SDC3 syndecan 3 [Homo sapiens (human)] - Gene

Summary

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
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Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
Hypoxia Promotes Syndecan-3 Expression in the Tumor Microenvironment.
Title: Hypoxia Promotes Syndecan-3 Expression in the Tumor Microenvironment.
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.
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.
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.
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

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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

Associated conditions

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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 more info	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

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Preferred Names: syndecan-3

Names: N-syndecan; syndecan neural type; syndecan proteoglycan 3

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

NG_013371.1 RefSeqGene

Range

4876..44168

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

30869466..30909735 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B4DIN4

Conserved Domains (1) summary

pfam01034
Location:388 → 429

Syndecan; Syndecan domain
XM_011542464.3 → XP_011540766.1 syndecan-3 isoform X2

UniProtKB/TrEMBL

B4DIN4

Conserved Domains (1) summary

pfam01034
Location:387 → 428

Syndecan; Syndecan domain
XM_011542466.2 → XP_011540768.1 syndecan-3 isoform X3

UniProtKB/TrEMBL

B4DIN4

Conserved Domains (1) summary

pfam01034
Location:357 → 398

Syndecan; Syndecan domain