PDGFA
platelet derived growth factor subunit A
Basic information
Region (hg38): 7:497258-520296
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 PDGFA 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 | 1 | |||||
| missense | 15 | 17 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 2 | 1 |
Variants in PDGFA
This is a list of pathogenic ClinVar variants found in the PDGFA region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-500484-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
| 7-500496-C-T | not specified | Uncertain significance (Nov 10, 2022) | ||
| 7-501118-G-A | not specified | Uncertain significance (Mar 07, 2025) | ||
| 7-501131-G-A | not specified | Uncertain significance (Apr 18, 2023) | ||
| 7-501139-G-A | not specified | Uncertain significance (Feb 05, 2025) | ||
| 7-501151-G-A | not specified | Uncertain significance (Aug 01, 2022) | ||
| 7-501164-C-T | not specified | Likely benign (Sep 01, 2021) | ||
| 7-501186-C-T | Benign (Mar 02, 2018) | |||
| 7-501224-C-T | not specified | Uncertain significance (Oct 12, 2024) | ||
| 7-510814-C-T | not specified | Uncertain significance (Feb 05, 2025) | ||
| 7-510815-G-C | not specified | Uncertain significance (Dec 06, 2023) | ||
| 7-510816-C-A | not specified | Uncertain significance (Dec 05, 2024) | ||
| 7-510858-G-C | not specified | Uncertain significance (Apr 12, 2024) | ||
| 7-510902-C-T | Splenomegaly;Delayed gross motor development;Hepatic fibrosis | Uncertain significance (Jun 13, 2024) | ||
| 7-510934-C-T | not specified | Uncertain significance (Sep 24, 2024) | ||
| 7-512374-G-C | not specified | Uncertain significance (Dec 22, 2024) | ||
| 7-512384-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
| 7-512414-C-A | not specified | Uncertain significance (Dec 17, 2023) | ||
| 7-512429-G-T | not specified | Uncertain significance (Apr 12, 2022) | ||
| 7-517412-G-T | not specified | Uncertain significance (Nov 23, 2021) | ||
| 7-517429-C-T | Likely benign (Jun 01, 2018) | |||
| 7-517443-C-G | not specified | Uncertain significance (Jun 07, 2024) | ||
| 7-517482-C-G | not specified | Uncertain significance (May 08, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PDGFA | protein_coding | protein_coding | ENST00000354513 | 6 | 23039 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.808 | 0.191 | 125617 | 0 | 3 | 125620 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.686 | 102 | 123 | 0.826 | 0.00000819 | 1349 |
| Missense in Polyphen | 31 | 51.783 | 0.59865 | 476 | ||
| Synonymous | -1.20 | 64 | 52.9 | 1.21 | 0.00000385 | 405 |
| Loss of Function | 2.61 | 1 | 9.82 | 0.102 | 4.17e-7 | 137 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000882 | 0.00000881 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| 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 for cells of mesenchymal origin. Required for normal lung alveolar septum formation during embryogenesis, normal development of the gastrointestinal tract, normal development of Leydig cells and spermatogenesis. Required for normal oligodendrocyte development and normal myelination in the spinal cord and cerebellum. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFB (By similarity). {ECO:0000250}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Melanoma - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Gap junction - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Glioma - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Fluid shear stress and atherosclerosis - 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);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);PDGF Pathway;Differentiation Pathway;Focal Adhesion;Lung fibrosis;MAPK Signaling Pathway;ESC Pluripotency Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;miRNA regulation of prostate cancer signaling pathways;PI3K-Akt Signaling Pathway;Regulation of Actin Cytoskeleton;Cytokines and Inflammatory Response;Disease;Signal Transduction;role of pi3k subunit p85 in regulation of actin organization and cell migration;phospholipids as signalling intermediaries;GPCR signaling-G alpha q;Signaling by PDGF;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Extracellular matrix organization;GPCR signaling-G alpha s Epac and ERK;pdgf signaling pathway;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;GPCR signaling-G alpha s PKA and ERK;PDGF receptor signaling network;Hemostasis;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;PIP3 activates AKT signaling;PDGF;Downstream signal transduction;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Non-integrin membrane-ECM interactions;Constitutive Signaling by Aberrant PI3K in Cancer;PI3K/AKT Signaling in Cancer;GPCR signaling-G alpha i;Signaling by Receptor Tyrosine Kinases;Intracellular signaling by second messengers;Diseases of signal transduction;Ceramide signaling pathway
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.64
Haploinsufficiency Scores
- pHI
- 0.139
- hipred
- Y
- hipred_score
- 0.786
- ghis
- 0.505
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pdgfa
- Phenotype
- homeostasis/metabolism phenotype; muscle phenotype; craniofacial 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); respiratory system phenotype; skeleton phenotype; renal/urinary system 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); 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); reproductive system phenotype; 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); embryo phenotype;
Zebrafish Information Network
- Gene name
- pdgfaa
- Affected structure
- trabecula communis
- Phenotype tag
- abnormal
- Phenotype quality
- cleft
Gene ontology
- Biological process
- MAPK cascade;angiogenesis;cell activation;hair follicle development;positive regulation of mesenchymal cell proliferation;platelet degranulation;cell-cell signaling;positive regulation of cell population proliferation;response to wounding;animal organ morphogenesis;regulation of signaling receptor activity;negative regulation of phosphatidylinositol biosynthetic process;negative regulation of platelet activation;positive regulation of phosphatidylinositol 3-kinase signaling;regulation of smooth muscle cell migration;cell projection assembly;actin cytoskeleton organization;extracellular matrix organization;positive regulation of cell migration;positive regulation of protein autophosphorylation;regulation of actin cytoskeleton organization;positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway;wound healing;positive regulation of MAP kinase activity;positive regulation of MAPK cascade;skin development;phosphatidylinositol phosphorylation;platelet-derived growth factor receptor signaling pathway;positive regulation of fibroblast proliferation;lung alveolus development;regulation of peptidyl-tyrosine phosphorylation;negative chemotaxis;positive regulation of cell division;positive regulation of protein kinase B signaling;regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling;positive regulation of ERK1 and ERK2 cascade;regulation of glomerular mesangial cell proliferation;embryonic lung development;regulation of DNA biosynthetic process
- Cellular component
- Golgi membrane;extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi lumen;microvillus;cell surface;platelet alpha granule lumen
- Molecular function
- Ras guanyl-nucleotide exchange factor activity;platelet-derived growth factor receptor binding;protein binding;collagen binding;growth factor activity;protein homodimerization activity;phosphatidylinositol-4,5-bisphosphate 3-kinase activity;protein heterodimerization activity;platelet-derived growth factor binding