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WNT2 Wnt family member 2 [ Homo sapiens (human) ]

Gene ID: 7472, updated on 5-Mar-2024

Summary

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Official Symbol
WNT2provided by HGNC
Official Full Name
Wnt family member 2provided by HGNC
Primary source
HGNC:HGNC:12780
See related
Ensembl:ENSG00000105989 MIM:147870; AllianceGenome:HGNC:12780
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
IRP; INT1L1
Summary
This gene is a member of the WNT gene family. The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]
Expression
Biased expression in placenta (RPKM 44.0), endometrium (RPKM 14.0) and 3 other tissues See more
Orthologs
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Genomic context

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Location:
7q31.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (117275451..117323058, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (118590786..118638396, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (116915505..116963112, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene heterogeneous nuclear ribonucleoprotein A1 like 2 pseudogene Neighboring gene MT-ND2 pseudogene 37 Neighboring gene MT-ND4 pseudogene 6 Neighboring gene MT-CYB pseudogene 6 Neighboring gene greater CFTR locus negative regulatory elements CR12 and CR13 Neighboring gene uncharacterized LOC124900596 Neighboring gene uncharacterized LOC105375467 Neighboring gene greater CFTR locus negative regulatory element CR15 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:116962406-116962980 Neighboring gene greater CFTR locus negative regulatory element CR17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26546 Neighboring gene greater CFTR locus negative regulatory element CR18 Neighboring gene ankyrin repeat, SAM and basic leucine zipper domain containing 1 Neighboring gene DNase I hypersensitive site -80 kb upstream of CFTR Neighboring gene CFTR -44 kb upstream enhancer Neighboring gene ANKRD49 pseudogene 4

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. A translational exploration of the effects of WNT2 variants on altered cortical structures in autism spectrum disorder. Chien YL, et al. J Psychiatry Neurosci, 2021 Nov-Dec. PMID 34862305, Free PMC Article
  2. Distinguishing colorectal adenoma from hyperplastic polyp by WNT2 expression. Wang B, et al. J Clin Lab Anal, 2021 Oct. PMID 34477243, Free PMC Article
  3. WNT2 activation through proximal germline deletion predisposes to small intestinal neuroendocrine tumors and intestinal adenocarcinomas. Aavikko M, et al. Hum Mol Genet, 2021 Nov 30. PMID 34274970, Free PMC Article
  4. Involvement of WNT2 in trophoblast cell behavior in preeclampsia development. Liu Y, et al. Cell Cycle, 2020 Sep. PMID 32779546, Free PMC Article
  5. Promoter Methylation Status of WNT2 in Placenta from Patients with Preeclampsia. Liu Y, et al. Med Sci Monit, 2017 Nov 7. PMID 29109390, Free PMC Article

See all (97) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A translational exploration of the effects of WNT2 variants on altered cortical structures in autism spectrum disorder.
    Title: A translational exploration of the effects of WNT2 variants on altered cortical structures in autism spectrum disorder.
  2. WNT2 activation through proximal germline deletion predisposes to small intestinal neuroendocrine tumors and intestinal adenocarcinomas.
    Title: WNT2 activation through proximal germline deletion predisposes to small intestinal neuroendocrine tumors and intestinal adenocarcinomas.
  3. Overexpression of IL-8 and Wnt2 is associated with prognosis of gastric cancer.
    Title: Overexpression of IL-8 and Wnt2 is associated with prognosis of gastric cancer.
  4. Distinguishing colorectal adenoma from hyperplastic polyp by WNT2 expression.
    Title: Distinguishing colorectal adenoma from hyperplastic polyp by WNT2 expression.
  5. LncRNA-HAGLR motivates triple negative breast cancer progression by regulation of WNT2 via sponging miR-335-3p.
    Title: LncRNA-HAGLR motivates triple negative breast cancer progression by regulation of WNT2 via sponging miR-335-3p.
  6. Prognostic Significance of Wnt1, Wnt2, E-Cadherin, and beta-catenin Expression in Operable Non-small Cell Lung Cancer.
    Title: Prognostic Significance of Wnt1, Wnt2, E-Cadherin, and β-catenin Expression in Operable Non-small Cell Lung Cancer.
  7. Involvement of WNT2 in trophoblast cell behavior in preeclampsia development.
    Title: Involvement of WNT2 in trophoblast cell behavior in preeclampsia development.
  8. MiR-548b suppresses proliferative capacity of colorectal cancer by binding WNT2.
    Title: MiR-548b suppresses proliferative capacity of colorectal cancer by binding WNT2.
  9. The increased expression of DKK1 and decreased expression of WNT2 may be involved in the pathogenesis of early-onset preeclampsia
    Title: Altered DNA methylation and transcription of WNT2 and DKK1 genes in placentas associated with early-onset preeclampsia.
  10. Down-regulation of miR-30a-3p/5p promotes esophageal squamous cell carcinoma cell proliferation by activating the Wnt signaling pathway through inhibition of Wnt2 and Fzd2.
    Title: Down-regulation of miR-30a-3p/5p promotes esophageal squamous cell carcinoma cell proliferation by activating the Wnt signaling pathway.
Submit: New GeneRIF Correction See all GeneRIFs (62)

