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    WNT16 Wnt family member 16 [ Homo sapiens (human) ]

    Gene ID: 51384, updated on 2-Nov-2024

    Summary

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    Official Symbol
    WNT16provided by HGNC
    Official Full Name
    Wnt family member 16provided by HGNC
    Primary source
    HGNC:HGNC:16267
    See related
    Ensembl:ENSG00000002745 MIM:606267; AllianceGenome:HGNC:16267
    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
    Summary
    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. This gene is a member of the WNT gene family. It contains two transcript variants diverging at the 5' termini. These two variants are proposed to be the products of separate promoters and not to be splice variants from a single promoter. They are differentially expressed in normal tissues, one of which (variant 2) is expressed at significant levels only in the pancreas, whereas another one (variant 1) is expressed more ubiquitously with highest levels in adult kidney, placenta, brain, heart, and spleen. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in skin (RPKM 9.9) and lymph node (RPKM 0.5) See more
    Orthologs
    mouse all
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    Genomic context

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    See WNT16 in Genome Data Viewer
    Location:
    7q31.31
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (121325367..121341104)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (122640682..122656420)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (120965421..120981158)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene cadherin like and PC-esterase domain containing 1 Neighboring gene RNA, 5S ribosomal pseudogene 241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26557 Neighboring gene uncharacterized LOC124901735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26560 Neighboring gene RNA, U6 small nuclear 517, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr7:120931342-120931494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26562 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:121025354-121025551 Neighboring gene FAM3 metabolism regulating signaling molecule C Neighboring gene hESC enhancers GRCh37_chr7:121035399-121035984 and GRCh37_chr7:121035985-121036569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18576 Neighboring gene CYCS pseudogene 19

    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 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. Wnt16 signaling in bone homeostasis and osteoarthristis. Ye X, et al. Front Endocrinol (Lausanne), 2022. PMID 36619549, Free PMC Article
    2. Treatment-induced damage to the tumor microenvironment promotes prostate cancer therapy resistance through WNT16B. Sun Y, et al. Nat Med, 2012 Sep. PMID 22863786, Free PMC Article
    3. Missense polymorphisms of the WNT16 gene are associated with bone mass, hip geometry and fractures. García-Ibarbia C, et al. Osteoporos Int, 2013 Sep. PMID 23417354
    4. Variation in the Kozak sequence of WNT16 results in an increased translation and is associated with osteoporosis related parameters. Hendrickx G, et al. Bone, 2014 Feb. PMID 24185276
    5. Wnt expression and canonical Wnt signaling in human bone marrow B lymphopoiesis. Døsen G, et al. BMC Immunol, 2006 Jun 29. PMID 16808837, Free PMC Article

