This gene is the central gene in a cluster of three vanin genes on chromosome 6q23-q24. Extensive alternative splicing has been described; the two most common variants are represented as RefSeqs. [provided by RefSeq, Apr 2014] See more...

Aliases for VNN3 Gene

Aliases for VNN3 Gene

  • Vanin 3 2 3 5
  • Vascular Non-Inflammatory Molecule 3 3 4
  • EC 3.5.1.92 4 52
  • Pantetheinase-Associated Gene Expressed In Leukocytes (PAGEL)-Alpha 3
  • Pantetheinase Pseudogene 3
  • Vanin 1 Pseudogene 3
  • HSA238982 3
  • EC 3.5.1 52
  • Vanin-3 4

External Ids for VNN3 Gene

Previous GeneCards Identifiers for VNN3 Gene

  • GC06M132667
  • GC06M132891
  • GC06M132979
  • GC06M133026
  • GC06M133027
  • GC06M133085
  • GC06M130618
  • GC06M133046

Summaries for VNN3 Gene

Entrez Gene Summary for VNN3 Gene

  • This gene is the central gene in a cluster of three vanin genes on chromosome 6q23-q24. Extensive alternative splicing has been described; the two most common variants are represented as RefSeqs. [provided by RefSeq, Apr 2014]

GeneCards Summary for VNN3 Gene

VNN3 (Vanin 3) is a Protein Coding gene. Among its related pathways are Metabolism of proteins and Post-translational modification- synthesis of GPI-anchored proteins. Gene Ontology (GO) annotations related to this gene include hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds and pantetheine hydrolase activity. An important paralog of this gene is VNN2.

UniProtKB/Swiss-Prot Summary for VNN3 Gene

  • Amidohydrolase that hydrolyzes specifically one of the carboamide linkages in D-pantetheine thus recycling pantothenic acid (vitamin B5) and releasing cysteamine.

Additional gene information for VNN3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VNN3 Gene

Genomics for VNN3 Gene

GeneHancer (GH) Regulatory Elements for VNN3 Gene

Promoters and enhancers for VNN3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J132732 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 525.9 +0.6 556 2.8 EP300 FOXK2 CTCF TCF12 NCOR1 POLR2A KDM6A TCF7 FOXA1 ZBTB25 VNN3 VNN1 ENSG00000234484 lnc-VNN2-2
GH06J132762 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 500.3 -28.5 -28531 2.2 POLR2A TCF12 GABPA PBX2 SPI1 BATF ELF1 RAD21 IKZF1 MTA3 RBM11P1 VNN2 lnc-RPS12-3 VNN3 SLC18B1 VNN1 ENSG00000234484
GH06J132736 Enhancer 0.9 FANTOM5 ENCODE 523.5 -1.6 -1601 0.3 FOS CEBPB JUND STAT3 RXRA MAX HNF4A REST ELF3 EGR1 VNN3 VNN2 VNN1 STX7 ENSG00000234484
GH06J132755 Promoter/Enhancer 1.7 EPDnew FANTOM5 Ensembl ENCODE 17.8 -22.9 -22884 3.3 EP300 RCOR1 BCL11A FOXA2 ZNF316 ZNF384 MAFK MEF2B NBN SPI1 VNN2 VNN3 STX7 ENSG00000234484
GH06J132669 Enhancer 0.9 Ensembl ENCODE 11.3 +61.4 61364 7.6 CTCF USF2 RAD21 RAD51 FOXA2 NFIC SMC3 ZBTB17 USF1 ZNF263 HLFP1 lnc-TAAR6-1 VNN1 ENSG00000234484 VNN2 VNN3 RPS12 SNORA33 SNORD100 SNORD101
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VNN3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VNN3

Top Transcription factor binding sites by QIAGEN in the VNN3 gene promoter:
  • E47
  • GATA-1
  • Hand1
  • Ik-1
  • PPAR-gamma1
  • PPAR-gamma2
  • RREB-1
  • STAT3
  • USF-1
  • USF1

Genomic Locations for VNN3 Gene

Genomic Locations for VNN3 Gene
chr6:132,722,787-132,734,765
(GRCh38/hg38)
Size:
11,979 bases
Orientation:
Minus strand
chr6:133,043,926-133,055,904
(GRCh37/hg19)
Size:
11,979 bases
Orientation:
Minus strand

Genomic View for VNN3 Gene

Genes around VNN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VNN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VNN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VNN3 Gene

Proteins for VNN3 Gene

  • Protein details for VNN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NY84-VNN3_HUMAN
    Recommended name:
    Vascular non-inflammatory molecule 3
    Protein Accession:
    Q9NY84
    Secondary Accessions:
    • B2DFY0
    • B2DFY1
    • B2DFY3
    • B2DFY5
    • B2DFY6
    • B2DFY7
    • B2DFY8
    • Q3SX90
    • Q9BQY2

    Protein attributes for VNN3 Gene

    Size:
    501 amino acids
    Molecular mass:
    56118 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • [Isoform 2]: Expressed in neutrophils, this isoform displays a frameshift at Glu-227 due to one missing nucleotide compared to isoform 1, this missing nucleotide could be a variation as it is also present on genomic sequence.