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 prognosis in advanced non-small cell lung cancer patients receiving platinum-based chemotherapy.
EBI GWAS Catalog
Wnt signaling and Dupuytren's disease.
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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat specifically associates with WNT2 promoter to upregulate WNT2 expression in T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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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 cytokine activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cytokine activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables frizzled binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables frizzled binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables receptor ligand activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables receptor ligand activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in atrial cardiac muscle tissue morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in canonical Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in canonical Wnt signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in canonical Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in canonical Wnt signaling pathway TAS
Traceable Author Statement
more info
 PubMed 
involved_in cardiac epithelial to mesenchymal transition IEA
Inferred from Electronic Annotation
more info
  
involved_in cardiac muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell proliferation in midbrain IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cell-cell signaling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to retinoic acid ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cellular response to transforming growth factor beta stimulus IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in epithelial cell proliferation involved in lung morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in iris morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in labyrinthine layer blood vessel development IEA
Inferred from Electronic Annotation
more info
  
involved_in lens development in camera-type eye ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in lung induction IEA
Inferred from Electronic Annotation
more info
  
involved_in mammary gland epithelium development IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in mesenchymal cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in midbrain dopaminergic neuron differentiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in neurogenesis TAS
Traceable Author Statement
more info
 PubMed 
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cardiac muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cell population proliferation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of epithelial cell proliferation involved in lung morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of fibroblast proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of mesenchymal cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of neurogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of Wnt signalosome IC
Inferred by Curator
more info
 PubMed 
located_in collagen-containing extracellular matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular region NAS
Non-traceable Author Statement
more info
 PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein Wnt-2
Names
Int-1-related protein
epididymis secretory sperm binding protein
int-1-like protein 1
secreted growth factor
wingless-type MMTV integration site family member 2

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_003391.3 → NP_003382.1  protein Wnt-2 precursor

    See identical proteins and their annotated locations for NP_003382.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AC006326, BC078170
    Consensus CDS
    CCDS5771.1
    UniProtKB/Swiss-Prot
    A4D0V1, P09544, Q75N05, Q9UDP9
    UniProtKB/TrEMBL
    A0A384MDX3
    Related
    ENSP00000265441.3, ENST00000265441.8
    Conserved Domains (1) summary
    pfam00110
    Location:43 → 349
    wnt; wnt family

RNA

  1. NR_024047.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region, compared to variant 1, that significantly impacts the predicted protein, and apparently results in a non-protein coding transcript.
    Source sequence(s)
    AC006326, BC078170
    Related
    ENST00000647844.1

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    117275451..117323058 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    118590786..118638396 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P09544.1 GenPept UniProtKB/Swiss-Prot:P09544

Gene LinkOut

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Chemical Information
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