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Aliases for SDC1 Gene

Aliases for SDC1 Gene

  • Syndecan 1 2 3 5
  • Syndecan Proteoglycan 1 2 3
  • CD138 Antigen 3 4
  • SYND1 3 4
  • SDC 3 4
  • Heparan Sulfate Proteoglycan Fibroblast Growth Factor Receptor 3
  • Syndecan-1 3
  • Syndecan 3
  • CD138 3

External Ids for SDC1 Gene

Previous HGNC Symbols for SDC1 Gene

  • SDC

Previous GeneCards Identifiers for SDC1 Gene

  • GC02M020292
  • GC02M020469
  • GC02M020368
  • GC02M020385
  • GC02M020322
  • GC02M020264
  • GC02M020400
  • GC02M020158

Summaries for SDC1 Gene

Entrez Gene Summary for SDC1 Gene

  • The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-1 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-1 expression has been detected in several different tumor types. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same protein. [provided by RefSeq, Jul 2008]

GeneCards Summary for SDC1 Gene

SDC1 (Syndecan 1) is a Protein Coding gene. Diseases associated with SDC1 include Granulomatous Endometritis and Diffuse Large B-Cell Lymphoma. Among its related pathways are Glycosaminoglycan metabolism and Response to elevated platelet cytosolic Ca2+. Gene Ontology (GO) annotations related to this gene include protein C-terminus binding. An important paralog of this gene is SDC3.

UniProtKB/Swiss-Prot for SDC1 Gene

  • Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413).

Gene Wiki entry for SDC1 Gene

Additional gene information for SDC1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SDC1 Gene

Genomics for SDC1 Gene

GeneHancer (GH) Regulatory Elements for SDC1 Gene

Promoters and enhancers for SDC1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I020205 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 589.9 +9.4 9449 21.3 HDGF PKNOX1 CLOCK FOXA2 ARNT MLX ARID4B SIN3A DMAP1 ZNF2 SDC1 PUM2 RNU7-113P RNU6-961P LAPTM4A ENSG00000228950 RHOB GC02M020197
GH02I020181 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 21.6 +40.8 40821 5.7 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A ZBTB7B YY1 SLC30A9 ZNF766 SDC1 MATN3 TTC32 PUM2 RNU7-113P HS1BP3 RNU6-961P GC02M020197
GH02I020177 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 25.6 +46.0 46007 3.8 ELF3 PKNOX1 FOXA2 SIN3A DMAP1 ZNF48 ZSCAN9 RAD21 YY1 FOS SDC1 RNU7-113P MATN3 RNU6-961P GC02M020197
GH02I020230 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 19.5 -8.8 -8769 7.2 ELF3 PKNOX1 CLOCK NEUROD1 SIN3A RAD21 RFX5 ZNF366 SCRT2 ZNF143 SDC1 RNU6-961P ENSG00000269976 GC02M020239
GH02I020135 Enhancer 1.3 Ensembl ENCODE dbSUPER 18.9 +89.2 89173 1 PKNOX1 ARID4B SIN3A DMAP1 YBX1 ZNF2 ZNF48 ZNF143 RUNX3 RXRA SDC1 RNU6-961P MATN3 GC02P020141 ENSG00000234378
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SDC1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SDC1 gene promoter:

Genomic Locations for SDC1 Gene

Genomic Locations for SDC1 Gene
24,637 bases
Minus strand

Genomic View for SDC1 Gene

Genes around SDC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SDC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SDC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SDC1 Gene

Proteins for SDC1 Gene

  • Protein details for SDC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • D6W523
    • Q53QV0
    • Q546D3
    • Q96HB7

    Protein attributes for SDC1 Gene

    310 amino acids
    Molecular mass:
    32462 Da
    Quaternary structure:
    • Interacts with CDCP1. Interacts (via C-terminus) with TIAM1 (via PDZ domain).