    Alternative splice isoforms for VNN3 Gene

neXtProt entry for VNN3 Gene

Selected DME Specific Peptides for VNN3 Gene

Q9NY84:
  • QGAHIIVTPED
  • YALGAFDG
  • YLEDIPDP

Post-translational modifications for VNN3 Gene

  • Glycosylation at Asn39, Asn147, Asn270, and Asn358
  • Modification sites at PhosphoSitePlus

Domains & Families for VNN3 Gene

Gene Families for VNN3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for VNN3 Gene

Blocks:
  • Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for VNN3 Gene

GenScript: Design optimal peptide antigens:
  • VNN3 protein (A0AUL5_HUMAN)
  • VNN3 protein (A7E205_HUMAN)
  • cDNA, FLJ95564, highly similar to Homo sapiens vanin 3 (VNN3), transcript variant 2, mRNA (B2RBK8_HUMAN)
  • Vascular non-inflammatory molecule 3 (VNN3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NY84

UniProtKB/Swiss-Prot:

VNN3_HUMAN :
  • Belongs to the carbon-nitrogen hydrolase superfamily. BTD/VNN family.
Family:
  • Belongs to the carbon-nitrogen hydrolase superfamily. BTD/VNN family.
genes like me logo Genes that share domains with VNN3: view

Function for VNN3 Gene

Molecular function for VNN3 Gene

UniProtKB/Swiss-Prot Function:
Amidohydrolase that hydrolyzes specifically one of the carboamide linkages in D-pantetheine thus recycling pantothenic acid (vitamin B5) and releasing cysteamine.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(R)-pantetheine + H2O = (R)-pantothenate + cysteamine; Xref=Rhea:RHEA:13445, ChEBI:CHEBI:15377, ChEBI:CHEBI:16753, ChEBI:CHEBI:29032, ChEBI:CHEBI:58029; EC=3.5.1.92;.
UniProtKB/Swiss-Prot Induction:
By Th17/Th1 type cytokines, but not by Th2-type.

Enzyme Numbers (IUBMB) for VNN3 Gene

Gene Ontology (GO) - Molecular Function for VNN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016787 hydrolase activity IEA --
GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides IEA --
GO:0017159 pantetheine hydrolase activity NAS,IBA 11491533
genes like me logo Genes that share ontologies with VNN3: view
genes like me logo Genes that share phenotypes with VNN3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VNN3

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VNN3 Gene

Localization for VNN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VNN3 Gene

Cell membrane; Lipid-anchor, GPI-anchor. Note=According to PubMed:11491533, secreted. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VNN3 gene
Compartment Confidence
plasma membrane 4
extracellular 4
peroxisome 1
nucleus 1
endoplasmic reticulum 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for VNN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005576 extracellular region TAS --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0031225 anchored component of membrane IEA --
genes like me logo Genes that share ontologies with VNN3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VNN3 Gene

Pathways & Interactions for VNN3 Gene

genes like me logo Genes that share pathways with VNN3: view

Interacting Proteins for VNN3 Gene

;

Gene Ontology (GO) - Biological Process for VNN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006807 nitrogen compound metabolic process IEA --
GO:0008150 biological_process ND --
GO:0015939 pantothenate metabolic process IBA 21873635
genes like me logo Genes that share ontologies with VNN3: view

No data available for SIGNOR curated interactions for VNN3 Gene

Drugs & Compounds for VNN3 Gene

(3) Drugs for VNN3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cysteamine Approved, Investigational Pharma 30
Water Approved Pharma 0
Pantothenic acid Approved, Vet_approved Nutra 35

(1) Additional Compounds for VNN3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pantetheine
  • (R)-Pantetheine
  • D-Pantetheine
  • Lactobacillus bulgaricus factor
  • LBF
  • Pantotheine
496-65-1
genes like me logo Genes that share compounds with VNN3: view

Transcripts for VNN3 Gene

mRNA/cDNA for VNN3 Gene

11 REFSEQ mRNAs :
22 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VNN3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VNN3 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8
SP1: - - -
SP2: - - - -
SP3: - - - - - -
SP4: - -
SP5:
SP6:

Relevant External Links for VNN3 Gene

GeneLoc Exon Structure for
VNN3

Expression for VNN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VNN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VNN3 Gene

This gene is overexpressed in Whole Blood (x32.6) and Liver (x12.5).

