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    RSPO3 R-spondin 3 [ Homo sapiens (human) ]

    Gene ID: 84870, updated on 9-Dec-2024

    Summary

    Official Symbol
    RSPO3provided by HGNC
    Official Full Name
    R-spondin 3provided by HGNC
    Primary source
    HGNC:HGNC:20866
    See related
    Ensembl:ENSG00000146374 MIM:610574; AllianceGenome:HGNC:20866
    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
    PWTSR; THSD2; CRISTIN1
    Summary
    This gene belongs to the R-spondin family. The encoded protein plays a role in the regulation of Wnt (wingless-type MMTV integration site family)/beta-catenin and Wnt/planar cell polarity (PCP) signaling pathways, which are involved in development, cell growth and disease pathogenesis. Genome-wide association studies suggest a correlation of this gene with bone mineral density and risk of fracture. This gene may be involved in tumor development. [provided by RefSeq, Jul 2013]
    Expression
    Broad expression in endometrium (RPKM 18.7), placenta (RPKM 8.3) and 14 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RSPO3 in Genome Data Viewer
    Location:
    6q22.33
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (127118671..127199481)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (128307592..128388425)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (127439816..127520626)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377992 Neighboring gene uncharacterized LOC105377993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17525 Neighboring gene uncharacterized LOC105377989 Neighboring gene uncharacterized LOC105377991 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:127297370-127297940 Neighboring gene uncharacterized LOC124901398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17527 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25039 Neighboring gene ring finger protein 146

    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
    Common variants at 6q22 and 17q21 are associated with intracranial volume.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genetic determinants of heel bone properties: genome-wide association meta-analysis and replication in the GEFOS/GENOMOS consortium.
    EBI GWAS Catalog
    Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations.
    EBI GWAS Catalog
    Genome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    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
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
    EBI GWAS Catalog
    Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.
    EBI GWAS Catalog
    Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.
    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
    Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ14440

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables frizzled binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables heparin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables signaling receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    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

    Preferred Names
    R-spondin-3
    Names
    R-spondin 3 homolog
    protein with TSP type-1 repeat
    roof plate-specific spondin-3
    thrombospondin type-1 domain-containing protein 2
    thrombospondin, type I, domain containing 2

    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.

    mRNA and Protein(s)

    1. NM_032784.5NP_116173.2  R-spondin-3 precursor

      See identical proteins and their annotated locations for NP_116173.2

      Status: REVIEWED

      Source sequence(s)
      AA568446, AF251057, AI095468, AL031776, AL590733
      Consensus CDS
      CCDS5135.1
      UniProtKB/Swiss-Prot
      B2RC27, Q5VTV4, Q96K87, Q9BXY4
      Related
      ENSP00000349131.4, ENST00000356698.9
      Conserved Domains (2) summary
      smart00209
      Location:150202
      TSP1; Thrombospondin type 1 repeats
      pfam15913
      Location:42143
      Furin-like_2; Furin-like repeat, cysteine-rich

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      127118671..127199481
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017011378.1XP_016866867.1  R-spondin-3 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      128307592..128388425
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356597.1XP_054212572.1  R-spondin-3 isoform X1