    Three dimensional structures from OCA and Proteopedia for SDC1 Gene

neXtProt entry for SDC1 Gene

Post-translational modifications for SDC1 Gene

  • Shedding is enhanced by a number of factors such as heparanase, thrombin or EGF. Also by stress and wound healing. PMA-mediated shedding is inhibited by TIMP3.
  • Glycosylation at isoforms=37, posLast=4343, posLast=4545, isoforms=47, isoforms=61, posLast=7777, isoforms=122, isoforms=188, posLast=206206, posLast=216216, and posLast=240240

Antibody Products

  • R&D Systems Antibodies for SDC1 (Syndecan-1/CD138)
  • Cell Signaling Technology (CST) Antibodies for SDC1 (syndecan-1)

Protein Products

No data available for DME Specific Peptides for SDC1 Gene

Domains & Families for SDC1 Gene

Gene Families for SDC1 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • CD markers
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins
  • Transporters

Suggested Antigen Peptide Sequences for SDC1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the syndecan proteoglycan family.
  • Belongs to the syndecan proteoglycan family.
genes like me logo Genes that share domains with SDC1: view

Function for SDC1 Gene

Molecular function for SDC1 Gene

GENATLAS Biochemistry:
syndecan,integral membrane heparan sulfate proteoglycan,matrix receptor,expressed in distinct stages of differentiation of normal lymphoid cells (pre-B) and in B chronic lymphoblastic leukemia (BCLL) in plamocytoid lymphomas and myelomas,underexpressed in squamous cell carcinoma of the head and neck
UniProtKB/Swiss-Prot Function:
Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413).

Phenotypes From GWAS Catalog for SDC1 Gene

Gene Ontology (GO) - Molecular Function for SDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15292202
GO:0008022 protein C-terminus binding IPI 16982797
GO:0042802 identical protein binding IPI 18093920
genes like me logo Genes that share ontologies with SDC1: view
genes like me logo Genes that share phenotypes with SDC1: view

Animal Models for SDC1 Gene

MGI Knock Outs for SDC1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SDC1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SDC1 Gene

Localization for SDC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SDC1 Gene

Membrane; Single-pass type I membrane protein. Secreted. Secreted, exosome. Note=Shedding of the ectodomain produces a soluble form. {ECO:0000269 PubMed:9169435}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SDC1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
lysosome 5
golgi apparatus 5
cytosol 3
cytoskeleton 2
nucleus 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Focal adhesion sites (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005796 Golgi lumen TAS --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 2324102
GO:0009897 external side of plasma membrane IEA --
genes like me logo Genes that share ontologies with SDC1: view

Pathways & Interactions for SDC1 Gene

genes like me logo Genes that share pathways with SDC1: view

Gene Ontology (GO) - Biological Process for SDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001523 retinoid metabolic process TAS --
GO:0001657 ureteric bud development IEA --
GO:0006024 glycosaminoglycan biosynthetic process TAS --
GO:0006027 glycosaminoglycan catabolic process TAS --
GO:0006954 inflammatory response IEA --
genes like me logo Genes that share ontologies with SDC1: view

No data available for SIGNOR curated interactions for SDC1 Gene

Drugs & Compounds for SDC1 Gene

(1) Additional Compounds for SDC1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
heparan sulfate
  • alpha-Idosane
  • Heparan N-sulfate
  • Heparan N-sulphate
  • Heparan sulfate
  • Heparan sulphate
genes like me logo Genes that share compounds with SDC1: view

Transcripts for SDC1 Gene

Unigene Clusters for SDC1 Gene

Syndecan 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for SDC1

Alternative Splicing Database (ASD) splice patterns (SP) for SDC1 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c · 6d · 6e · 6f · 6g ^ 7 ^ 8a · 8b
SP1: - - -
SP2: - - - - -
SP3: - - - - - - -
SP4: - -
SP5: - - - -
SP6: - -

Relevant External Links for SDC1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SDC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SDC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SDC1 Gene

This gene is overexpressed in Liver (x8.6), Esophagus - Mucosa (x8.2), Skin - Not Sun Exposed (Suprapubic) (x7.8), and Skin - Sun Exposed (Lower leg) (x7.1).

