PDGFC
platelet derived growth factor C
Basic information
Region (hg38): 4:156760454-156971799
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDGFC gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 10 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 3 | 1 |
Variants in PDGFC
This is a list of pathogenic ClinVar variants found in the PDGFC region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-156763185-T-C | not specified | Uncertain significance (Nov 30, 2022) | ||
| 4-156767839-G-C | Benign/Likely benign (Jun 01, 2023) | |||
| 4-156767853-C-T | not specified | Uncertain significance (Jan 09, 2024) | ||
| 4-156767900-C-G | not specified | Uncertain significance (May 20, 2024) | ||
| 4-156772747-A-T | not specified | Uncertain significance (Apr 27, 2024) | ||
| 4-156772843-T-G | PDGFC-related disorder | Likely benign (Jan 06, 2020) | ||
| 4-156772857-G-C | not specified | Uncertain significance (Feb 06, 2023) | ||
| 4-156810839-G-T | not specified | Uncertain significance (Jan 22, 2024) | ||
| 4-156810923-C-T | not specified | Uncertain significance (Nov 03, 2022) | ||
| 4-156850397-A-T | not specified | Uncertain significance (Jul 07, 2022) | ||
| 4-156850408-C-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| 4-156970791-T-C | Benign (Dec 31, 2019) | |||
| 4-156970811-C-A | PDGFC-related disorder | Likely benign (Nov 13, 2019) | ||
| 4-156970839-G-A | not specified | Uncertain significance (Jan 20, 2023) | ||
| 4-156970845-G-A | not specified | Uncertain significance (Dec 21, 2023) | ||
| 4-156970863-G-C | not specified | Uncertain significance (Apr 10, 2023) | ||
| 4-156970888-G-A | not specified | Uncertain significance (Apr 15, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PDGFC | protein_coding | protein_coding | ENST00000502773 | 6 | 210941 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.994 | 0.00626 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.17 | 139 | 184 | 0.756 | 0.00000887 | 2254 |
| Missense in Polyphen | 38 | 75.146 | 0.50568 | 885 | ||
| Synonymous | 0.323 | 66 | 69.4 | 0.951 | 0.00000363 | 665 |
| Loss of Function | 3.60 | 0 | 15.1 | 0.00 | 7.01e-7 | 190 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen and chemoattractant for cells of mesenchymal origin. Required for normal skeleton formation during embryonic development, especially for normal development of the craniofacial skeleton and for normal development of the palate. Required for normal skin morphogenesis during embryonic development. Plays an important role in wound healing, where it appears to be involved in three stages: inflammation, proliferation and remodeling. Plays an important role in angiogenesis and blood vessel development. Involved in fibrotic processes, in which transformation of interstitial fibroblasts into myofibroblasts plus collagen deposition occurs. The CUB domain has mitogenic activity in coronary artery smooth muscle cells, suggesting a role beyond the maintenance of the latency of the PDGF domain. In the nucleus, PDGFC seems to have additional function. {ECO:0000269|PubMed:10806482, ECO:0000269|PubMed:10858496, ECO:0000269|PubMed:11297552, ECO:0000269|PubMed:11854040, ECO:0000269|PubMed:12032822, ECO:0000269|PubMed:15061151, ECO:0000269|PubMed:15372073, ECO:0000269|PubMed:15389578, ECO:0000269|PubMed:15728360, ECO:0000269|PubMed:15911618, ECO:0000269|PubMed:16439802, ECO:0000269|PubMed:18055825}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Melanoma - Homo sapiens (human);Gap junction - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Signal Transduction;Signaling by PDGF;PDGF receptor signaling network;Signaling by Receptor Tyrosine Kinases
(Consensus)
Recessive Scores
- pRec
- 0.192
Intolerance Scores
- loftool
- 0.214
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.92
Haploinsufficiency Scores
- pHI
- 0.325
- hipred
- Y
- hipred_score
- 0.738
- ghis
- 0.518
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.576
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pdgfc
- Phenotype
- renal/urinary system phenotype; skeleton phenotype; vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); pigmentation phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; respiratory system phenotype; embryo phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; muscle phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Gene ontology
- Biological process
- activation of transmembrane receptor protein tyrosine kinase activity;central nervous system development;positive regulation of cell population proliferation;animal organ morphogenesis;regulation of signaling receptor activity;positive regulation of phosphatidylinositol 3-kinase signaling;positive regulation of cell migration;positive regulation of protein autophosphorylation;positive regulation of MAP kinase activity;platelet-derived growth factor receptor signaling pathway;positive regulation of fibroblast proliferation;digestive tract development;embryonic organ development;regulation of peptidyl-tyrosine phosphorylation;positive regulation of cell division;bone development;positive regulation of ERK1 and ERK2 cascade;cellular response to amino acid stimulus;positive regulation of cold-induced thermogenesis
- Cellular component
- Golgi membrane;extracellular region;extracellular space;nucleus;endoplasmic reticulum lumen;cytosol;plasma membrane;cell surface;extracellular exosome
- Molecular function
- platelet-derived growth factor receptor binding;protein binding;growth factor activity;protein homodimerization activity