VNN2 Gene (Protein Coding)

Vanin 2

GC06M132743
GIFtS:
41
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, ... See more...

Aliases for VNN2 Gene

Aliases for VNN2 Gene

  • Vanin 2 2 3 5
  • Glycosylphosphatidyl Inositol-Anchored Protein GPI-80 3 4
  • Vascular Non-Inflammatory Molecule 2 3 4
  • Pantetheinase 2 3
  • EC 3.5.1.92 4 52
  • Protein FOAP-4 4
  • Vannin 2 3
  • EC 3.5.1 52
  • Vanin-2 4
  • FOAP-4 3
  • GPI-80 3

External Ids for VNN2 Gene

Previous GeneCards Identifiers for VNN2 Gene

  • GC06M132688
  • GC06M132912
  • GC06M133000
  • GC06M133045
  • GC06M133106
  • GC06M130639
  • GC06M133065

Summaries for VNN2 Gene

Entrez Gene Summary for VNN2 Gene

  • 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]

GeneCards Summary for VNN2 Gene

VNN2 (Vanin 2) is a Protein Coding gene. Diseases associated with VNN2 include Trichuriasis and Biotinidase Deficiency. Among its related pathways are Metabolism of proteins and Metabolism of water-soluble vitamins and cofactors. 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 VNN1.

UniProtKB/Swiss-Prot Summary for VNN2 Gene

  • Amidohydrolase that hydrolyzes specifically one of the carboamide linkages in D-pantetheine thus recycling pantothenic acid (vitamin B5) and releasing cysteamine. Involved in the thymus homing of bone marrow cells. May regulate beta-2 integrin-mediated cell adhesion, migration and motility of neutrophil.

Gene Wiki entry for VNN2 Gene

Additional gene information for VNN2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VNN2 Gene

Genomics for VNN2 Gene

GeneHancer (GH) Regulatory Elements for VNN2 Gene

Promoters and enhancers for VNN2 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
GH06J132755 Promoter/Enhancer 1.7 EPDnew FANTOM5 Ensembl ENCODE 563.9 +5.8 5810 3.3 EP300 RCOR1 BCL11A FOXA2 ZNF316 ZNF384 MAFK MEF2B NBN SPI1 VNN2 VNN3 STX7 ENSG00000234484
GH06J132762 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 500.7 +0.2 163 2.2 POLR2A TCF12 GABPA PBX2 SPI1 BATF ELF1 RAD21 IKZF1 MTA3 RBM11P1 VNN2 lnc-RPS12-3 VNN3 SLC18B1 VNN1 ENSG00000234484
GH06J132764 Enhancer 0.5 ENCODE 500.7 -1.0 -985 0 FOS RAD21 POLR2A PRDM1 YY1 MYC RBM11P1 VNN2 lnc-RPS12-3 VNN3
GH06J132749 Enhancer 0.8 FANTOM5 78.4 +14.2 14207 0.2 CEBPB GABPA TRIM24 CEBPG GABPB1 JUND FOXP1 ZGPAT KLF6 EP300 VNN2 STX7 ENSG00000234484 VNN3
GH06J132746 Enhancer 0.6 FANTOM5 ENCODE 89.1 +17.2 17151 0.3 CTCF FOS STAT3 VNN2 STX7 SLC18B1 ENSG00000234484 VNN3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VNN2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VNN2

Top Transcription factor binding sites by QIAGEN in the VNN2 gene promoter:
  • AP-1
  • c-Fos
  • c-Jun
  • C/EBPalpha
  • TBP
  • TFIID

Genomic Locations for VNN2 Gene

Genomic Locations for VNN2 Gene
chr6:132,743,870-132,763,459
(GRCh38/hg38)
Size:
19,590 bases
Orientation:
Minus strand
chr6:133,065,009-133,084,598
(GRCh37/hg19)
Size:
19,590 bases
Orientation:
Minus strand

Genomic View for VNN2 Gene

Genes around VNN2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VNN2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VNN2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for VNN2 Gene

Proteins for VNN2 Gene

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  • Protein details for VNN2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95498-VNN2_HUMAN
    Recommended name:
    Vascular non-inflammatory molecule 2
    Protein Accession:
    O95498
    Secondary Accessions:
    • A0AUZ3
    • A6NDY1
    • A8K4E3
    • A8K7W0
    • B2DFZ0
    • B2DFZ1
    • B2DFZ2
    • B2DFZ3
    • F6XL73
    • Q2XUN1
    • Q9UJF3
    • Q9UMW2

