VNN2 vanin 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: VNN2provided by HGNC
Official Full Name: vanin 2provided by HGNC
Primary source: HGNC:HGNC:12706
See related: Ensembl:ENSG00000112303 MIM:603571
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

Location:: 6q23.2

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
109.20211119	current	GRCh38.p13 (GCF_000001405.39)	6	NC_000006.12 (132743503..132763489, complement)
105.20201022	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (133065009..133084594, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

GPI-80 Augments NF-kappaB Activation in Tumor Cells.
Title: GPI-80 Augments NF-κB Activation in Tumor Cells.
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.
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.
Low VNN2 expression is associated with invasion of osteosarcoma.
Title: MicroRNA‑106a regulates the proliferation and invasion of human osteosarcoma cells by targeting VNN2.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Homologs of the VNN2 gene: The VNN2 gene is conserved in chimpanzee, Rhesus monkey, cow, and fruit fly.
Orthologs from Annotation Pipeline: 65 organisms have orthologs with human gene VNN2
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables pantetheine hydrolase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	PubMed
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 anchored component of membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular region	TAS Traceable Author Statement more info
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: vascular non-inflammatory molecule 2

Names: Vannin 2; glycosylphosphatidyl inositol-anchored protein GPI-80; pantetheinase

NP_001229279.2

EC 3.5.1.92

NP_004656.3

EC 3.5.1.92

NP_511043.2

EC 3.5.1.92

XP_006715656.1

EC 3.5.1.92

XP_011534533.1

EC 3.5.1.92

XP_016866897.1

EC 3.5.1.92

XP_016866898.1

EC 3.5.1.92

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

NG_050645.1 RefSeqGene

Range

5001..24590

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001242350.3 → NP_001229279.2 vascular non-inflammatory molecule 2 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
NM_004665.6 → NP_004656.3 vascular non-inflammatory molecule 2 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

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
NM_078488.3 → NP_511043.2 vascular non-inflammatory molecule 2 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

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
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
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
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
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
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: Homo sapiens Updated Annotation Release 109.20211119

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p13 Primary Assembly

Range

132743503..132763489 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017011408.1 → XP_016866897.1 vascular non-inflammatory molecule 2 isoform X3
XM_017011409.1 → XP_016866898.1 vascular non-inflammatory molecule 2 isoform X3
XM_006715593.3 → XP_006715656.1 vascular non-inflammatory molecule 2 isoform X1

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
XM_011536231.1 → XP_011534533.1 vascular non-inflammatory molecule 2 isoform X2

Conserved Domains (1) summary

cd07567
Location:26 → 329

biotinidase_like; biotinidase and vanins (class 4 nitrilases)