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PDGFC platelet derived growth factor C [ Homo sapiens (human) ]

Gene ID: 56034, updated on 12-Nov-2024

Summary

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Official Symbol
PDGFCprovided by HGNC
Official Full Name
platelet derived growth factor Cprovided by HGNC
Primary source
HGNC:HGNC:8801
See related
Ensembl:ENSG00000145431 MIM:608452; AllianceGenome:HGNC:8801
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
SCDGF; FALLOTEIN
Summary
The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of this family are mitogenic factors for cells of mesenchymal origin and are characterized by a core motif of eight cysteines. This gene product appears to form only homodimers. It differs from the platelet-derived growth factor alpha and beta polypeptides in having an unusual N-terminal domain, the CUB domain. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2010]
Expression
Ubiquitous expression in endometrium (RPKM 16.6), prostate (RPKM 13.9) and 24 other tissues See more
Orthologs
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Genomic context

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See PDGFC in Genome Data Viewer
Location:
4q32.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (156760454..156971799, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (160106105..160317463, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (157681606..157892951, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377508 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_74995 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:157426362-157427068 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75051 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:157519367-157520566 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:157521211-157521946 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:157526591-157527116 Neighboring gene NANOG hESC enhancer GRCh37_chr4:157555350-157555851 Neighboring gene long intergenic non-protein coding RNA 2272 Neighboring gene NANOG hESC enhancer GRCh37_chr4:157692390-157692891 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:157718592-157719092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:157892738-157893238 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:157919659-157920439 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:157920440-157921219 Neighboring gene ribonuclease P RNA component H1, 3 pseudogene Neighboring gene Sharpr-MPRA regulatory region 1911 Neighboring gene glycine receptor beta

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Maternal transmission effect of a PDGF-C SNP on nonsyndromic cleft lip with or without palate from a Chinese population. Wu D, et al. PLoS One, 2012. PMID 23029525, Free PMC Article
  2. Regulation of fibrogenic/fibrolytic genes by platelet-derived growth factor C, a novel growth factor, in human dermal fibroblasts. Jinnin M, et al. J Cell Physiol, 2005 Feb. PMID 15389578
  3. Presymptomatic activation of the PDGF-CC pathway accelerates onset of ALS neurodegeneration. Lewandowski SA, et al. Acta Neuropathol, 2016 Mar. PMID 26687981, Free PMC Article
  4. PDGF-C expression in the developing and normal adult human kidney and in glomerular diseases. Eitner F, et al. J Am Soc Nephrol, 2003 May. PMID 12707385
  5. Platelet-derived growth factor (PDGF)-C, a PDGF family member with a vascular endothelial growth factor-like structure. Reigstad LJ, et al. J Biol Chem, 2003 May 9. PMID 12598536

See all (79) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Platelet-Derived Growth Factor C Facilitates Malignant Behavior of Pancreatic Ductal Adenocarcinoma by Regulating SREBP1 Mediated Lipid Metabolism.
    Title: Platelet-Derived Growth Factor C Facilitates Malignant Behavior of Pancreatic Ductal Adenocarcinoma by Regulating SREBP1 Mediated Lipid Metabolism.
  2. PDGF-C promotes cell proliferation partially via downregulating BOP1.
    Title: PDGF-C promotes cell proliferation partially via downregulating BOP1.
  3. Impact of Acute High Glucose on Mitochondrial Function in a Model of Endothelial Cells: Role of PDGF-C.
    Title: Impact of Acute High Glucose on Mitochondrial Function in a Model of Endothelial Cells: Role of PDGF-C.
  4. RNA N6-methyladenosine demethylase FTO promotes pancreatic cancer progression by inducing the autocrine activity of PDGFC in an m(6)A-YTHDF2-dependent manner.
    Title: RNA N6-methyladenosine demethylase FTO promotes pancreatic cancer progression by inducing the autocrine activity of PDGFC in an m(6)A-YTHDF2-dependent manner.
  5. Expression and function of PDGF-C in development and stem cells.
    Title: Expression and function of PDGF-C in development and stem cells.
  6. Cancer-associated fibroblast secretion of PDGFC promotes gastrointestinal stromal tumor growth and metastasis.
    Title: Cancer-associated fibroblast secretion of PDGFC promotes gastrointestinal stromal tumor growth and metastasis.
  7. Platelet-Derived Growth Factor C in Alcoholics.
    Title: Platelet-Derived Growth Factor C in Alcoholics.
  8. The authors found PDGF-C to be highly expressed in breast carcinoma cell lines. I
    Title: An oncogenic activity of PDGF-C and its splice variant in human breast cancer.
  9. High PDGFC expression is associated with glioblastoma.
    Title: MicroRNA-29a inhibits glioblastoma stem cells and tumor growth by regulating the PDGF pathway.
  10. PDGF-C and PDGF-D are relatively new members of the PDGF family and are potent angiogenic and survival factors. Recent studies have demonstrated their important roles in different types of eye diseases. [review]
    Title: PDGF-C and PDGF-D in ocular diseases.
Submit: New GeneRIF Correction See all GeneRIFs (48)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
EBI GWAS Catalog
First genome-wide association scan on neurophysiological endophenotypes points to trans-regulation effects on SLC2A3 in dyslexic children.
EBI GWAS Catalog
Genome-wide association analyses identify variants in developmental genes associated with hypospadias.
EBI GWAS Catalog

