U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    SDC3 syndecan 3 [ Homo sapiens (human) ]

    Gene ID: 9672, updated on 10-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    SDC3provided by HGNC
    Official Full Name
    syndecan 3provided by HGNC
    Primary source
    HGNC:HGNC:10660
    See related
    Ensembl:ENSG00000162512 MIM:186357; AllianceGenome:HGNC:10660
    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
    SDCN; SYND3
    Summary
    The protein encoded by this gene belongs to the syndecan proteoglycan family. It may play a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism. Allelic variants of this gene have been associated with obesity. [provided by RefSeq, Oct 2009]
    Expression
    Broad expression in brain (RPKM 64.6), spleen (RPKM 56.5) and 21 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See SDC3 in Genome Data Viewer
    Location:
    1p35.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (30869466..30909735, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (30721742..30761962, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (31342313..31381605, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31317155-31317674 Neighboring gene Sharpr-MPRA regulatory region 1191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31320286-31321089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31322620-31323120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31323121-31323621 Neighboring gene Sharpr-MPRA regulatory region 1173 Neighboring gene RN7SK pseudogene 91 Neighboring gene uncharacterized LOC400748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31343383-31344254 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 562 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31358623-31359123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31363707-31364422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31368603-31369362 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 563 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:31392155-31393153 Neighboring gene RNA, 7SL, cytoplasmic 371, pseudogene Neighboring gene small nucleolar RNA, C/D box 103A Neighboring gene pumilio RNA binding family member 1

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. The Cell Surface Heparan Sulfate Proteoglycan Syndecan-3 Promotes Ovarian Cancer Pathogenesis. Hillemeyer L, et al. Int J Mol Sci, 2022 May 21. PMID 35628603, Free PMC Article
    2. Role of syndecan-3 polymorphisms in obesity and female hyperandrogenism. Schüring AN, et al. J Mol Med (Berl), 2009 Dec. PMID 19820907
    3. Positive association of obesity with single nucleotide polymorphisms of syndecan 3 in the Korean population. Ha E, et al. J Clin Endocrinol Metab, 2006 Dec. PMID 17018662
    4. Cloning and characterization of human syndecan-3. Berndt C, et al. J Cell Biochem, 2001. PMID 11527150
    5. Soluble syndecan-3 binds chemokines, reduces leukocyte migration in vitro and ameliorates disease severity in models of rheumatoid arthritis. Eustace AD, et al. Arthritis Res Ther, 2019 Jul 12. PMID 31300004, Free PMC Article

    See all (70) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A genome-wide association study identifies a novel association between SDC3 and apparent treatment-resistant hypertension.
      Title: A genome-wide association study identifies a novel association between SDC3 and apparent treatment-resistant hypertension.
    2. The Cell Surface Heparan Sulfate Proteoglycan Syndecan-3 Promotes Ovarian Cancer Pathogenesis.
      Title: The Cell Surface Heparan Sulfate Proteoglycan Syndecan-3 Promotes Ovarian Cancer Pathogenesis.
    3. Syndecan Family Gene and Protein Expression and Their Prognostic Values for Prostate Cancer.
      Title: Syndecan Family Gene and Protein Expression and Their Prognostic Values for Prostate Cancer.
    4. LncRNA TRPM2-AS promotes ovarian cancer progression and cisplatin resistance by sponging miR-138-5p to release SDC3 mRNA.
      Title: LncRNA TRPM2-AS promotes ovarian cancer progression and cisplatin resistance by sponging miR-138-5p to release SDC3 mRNA.
    5. The Interplay of Apoes with Syndecans in Influencing Key Cellular Events of Amyloid Pathology.
      Title: The Interplay of Apoes with Syndecans in Influencing Key Cellular Events of Amyloid Pathology.
    6. Hypoxia Promotes Syndecan-3 Expression in the Tumor Microenvironment.
      Title: Hypoxia Promotes Syndecan-3 Expression in the Tumor Microenvironment.
    7. Contribution of syndecans to cellular uptake and fibrillation of alpha-synuclein and tau.
      Title: Contribution of syndecans to cellular uptake and fibrillation of α-synuclein and tau.
    8. Data show that soluble syndecan-3 occurred naturally in the sera of patients with rheumatoid arthritis.
      Title: Soluble syndecan-3 binds chemokines, reduces leukocyte migration in vitro and ameliorates disease severity in models of rheumatoid arthritis.
    9. High PTN and N-syndecan expression was closely associated with metastasis and poor prognosis, suggesting that they may promote tumor progression and perineural invasion in the orthotopic mouse model of pancreatic cancer.
      Title: Pleiotrophin and N-syndecan promote perineural invasion and tumor progression in an orthotopic mouse model of pancreatic cancer.
    10. Syndecan-3 and TFPI colocalize on the surface of endothelial-, smooth muscle-, and cancer cells
      Title: Syndecan-3 and TFPI colocalize on the surface of endothelial-, smooth muscle-, and cancer cells.
    Submit: New GeneRIF Correction See all GeneRIFs (27)