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genetic Variants in WNT16 and PKD2L1 Locus Affect Heel Ultrasound Bone Stiffness: Analyses from the General Population and Patients Evaluated for Osteoporosis.
      Title: Genetic Variants in WNT16 and PKD2L1 Locus Affect Heel Ultrasound Bone Stiffness: Analyses from the General Population and Patients Evaluated for Osteoporosis.
    2. Whole-genome sequencing identifies rare missense variants of WNT16 and ERVW-1 causing the systemic lupus erythematosus.
      Title: Whole-genome sequencing identifies rare missense variants of WNT16 and ERVW-1 causing the systemic lupus erythematosus.
    3. Associations between WNT signaling pathway-related gene polymorphisms and risks of osteoporosis development in Chinese postmenopausal women: a case-control study.
      Title: Associations between WNT signaling pathway-related gene polymorphisms and risks of osteoporosis development in Chinese postmenopausal women: a case-control study.
    4. WNT16 from decidual stromal cells regulates HTR8/SVneo trophoblastic cell function via AKT/beta-catenin pathway.
      Title: WNT16 from decidual stromal cells regulates HTR8/SVneo trophoblastic cell function via AKT/beta-catenin pathway.
    5. Bone mineral density in high-level endurance runners: Part B-genotype-dependent characteristics.
      Title: Bone mineral density in high-level endurance runners: Part B-genotype-dependent characteristics.
    6. WNT16 elevation induced cell senescence of osteoblasts in ankylosing spondylitis.
      Title: WNT16 elevation induced cell senescence of osteoblasts in ankylosing spondylitis.
    7. Lower WNT16 expression in patients with adolescent idiopathic scoliosis - potential link to lower bone mass in AIS?
      Title: Lower WNT16 expression in patients with adolescent idiopathic scoliosis - potential link to lower bone mass in AIS?
    8. Short Communication: The Association of WNT16 Polymorphisms with the CD4(+) T Cell Count in the HIV-Infected Population.
      Title: Short Communication: The Association of WNT16 Polymorphisms with the CD4(+) T Cell Count in the HIV-Infected Population.
    9. significant differences in the polymorphisms of the WNT16 rs2908004 genetic variant contributes to the pathogenesis of osteoporosis
      Title: Genetic Predisposition for Osteoporosis and Fractures in Postmenopausal Women.
    10. Study identified two rare variants in functional regions of WNT16 (rs190011371 in WNT16b 3'UTR and rs570754792 in the SOST TATA box) found present in women with low BMD.
      Title: Common and rare variants of WNT16, DKK1 and SOST and their relationship with bone mineral density.
    Submit: New GeneRIF Correction See all GeneRIFs (36)

    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
    Genetic determinants of heel bone properties: genome-wide association meta-analysis and replication in the GEFOS/GENOMOS consortium.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    Meta-analysis of genome-wide scans for total body BMD in children and adults reveals allelic heterogeneity and age-specific effects at the WNT16 locus.
    EBI GWAS Catalog
    Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
    EBI GWAS Catalog
    Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
    EBI GWAS Catalog
    WNT16 influences bone mineral density, cortical bone thickness, bone strength, and osteoporotic fracture risk.
    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

    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 frizzled binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in bone remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in canonical Wnt signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cardiac epithelial to mesenchymal transition IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell fate commitment IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in keratinocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in keratinocyte proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of apoptotic signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in optic cup formation involved in camera-type eye development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in oxidative stress-induced premature senescence IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of JNK cascade IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in replicative senescence IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    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
    		  
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein Wnt-16
    Names
    wingless-type MMTV integration site family member 16b
    wingless-type MMTV integration site family, member 16

    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_029242.1 RefSeqGene

      Range
      8634..20738
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_016087.2 → NP_057171.2  protein Wnt-16 isoform 2

      See identical proteins and their annotated locations for NP_057171.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs from variant 1 at the 5' terminus including 5' UTR and the coding region for the N-terminus. It encodes a shorter isoform than variant 1.
      Source sequence(s)
      AF152584, AF169963
      Consensus CDS
      CCDS5780.1
      UniProtKB/TrEMBL
      A4D0W7, E9PH60
      Related
      ENSP00000355065.2, ENST00000361301.6
      Conserved Domains (1) summary
      pfam00110
      Location:42 → 355
      wnt; wnt family

    2. NM_057168.2 → NP_476509.1  protein Wnt-16 isoform 1 precursor

      See identical proteins and their annotated locations for NP_476509.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs from variant 2 at the 5' terminus including 5' UTR and the coding region for the N-terminus. Isoform 1, encoded by this variant, is 90% identical to the mouse Wnt16 protein at the amino acid level.
      Source sequence(s)
      AC006364
      Consensus CDS
      CCDS5781.1
      UniProtKB/Swiss-Prot
      Q2M3G1, Q9UBV4, Q9Y5C0
      UniProtKB/TrEMBL
      A4D0W8
      Related
      ENSP00000222462.2, ENST00000222462.3
      Conserved Domains (1) summary
      pfam00110
      Location:52 → 365
      wnt; wnt family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      121325367..121341104
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      122640682..122656420
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UBV4.1 GenPept UniProtKB/Swiss-Prot:Q9UBV4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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