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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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