PDGFD
platelet derived growth factor D
Basic information
Region (hg38): 11:103907189-104164379
Links
Phenotypes
GenCC
Source:
- pulmonary arterial hypertension (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (106 variants)
- not_provided (5 variants)
- Premature_ovarian_insufficiency (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDGFD gene is commonly pathogenic or not. These statistics are base on transcript: NM_000025208.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 42 | 42 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 42 | 0 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PDGFD | protein_coding | protein_coding | ENST00000393158 | 7 | 257194 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00171 | 0.993 | 125728 | 0 | 20 | 125748 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.344 | 199 | 213 | 0.934 | 0.0000117 | 2425 |
| Missense in Polyphen | 78 | 86.936 | 0.89721 | 990 | ||
| Synonymous | -0.0197 | 80 | 79.8 | 1.00 | 0.00000446 | 702 |
| Loss of Function | 2.46 | 8 | 19.8 | 0.404 | 0.00000109 | 223 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000120 | 0.000120 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.000140 | 0.000139 |
| European (Non-Finnish) | 0.0000708 | 0.0000703 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000136 | 0.000131 |
| 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. Plays an important role in wound healing. Induces macrophage recruitment, increased interstitial pressure, and blood vessel maturation during angiogenesis. Can initiate events that lead to a mesangial proliferative glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix (By similarity). {ECO:0000250, ECO:0000269|PubMed:11331881, ECO:0000269|PubMed:15271796}.;
- 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);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;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling
(Consensus)
Recessive Scores
- pRec
- 0.172
Intolerance Scores
- loftool
- 0.701
- rvis_EVS
- -0.54
- rvis_percentile_EVS
- 20.54
Haploinsufficiency Scores
- pHI
- 0.227
- hipred
- Y
- hipred_score
- 0.605
- ghis
- 0.540
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.165
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pdgfd
- Phenotype
Gene ontology
- Biological process
- multicellular organism development;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of phosphatidylinositol 3-kinase signaling;positive regulation of cell migration;positive regulation of protein autophosphorylation;cellular response to platelet-derived growth factor stimulus;positive regulation of MAP kinase activity;platelet-derived growth factor receptor signaling pathway;positive regulation of fibroblast proliferation;positive regulation of smooth muscle cell proliferation;regulation of peptidyl-tyrosine phosphorylation;positive regulation of cell division;cellular response to hydrogen peroxide;positive regulation of ERK1 and ERK2 cascade;cellular response to amino acid stimulus;cellular response to transforming growth factor beta stimulus;positive regulation of smooth muscle cell chemotaxis;positive regulation of glomerular mesangial cell proliferation;positive regulation of monocyte extravasation
- Cellular component
- Golgi membrane;extracellular region;extracellular space;endoplasmic reticulum lumen
- Molecular function
- platelet-derived growth factor receptor binding;growth factor activity