    Protein attributes for VNN2 Gene

    Size:
    520 amino acids
    Molecular mass:
    58503 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • [Isoform 3]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    • [Isoform 4]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    • [Isoform 5]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Alternative splice isoforms for VNN2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VNN2 Gene

Protein Expression for VNN2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for VNN2 Gene

O95498:
  • TRFEMFSLSGTFGT
  • YLEDIPDP
  • LVARYHK
  • FHSAWAMGM

Post-translational modifications for VNN2 Gene

  • Glycosylation at Asn39, Asn411, Asn273, Asn468, Asn347, and Asn357
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Other Protein References for VNN2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Protein Products

  • Abcam proteins for VNN2

Domains & Families for VNN2 Gene

Gene Families for VNN2 Gene

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

Protein Domains for VNN2 Gene

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

Suggested Antigen Peptide Sequences for VNN2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ75896, highly similar to Homo sapiens vanin 2 (VNN2), transcript variant 2, mRNA (A8K7W0_HUMAN)
  • cDNA FLJ55137, highly similar to Vascular non-inflammatory molecule 2 (B4DQB2_HUMAN)
  • Protein FOAP-4 (VNN2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O95498

UniProtKB/Swiss-Prot:

VNN2_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 VNN2: view

Function for VNN2 Gene

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Molecular function for VNN2 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. Involved in the thymus homing of bone marrow cells. May regulate beta-2 integrin-mediated cell adhesion, migration and motility of neutrophil.
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;.
GENATLAS Biochemistry:
vanin 2,53kDa,expressed in kidney,homolog to mouse VNN1,VNN2,involved in lymphocyte migration and cell adhesion

Enzyme Numbers (IUBMB) for VNN2 Gene

Phenotypes From GWAS Catalog for VNN2 Gene

Gene Ontology (GO) - Molecular Function for VNN2 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 IBA,IDA 11491533
genes like me logo Genes that share ontologies with VNN2: view
genes like me logo Genes that share phenotypes with VNN2: view

Animal Model Products

CRISPR Products

miRNA for VNN2 Gene

miRTarBase miRNAs that target VNN2

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VNN2 Gene

Localization for VNN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VNN2 Gene

Cell membrane; Lipid-anchor, GPI-anchor.

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 VNN2 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for VNN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
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 VNN2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VNN2 Gene

Pathways & Interactions for VNN2 Gene

genes like me logo Genes that share pathways with VNN2: view

Gene Ontology (GO) - Biological Process for VNN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006807 nitrogen compound metabolic process IEA --
GO:0015939 pantothenate metabolic process TAS --
genes like me logo Genes that share ontologies with VNN2: view

No data available for SIGNOR curated interactions for VNN2 Gene

Drugs & Compounds for VNN2 Gene

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  1. Drug

(4) Drugs for VNN2 Gene - From: HMDB and Novoseek

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

(5) Additional Compounds for VNN2 Gene - From: HMDB and Novoseek

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 VNN2: view

Transcripts for VNN2 Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
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mRNA/cDNA for VNN2 Gene

3 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
16 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VNN2 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c · 3d · 3e ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12
SP1: - -
SP2: - - -
SP3: - - - - - -
SP4: - -
SP5: - - - - - - -
SP6: - - - -
SP7:
SP8: -

Relevant External Links for VNN2 Gene

GeneLoc Exon Structure for
VNN2

Expression for VNN2 Gene

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  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VNN2 Gene

mRNA expression in normal human tissues for VNN2 Gene
mRNA expression by GTEx for VNN2 GenemRNA expression by BioGPS for VNN2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VNN2 Gene

This gene is overexpressed in Whole Blood (x49.3).

Protein differential expression in normal tissues from HIPED for VNN2 Gene

This gene is overexpressed in Blymphocyte (35.9), Peripheral blood mononuclear cells (8.1), and Islet of Langerhans (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VNN2 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VNN2

SOURCE GeneReport for Unigene cluster for VNN2 Gene:

Hs.293130

mRNA Expression by UniProt/SwissProt for VNN2 Gene:

O95498-VNN2_HUMAN
Tissue specificity: Widely expressed with higher expression in spleen and blood.

