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

Gene ID: 51384, updated on 23-Nov-2023

Summary

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
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Genomic context

See WNT16 in Genome Data Viewer
Location:
7q31.31
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (121325367..121341104)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (122640682..122656420)
105.20220307 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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)

NEW Try the new Transcript table

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_016087.2NP_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:42355
    wnt; wnt family
  2. NM_057168.2NP_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:52365
    wnt; wnt family

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
    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)