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
Tat tat Treatment of human neuroblastoma cells or rat primary neurons with HIV-1 Tat downregulates PDGF-C expression PubMed
tat PDGF-C mediated neuroprotection against HIV-1 Tat results from inactivation of the downstream mediator GSK3 beta by its phosphorylation at Ser-9 in human neuroblastoma cells PubMed
tat PI3K/Akt, TRPC, and GSK3 beta signaling pathways are all involved in PDGF-C mediated neuroprotection against HIV-1 Tat in human neuroblastoma cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables growth factor activity IEA
Inferred from Electronic Annotation
more info
  
enables platelet-derived growth factor receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables platelet-derived growth factor receptor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in animal organ morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in bone development IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in central nervous system development TAS
Traceable Author Statement
more info
 PubMed 
involved_in digestive tract development IEA
Inferred from Electronic Annotation
more info
  
involved_in fibroblast proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in platelet-derived growth factor receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in platelet-derived growth factor receptor signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of ERK1 and ERK2 cascade IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cell population proliferation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cell population proliferation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in positive regulation of fibroblast proliferation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
located_in cell surface IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA 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 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
platelet-derived growth factor C
Names
PDGF-C
VEGF-E
secretory growth factor-like protein
spinal cord-derived growth factor

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.

mRNA and Protein(s)

  1. NM_016205.3 → NP_057289.1  platelet-derived growth factor C precursor

    See identical proteins and their annotated locations for NP_057289.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.
    Source sequence(s)
    AC092608, AC093325, AF091434, AI446155
    Consensus CDS
    CCDS3795.1
    UniProtKB/Swiss-Prot
    B4DU34, B9EGR8, Q4W5M9, Q9NRA1, Q9UL22
    UniProtKB/TrEMBL
    B2R9K6
    Related
    ENSP00000422464.1, ENST00000502773.6
    Conserved Domains (2) summary
    cd00041
    Location:49 → 162
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    cd00135
    Location:248 → 340
    PDGF; Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and ...

RNA

  1. NR_036641.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as PDGF-Cb) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC092608, AC093325, AF091434, AI446155, AM922296

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    156760454..156971799 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008455.2 → XP_016863944.1  platelet-derived growth factor C isoform X1

    UniProtKB/TrEMBL
    B2R9K6

  2. XM_047415970.1 → XP_047271926.1  platelet-derived growth factor C isoform X3

  3. XM_047415972.1 → XP_047271928.1  platelet-derived growth factor C isoform X3

  4. XM_047415969.1 → XP_047271925.1  platelet-derived growth factor C isoform X2

  5. XM_047415971.1 → XP_047271927.1  platelet-derived growth factor C isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    160106105..160317463 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350511.1 → XP_054206486.1  platelet-derived growth factor C isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NRA1.2 GenPept UniProtKB/Swiss-Prot:Q9NRA1

Gene LinkOut

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

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