS genome-wide breast cancer association study to identify genes that may modify risk in BRCA1/2 mutation carriers.
    8. some of the GPI-80 on pseudopodia of migrating neutrophils during the late phase was associated with urokinase-type plasminogen activator receptor (uPAR), a regulator of beta2 integrin-dependent adherence and migration
      Title: GPI-80, a beta2 integrin associated glycosylphosphatidylinositol-anchored protein, concentrates on pseudopodia without association with beta2 integrin during neutrophil migration.
    9. elevated GPI-80 expression is associated with development and progression of thymoma
      Title: Glycosylphosphatidyl inositol-anchored protein (GPI-80) gene expression is correlated with human thymoma stage.
    10. GPI-80 positive monocytes belong to a monocyte subpopulation that is superior in phagocytosis and reactive oxygen production, but inferior in antigen presentation
      Title: Localization of GPI-80, a beta2-integrin-associated glycosylphosphatidyl-inositol anchored protein, on strongly CD14-positive human monocytes.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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

    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 pantetheine hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables pantetheine hydrolase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables pantetheine hydrolase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in pantothenate metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in pantothenate metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in pantothenate metabolic process TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    pantetheine hydrolase VNN2
    Names
    Vannin 2
    glycosylphosphatidyl inositol-anchored protein GPI-80
    pantetheinase
    vascular non-inflammatory molecule 2
    NP_001229279.2
    NP_004656.3
    NP_511043.2
    XP_006715656.1
    XP_011534533.1
    XP_047275433.1
    XP_047275434.1
    XP_047275435.1
    XP_047275436.1
    XP_047275437.1
    XP_054212659.1
    XP_054212660.1
    XP_054212661.1
    XP_054212662.1
    XP_054212663.1
    XP_054212664.1
    XP_054212665.1

    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_050645.2 RefSeqGene

      Range
      10551..24585
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001242350.3 → NP_001229279.2  pantetheine hydrolase VNN2 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks two alternate in-frame exons in the coding region, compared to variant 1. The resulting protein (isoform 3) is shorter but has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      AL032821
      Consensus CDS
      CCDS56451.1
      Related
      ENSP00000436935.1, ENST00000525289.5
      Conserved Domains (2) summary
      pfam19018
      Location:165 → 266
      Vanin_C; Vanin C-terminal domain
      cl11424
      Location:26 → 180
      nitrilase; Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes

    2. NM_004665.6 → NP_004656.3  pantetheine hydrolase VNN2 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL032821
      Consensus CDS
      CCDS5161.1
      UniProtKB/Swiss-Prot
      A0AUZ3, A6NDY1, A8K4E3, A8K7W0, B2DFZ0, B2DFZ1, B2DFZ2, B2DFZ3, F6XL73, O95498, Q2XUN1, Q9UJF3, Q9UMW2
      Related
      ENSP00000322276.6, ENST00000326499.11
      Conserved Domains (2) summary
      cd07567
      Location:26 → 329
      biotinidase_like; biotinidase and vanins (class 4 nitrilases)
      pfam19018
      Location:344 → 487
      Vanin_C; Vanin C-terminal domain

    3. NM_078488.3 → NP_511043.2  pantetheine hydrolase VNN2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream codon, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AL032821
      Consensus CDS
      CCDS5162.1
      Related
      ENSP00000436822.1, ENST00000525270.5
      Conserved Domains (2) summary
      cd07567
      Location:1 → 276
      biotinidase_like; biotinidase and vanins (class 4 nitrilases)
      pfam19018
      Location:291 → 434
      Vanin_C; Vanin C-terminal domain

    RNA

    1. NR_034173.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate 5' exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL032821

    2. NR_034174.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate 5' exon and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL032821

    3. NR_110143.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) uses an alternate internal splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL032821
      Related
      ENST00000392389.6

    4. NR_110144.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) uses an alternate internal splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL032821
      Related
      ENST00000418593.6

    5. NR_110145.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate 5' exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL032821

    6. NR_110146.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks multiple consecutive exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL032821

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      132743870..132763455 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419477.1 → XP_047275433.1  pantetheine hydrolase VNN2 isoform X1

      UniProtKB/Swiss-Prot
      A0AUZ3, A6NDY1, A8K4E3, A8K7W0, B2DFZ0, B2DFZ1, B2DFZ2, B2DFZ3, F6XL73, O95498, Q2XUN1, Q9UJF3, Q9UMW2

    2. XM_006715593.4 → XP_006715656.1  pantetheine hydrolase VNN2 isoform X3

      UniProtKB/Swiss-Prot
      O95498
      Conserved Domains (2) summary
      cd07567
      Location:1 → 276
      biotinidase_like; biotinidase and vanins (class 4 nitrilases)
      pfam19018
      Location:291 → 434
      Vanin_C; Vanin C-terminal domain

    3. XM_047419478.1 → XP_047275434.1  pantetheine hydrolase VNN2 isoform X1

      UniProtKB/Swiss-Prot
      A0AUZ3, A6NDY1, A8K4E3, A8K7W0, B2DFZ0, B2DFZ1, B2DFZ2, B2DFZ3, F6XL73, O95498, Q2XUN1, Q9UJF3, Q9UMW2

    4. XM_047419481.1 → XP_047275437.1  pantetheine hydrolase VNN2 isoform X3

    5. XM_047419479.1 → XP_047275435.1  pantetheine hydrolase VNN2 isoform X1

      UniProtKB/Swiss-Prot
      A0AUZ3, A6NDY1, A8K4E3, A8K7W0, B2DFZ0, B2DFZ1, B2DFZ2, B2DFZ3, F6XL73, O95498, Q2XUN1, Q9UJF3, Q9UMW2

    6. XM_047419480.1 → XP_047275436.1  pantetheine hydrolase VNN2 isoform X2

    7. XM_011536231.1 → XP_011534533.1  pantetheine hydrolase VNN2 isoform X4

      Conserved Domains (1) summary
      cd07567
      Location:26 → 329
      biotinidase_like; biotinidase and vanins (class 4 nitrilases)

    RNA

    1. XR_007059352.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      133938837..133958444 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356684.1 → XP_054212659.1  pantetheine hydrolase VNN2 isoform X1

    2. XM_054356688.1 → XP_054212663.1  pantetheine hydrolase VNN2 isoform X3

    3. XM_054356685.1 → XP_054212660.1  pantetheine hydrolase VNN2 isoform X1

    4. XM_054356687.1 → XP_054212662.1  pantetheine hydrolase VNN2 isoform X3

    5. XM_054356690.1 → XP_054212665.1  pantetheine hydrolase VNN2 isoform X5

    6. XM_054356686.1 → XP_054212661.1  pantetheine hydrolase VNN2 isoform X2

    7. XM_054356689.1 → XP_054212664.1  pantetheine hydrolase VNN2 isoform X4

    RNA

    1. XR_008487456.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95498.3 GenPept UniProtKB/Swiss-Prot:O95498

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