Protein differential expression in normal tissues from HIPED for VNN3 Gene

This gene is overexpressed in Plasma (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VNN3 Gene



Protein tissue co-expression partners for VNN3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VNN3

SOURCE GeneReport for Unigene cluster for VNN3 Gene:

Hs.183656

mRNA Expression by UniProt/SwissProt for VNN3 Gene:

Q9NY84-VNN3_HUMAN
Tissue specificity: Widely expressed with higher expression in liver and blood. Expressed in differentiated keratinocytes in epidermis and in epithelial cells in dermis. Overexpressed in lesional psoriatic skin.

Evidence on tissue expression from TISSUES for VNN3 Gene

  • Blood(4.2)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with VNN3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for VNN3 Gene

Orthologs for VNN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for VNN3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VNN3 31
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vnn3 31
  • 29 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VNN3 31
  • 28 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 27 (a)
OneToMany
-- 31
  • 4 (a)
OneToMany
chicken
(Gallus gallus)
Aves VNN1 31
  • 28 (a)
ManyToMany
-- 31
  • 27 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 26 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Btd 31
  • 10 (a)
ManyToMany
CG32751 31
  • 9 (a)
ManyToMany
vanin-like 31 32
  • 8 (a)
ManyToMany
CG32750 31
  • 8 (a)
ManyToMany
Species where no ortholog for VNN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for VNN3 Gene

ENSEMBL:
Gene Tree for VNN3 (if available)
TreeFam:
Gene Tree for VNN3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VNN3: view image

Paralogs for VNN3 Gene

Paralogs for VNN3 Gene

(3) SIMAP similar genes for VNN3 Gene using alignment to 7 proteins:

  • VNN3_HUMAN
  • A0AUL5_HUMAN
  • A7E205_HUMAN
  • B2RBK8_HUMAN
  • F5GYI1_HUMAN
  • F5GYM6_HUMAN
  • H0YFQ7_HUMAN
genes like me logo Genes that share paralogs with VNN3: view

Variants for VNN3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VNN3 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
776162 Benign: not provided 132,724,775(-) T/G MISSENSE_VARIANT
rs12174042 - p.Glu91Lys
rs36012859 - p.Thr89Ala
rs6569834 - p.Val222Ala
rs764264 - p.His33Arg

Additional dbSNP identifiers (rs#s) for VNN3 Gene

Structural Variations from Database of Genomic Variants (DGV) for VNN3 Gene

Variant ID Type Subtype PubMed ID
esv3610840 CNV loss 21293372

Variation tolerance for VNN3 Gene

Gene Damage Index Score: 13.89; 95.92% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VNN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VNN3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VNN3 Gene

Disorders for VNN3 Gene

Additional Disease Information for VNN3

No disorders were found for VNN3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VNN3 Gene

Publications for VNN3 Gene

  1. Expression of the vanin gene family in normal and inflamed human skin: induction by proinflammatory cytokines. (PMID: 19322213) Jansen PA … Schalkwijk J (The Journal of investigative dermatology 2009) 2 3 4 23 54
  2. Alternative spliced variants in the pantetheinase family of genes expressed in human neutrophils. (PMID: 18805469) Nitto T … Node K (Gene 2008) 3 4 23 54
  3. Vanin genes are clustered (human 6q22-24 and mouse 10A2B1) and encode isoforms of pantetheinase ectoenzymes. (PMID: 11491533) Martin F … Galland F (Immunogenetics 2001) 3 4 23 54
  4. An ESTs description of the new Vanin gene family conserved from fly to human. (PMID: 10501839) Granjeaud S … Galland F (Immunogenetics 1999) 2 3 4 54
  5. Pharmacologic concentrations of ascorbic acid cause diverse influence on differential expressions of angiogenic chemokine genes in different hepatocellular carcinoma cell lines. (PMID: 19932582) Lin ZY … Chuang WL (Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 2010) 2 3 54

Products for VNN3 Gene

  • Signalway ELISA kits for VNN3
  • Signalway Proteins for VNN3

Sources for VNN3 Gene