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

Summary

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: mouse all
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Genomic context

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_000004.12 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?

PDGF-C promotes cell proliferation partially via downregulating BOP1.
Title: PDGF-C promotes cell proliferation partially via downregulating BOP1.
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.
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.
Expression and function of PDGF-C in development and stem cells.
Title: Expression and function of PDGF-C in development and stem cells.
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.
Platelet-Derived Growth Factor C in Alcoholics.
Title: Platelet-Derived Growth Factor C in Alcoholics.
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.
High PDGFC expression is associated with glioblastoma.
Title: MicroRNA-29a inhibits glioblastoma stem cells and tumor growth by regulating the PDGF pathway.
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.
Numerous studies have shown that PDGF-C and PDGF-D are critical regulators of the cardiovascular system as angiogenic and survival factors. PDGF-C and PDGFD are widely expressed in many different types of cells with pleotropic effects. [review]
Title: Platelet-derived growth factor-C and -D in the cardiovascular system and diseases.

Submit: New GeneRIF Correction See all GeneRIFs (47)

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 EBI GWAS CatalogPubMed
First genome-wide association scan on neurophysiological endophenotypes points to trans-regulation effects on SLC2A3 in dyslexic children. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analyses identify variants in developmental genes associated with hypospadias. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D4S949 (e-PCR)
- UniSTS:56595

AFM290vc5 (e-PCR), detects polymorphism
- UniSTS:90660

D4S1589 (e-PCR), detects polymorphism
- UniSTS:29997

RH104283 (e-PCR)
- UniSTS:98608

SHGC-59762 (e-PCR)
- UniSTS:11949

SHGC-50156 (e-PCR)
- UniSTS:73156

G63726 (e-PCR)
- UniSTS:140757

SHGC-68226 (e-PCR)
- UniSTS:3058

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 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
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)

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

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

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

156760454..156971799 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B2R9K6
XM_047415970.1 → XP_047271926.1 platelet-derived growth factor C isoform X3
XM_047415972.1 → XP_047271928.1 platelet-derived growth factor C isoform X3
XM_047415969.1 → XP_047271925.1 platelet-derived growth factor C isoform X2
XM_047415971.1 → XP_047271927.1 platelet-derived growth factor C isoform X3