Protein differential expression in normal tissues from HIPED for SDC1 Gene

This gene is overexpressed in Hair follicle (13.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SDC1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SDC1 Gene:


SOURCE GeneReport for Unigene cluster for SDC1 Gene:


Evidence on tissue expression from TISSUES for SDC1 Gene

  • Liver(4.7)
  • Kidney(4.6)
  • Lung(3.7)
  • Bone marrow(3.3)
  • Skin(3.1)
  • Intestine(3)
  • Blood(2.7)
  • Lymph node(2.6)
  • Spleen(2.2)
  • Stomach(2.2)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with SDC1: view

Primer Products

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SDC1 Gene

Orthologs for SDC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SDC1 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia SDC1 33 34
  • 83.33 (n)
(Bos Taurus)
Mammalia SDC1 33 34
  • 80.95 (n)
(Rattus norvegicus)
Mammalia Sdc1 33
  • 80.75 (n)
(Mus musculus)
Mammalia Sdc1 33 16 34
  • 80.15 (n)
(Ornithorhynchus anatinus)
Mammalia SDC1 34
  • 40 (a)
(Gallus gallus)
Aves SDC1 33 34
  • 51.11 (n)
(Anolis carolinensis)
Reptilia SDC1 34
  • 31 (a)
fruit fly
(Drosophila melanogaster)
Insecta Sdc 34
  • 14 (a)
(Caenorhabditis elegans)
Secernentea sdn-1 34
  • 23 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3537 34
  • 27 (a)
Species where no ortholog for SDC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for SDC1 Gene

Gene Tree for SDC1 (if available)
Gene Tree for SDC1 (if available)

Paralogs for SDC1 Gene

Paralogs for SDC1 Gene

genes like me logo Genes that share paralogs with SDC1: view

Variants for SDC1 Gene

Sequence variations from dbSNP and Humsavar for SDC1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs777304384 likely-benign, Long QT syndrome 20,204,252(-) G/A coding_sequence_variant, missense_variant
rs1000022786 -- 20,200,915(-) C/T 3_prime_UTR_variant
rs1000024390 -- 20,207,701(-) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000269171 -- 20,210,140(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000615386 -- 20,202,159(-) G/C 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for SDC1 Gene

Variant ID Type Subtype PubMed ID
nsv819169 CNV gain 19587683
nsv581164 CNV loss 21841781
nsv581163 CNV gain 21841781
nsv581162 CNV gain+loss 21841781
nsv581161 CNV loss 21841781
nsv581160 CNV gain+loss 21841781
nsv581157 CNV loss 21841781
nsv1072400 CNV deletion 25765185
esv3402038 CNV duplication 20981092
esv29979 CNV loss 17803354
esv29269 CNV loss 19812545
dgv6731n54 CNV gain 21841781
dgv3737n100 CNV gain 25217958

Variation tolerance for SDC1 Gene

Residual Variation Intolerance Score: 60.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.37; 53.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SDC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SDC1 Gene

Disorders for SDC1 Gene

MalaCards: The human disease database

(19) MalaCards diseases for SDC1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
granulomatous endometritis
diffuse large b-cell lymphoma
  • large b-cell diffuse lymphoma
mucinous bronchioloalveolar adenocarcinoma
  • bronchiolo-alveolar carcinoma, mucinous
intestinal disease
  • intestinal diseases
ameloblastic carcinoma
- elite association - COSMIC cancer census association via MalaCards
Search SDC1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SDC1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SDC1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SDC1 Gene

Publications for SDC1 Gene

  1. The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics. (PMID: 23395182) Liu X … Fuentes EJ (Structure (London, England : 1993) 2013) 3 4 58
  2. Syndecan-syntenin-ALIX regulates the biogenesis of exosomes. (PMID: 22660413) Baietti MF … David G (Nature cell biology 2012) 3 4 58
  3. Bone marrow stromal cell interaction reduces syndecan-1 expression and induces kinomic changes in myeloma cells. (PMID: 20307537) Fuhler GM … Bos NA (Experimental cell research 2010) 3 22 58
  4. Syndecan-1 regulates alphavbeta3 and alphavbeta5 integrin activation during angiogenesis and is blocked by synstatin, a novel peptide inhibitor. (PMID: 19255147) Beauvais DM … Rapraeger AC (The Journal of experimental medicine 2009) 3 22 58
  5. Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study. (PMID: 19107206) Dalmasso C … ANRS Genome Wide Association 01 (PloS one 2008) 3 44 58

Products for SDC1 Gene

  • Addgene plasmids for SDC1

Sources for SDC1 Gene

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