Evidence on tissue expression from TISSUES for VNN2 Gene

  • Blood(4.9)
  • Bone marrow(4.3)
  • Kidney(4.1)
genes like me logo Genes that share expression patterns with VNN2: view

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for VNN2 Gene

Orthologs for VNN2 Gene

This gene was present in the common ancestor of animals.

Orthologs for VNN2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia VNN2 31 30
  • 99.33 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia VNN2 31 30
  • 86.22 (n)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia VNN2 31
  • 66 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves VNN1 31
  • 63 (a)
 ManyToMany
-- 31
  • 61 (a)
 ManyToMany
lizard
(Anolis carolinensis)
 Reptilia -- 31
  • 62 (a)
 OneToMany
fruit fly
(Drosophila melanogaster)
 Insecta Btd 31 30
  • 44.78 (n)
 ManyToMany
CG3599 32
  • 30 (a)
CG32751 31
  • 25 (a)
 ManyToMany
vanin-like 31 32
  • 24 (a)
 ManyToMany
CG32750 31
  • 23 (a)
 ManyToMany
Species where no ortholog for VNN2 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)
  • 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)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • 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 VNN2 Gene

ENSEMBL:
Gene Tree for VNN2 (if available)
TreeFam:
Gene Tree for VNN2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VNN2: view image

Paralogs for VNN2 Gene

Paralogs for VNN2 Gene

(3) SIMAP similar genes for VNN2 Gene using alignment to 10 proteins:

  • VNN2_HUMAN
  • B4DQB2_HUMAN
  • E9PK31_HUMAN
  • E9PL76_HUMAN
  • E9PLK5_HUMAN
  • E9PQ75_HUMAN
  • E9PRD9_HUMAN
  • J3KQ55_HUMAN
  • J3KQQ7_HUMAN
  • J3QT03_HUMAN
genes like me logo Genes that share paralogs with VNN2: view

Variants for VNN2 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VNN2 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
708437 Benign: not provided 132,757,494(-) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
721182 Likely Benign: not provided 132,757,747(-) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR_VARIANT
778252 Benign: not provided 132,757,834(-) G/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT
784097 Benign: not provided 132,751,167(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT
rs864622023 Uncertain Significance: Malignant tumor of prostate 132,755,930(-) G/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for VNN2 Gene

Structural Variations from Database of Genomic Variants (DGV) for VNN2 Gene

Variant ID Type Subtype PubMed ID
dgv1219e214 CNV loss 21293372
esv2662373 CNV deletion 23128226
esv3610841 CNV loss 21293372
esv3610842 CNV gain 21293372
esv3610843 CNV loss 21293372
esv3610846 CNV gain 21293372
esv3610847 CNV loss 21293372
nsv517934 CNV loss 19592680

Variation tolerance for VNN2 Gene

Residual Variation Intolerance Score: 37.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.57; 44.72% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VNN2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VNN2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VNN2 Gene

Disorders for VNN2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for VNN2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
trichuriasis
  • infection by trichuris trichura
biotinidase deficiency
  • btd deficiency
pyruvate kinase deficiency of red cells
  • pkd
congenital nonspherocytic hemolytic anemia
  • hereditary nonspherocytic hemolytic anemia
- elite association - COSMIC cancer census association via MalaCards
Search VNN2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VNN2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VNN2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VNN2 Gene

Publications for VNN2 Gene

  1. Two human genes related to murine vanin-1 are located on the long arm of human chromosome 6. (PMID: 9790769) Galland F … Naquet P (Genomics 1998) 2 3 4 23 54
  2. Vanin genes are clustered (human 6q22-24 and mouse 10A2B1) and encode isoforms of pantetheinase ectoenzymes. (PMID: 11491533) Martin F … Galland F (Immunogenetics 2001) 2 3 4 54
  3. A novel glycosylphosphatidyl inositol-anchored protein on human leukocytes: a possible role for regulation of neutrophil adherence and migration. (PMID: 10201959) Suzuki K … Sendo F (Journal of immunology (Baltimore, Md. : 1950) 1999) 3 4 23 54
  4. 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) 4 23 54
  5. 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. (PMID: 18095154) Walker LC … Spurdle AB (Breast cancer research and treatment 2008) 3 41 54

ExternalLinks

View latest publications for VNN2 gene in Mastermind

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