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Inherited obesity
    MedGen: C4054476 OMIM: 601665 GeneReviews: Not available
    		Compare labs

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

    Go to the top of the page Help

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env The V3 region (amino acids 298-329) of HIV-1 gp120 contains the syndecan-binding site for HIV-1 via 6-O sulfated motifs; a single conserved arginine (Arg-298) in the V3 region of gp120 governs HIV-1 binding to syndecans PubMed
    Envelope transmembrane glycoprotein gp41 env A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 downregulates the expression of syndecan 3 (SDC3) in peptide-treated PBMCs PubMed
    Nef nef HIV-1 Nef inhibits the expression of syndecan 3 in human podocyte PubMed
    Tat tat Binding of HIV-1 Tat to heparan sulfate proteoglycans is competed out by the heparin-binding factor bFGF PubMed
    tat Cell membrane heparin sulfate proteoglycans bind to the basic region of HIV-1 Tat (amino acids 49-57) and act as receptors for extracellular Tat uptake, an effect that may contribute to the angiogenic properties of Tat in promoting Kaposi's sarcoma PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi lumen TAS
    Traceable Author Statement
    more info
    		  
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in microspike ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    syndecan-3
    Names
    N-syndecan
    syndecan neural type
    syndecan proteoglycan 3

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_013371.1 RefSeqGene

      Range
      4876..44168
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014654.4 → NP_055469.3  syndecan-3

      See identical proteins and their annotated locations for NP_055469.3

      Status: REVIEWED

      Source sequence(s)
      AF248634, AL445235, BQ887307
      Consensus CDS
      CCDS30661.1
      UniProtKB/Swiss-Prot
      O75056, Q5T1Z6, Q5T1Z7, Q96CT3, Q96PR8
      UniProtKB/TrEMBL
      A0A0S2Z540, A0A9K3Y886, F8W8E9
      Related
      ENSP00000344468.6, ENST00000339394.7
      Conserved Domains (1) summary
      pfam01034
      Location:399 → 440
      Syndecan; Syndecan domain

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      30869466..30909735 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011542463.1 → XP_011540765.1  syndecan-3 isoform X1

      UniProtKB/TrEMBL
      B4DIN4
      Conserved Domains (1) summary
      pfam01034
      Location:388 → 429
      Syndecan; Syndecan domain

    2. XM_011542464.3 → XP_011540766.1  syndecan-3 isoform X2

      UniProtKB/TrEMBL
      B4DIN4
      Conserved Domains (1) summary
      pfam01034
      Location:387 → 428
      Syndecan; Syndecan domain

    3. XM_011542466.2 → XP_011540768.1  syndecan-3 isoform X3

      UniProtKB/TrEMBL
      B4DIN4
      Conserved Domains (1) summary
      pfam01034
      Location:357 → 398
      Syndecan; Syndecan domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      30721742..30761962 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339740.1 → XP_054195715.1  syndecan-3 isoform X1

      UniProtKB/TrEMBL
      B4DIN4

    2. XM_054339741.1 → XP_054195716.1  syndecan-3 isoform X2

      UniProtKB/TrEMBL
      B4DIN4

    3. XM_054339742.1 → XP_054195717.1  syndecan-3 isoform X3

      UniProtKB/TrEMBL
      B4DIN4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75056.2 GenPept UniProtKB/Swiss-Prot:O75056

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous