PDGFRB
platelet derived growth factor receptor beta, the group of I-set domain containing|CD molecules|Receptor tyrosine kinases
Basic information
Region (hg38): 5:150113838-150155872
Previous symbols: [ "PDGFR" ]
Links
Phenotypes
GenCC
Source:
- myofibromatosis, infantile, 1 (Definitive), mode of inheritance: AD
- acroosteolysis-keloid-like lesions-premature aging syndrome (Definitive), mode of inheritance: AD
- skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome (Definitive), mode of inheritance: AD
- basal ganglia calcification, idiopathic, 4 (Strong), mode of inheritance: AD
- basal ganglia calcification, idiopathic, 4 (Strong), mode of inheritance: AD
- basal ganglia calcification, idiopathic, 4 (Moderate), mode of inheritance: AD
- skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome (Moderate), mode of inheritance: AD
- bilateral striopallidodentate calcinosis (Supportive), mode of inheritance: AD
- infantile myofibromatosis (Supportive), mode of inheritance: AD
- acroosteolysis-keloid-like lesions-premature aging syndrome (Supportive), mode of inheritance: AD
- basal ganglia calcification, idiopathic, 4 (Strong), mode of inheritance: AD
- skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome (Strong), mode of inheritance: AD
- myofibromatosis, infantile, 1 (Strong), mode of inheritance: AD
- acroosteolysis-keloid-like lesions-premature aging syndrome (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Myofibromatosis, infantile 1; Kosaki overgrowth syndrome | AD | Cardiovascular; Oncologic | Myofibromatosis, infantile 1 involves benign tumors affecting the skin, muscle, bone, and viscera, and awareness of visceral neoplasms may be beneficial in order to diagnose and manage lesions; Individuals with Kosaki overgrowth syndrome have been described with coronary artery anomalies, and vascular screening and optimal blood pressure control have been recommended | Craniofacial; Cardiovascular; Dermatologic; Musculoskeletal; Neurologic | 9056558; 23255827; 23720404; 23731537; 23731542; 25454926; 26279204; 33382209 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (230 variants)
- Inborn genetic diseases (58 variants)
- Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Acroosteolysis-keloid-like lesions-premature aging syndrome (47 variants)
- Acroosteolysis-keloid-like lesions-premature aging syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome (30 variants)
- Basal ganglia calcification, idiopathic, 4;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Infantile myofibromatosis;Acroosteolysis-keloid-like lesions-premature aging syndrome (30 variants)
- Basal ganglia calcification, idiopathic, 4;Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Infantile myofibromatosis (22 variants)
- not specified (18 variants)
- Myeloproliferative disorder, chronic, with eosinophilia (17 variants)
- Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Acroosteolysis-keloid-like lesions-premature aging syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis (16 variants)
- Infantile myofibromatosis;Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4 (15 variants)
- Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Infantile myofibromatosis;Basal ganglia calcification, idiopathic, 4 (13 variants)
- Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis;Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome (13 variants)
- Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Infantile myofibromatosis;Basal ganglia calcification, idiopathic, 4;Acroosteolysis-keloid-like lesions-premature aging syndrome (12 variants)
- Basal ganglia calcification, idiopathic, 4 (12 variants)
- Infantile myofibromatosis (11 variants)
- PDGFRB-related condition (11 variants)
- Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome (10 variants)
- Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis (10 variants)
- Basal ganglia calcification, idiopathic, 4;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Acroosteolysis-keloid-like lesions-premature aging syndrome;Infantile myofibromatosis (8 variants)
- Infantile myofibromatosis;Acroosteolysis-keloid-like lesions-premature aging syndrome;Basal ganglia calcification, idiopathic, 4;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome (7 variants)
- Acroosteolysis-keloid-like lesions-premature aging syndrome;Infantile myofibromatosis;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4 (7 variants)
- Infantile myofibromatosis;Basal ganglia calcification, idiopathic, 4;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Acroosteolysis-keloid-like lesions-premature aging syndrome (7 variants)
- Acroosteolysis-keloid-like lesions-premature aging syndrome (6 variants)
- Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Acroosteolysis-keloid-like lesions-premature aging syndrome;Infantile myofibromatosis;Basal ganglia calcification, idiopathic, 4 (6 variants)
- Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4;Acroosteolysis-keloid-like lesions-premature aging syndrome;Infantile myofibromatosis (5 variants)
- Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis;Acroosteolysis-keloid-like lesions-premature aging syndrome (5 variants)
- Infantile myofibromatosis;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Acroosteolysis-keloid-like lesions-premature aging syndrome;Basal ganglia calcification, idiopathic, 4 (4 variants)
- Myofibromatosis, infantile, 1 (4 variants)
- Infantile myofibromatosis;Basal ganglia calcification, idiopathic, 4;Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome (3 variants)
- Acroosteolysis-keloid-like lesions-premature aging syndrome;Basal ganglia calcification, idiopathic, 4;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Infantile myofibromatosis (2 variants)
- Acroosteolysis-keloid-like lesions-premature aging syndrome;Infantile myofibromatosis;Basal ganglia calcification, idiopathic, 4;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome (2 variants)
- See cases (2 variants)
- Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Infantile myofibromatosis;Acroosteolysis-keloid-like lesions-premature aging syndrome;Basal ganglia calcification, idiopathic, 4 (2 variants)
- Basal ganglia calcification, idiopathic, 4;Acroosteolysis-keloid-like lesions-premature aging syndrome;Infantile myofibromatosis;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome (2 variants)
- Cerebral palsy (1 variants)
- Infantile myofibromatosis;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4;Acroosteolysis-keloid-like lesions-premature aging syndrome (1 variants)
- Dandy-Walker syndrome (1 variants)
- Myofibromatosis, infantile, 1;Hydrocephalus (1 variants)
- Parkinsonism (1 variants)
- 6 conditions (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDGFRB 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 | 81 | 28 | 110 | |||
| missense | 126 | 61 | 17 | 216 | ||
| nonsense | 2 | |||||
| start loss | 0 | |||||
| frameshift | 3 | |||||
| inframe indel | 7 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| splice region ? | 6 | 7 | 6 | 19 | ||
| non coding ? | 59 | 66 | 129 | |||
| Total | 10 | 5 | 142 | 201 | 111 |
Highest pathogenic variant AF is 0.00000657
Variants in PDGFRB
This is a list of pathogenic ClinVar variants found in the PDGFRB region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-150115690-T-C | Benign (Jan 10, 2019) | |||
| 5-150115722-AG-A | Likely benign (Aug 04, 2019) | |||
| 5-150115724-G-C | Benign (Jan 10, 2019) | |||
| 5-150115724-G-T | Benign (Mar 20, 2019) | |||
| 5-150115787-C-T | Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4;Acroosteolysis-keloid-like lesions-premature aging syndrome;Infantile myofibromatosis | Likely benign (Sep 01, 2022) | ||
| 5-150115788-G-A | Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis | Likely benign (May 03, 2022) | ||
| 5-150115789-C-T | Uncertain significance (Sep 24, 2019) | |||
| 5-150115792-G-A | Basal ganglia calcification, idiopathic, 4;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Acroosteolysis-keloid-like lesions-premature aging syndrome;Infantile myofibromatosis | Uncertain significance (Oct 21, 2021) | ||
| 5-150115796-C-T | Acroosteolysis-keloid-like lesions-premature aging syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome • PDGFRB-related disorder | Benign/Likely benign (Sep 07, 2022) | ||
| 5-150115797-G-A | Infantile myofibromatosis;Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4 • Myofibromatosis, infantile, 1 • Inborn genetic diseases | Benign/Likely benign (Jan 26, 2024) | ||
| 5-150115805-C-A | Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis | Likely benign (Nov 08, 2022) | ||
| 5-150115808-C-T | Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis | Benign (Nov 18, 2023) | ||
| 5-150115809-G-A | Inborn genetic diseases • Infantile myofibromatosis;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Acroosteolysis-keloid-like lesions-premature aging syndrome;Basal ganglia calcification, idiopathic, 4 | Conflicting classifications of pathogenicity (Jan 26, 2023) | ||
| 5-150115810-A-T | Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Infantile myofibromatosis;Basal ganglia calcification, idiopathic, 4;Acroosteolysis-keloid-like lesions-premature aging syndrome | Uncertain significance (Nov 29, 2022) | ||
| 5-150115814-C-T | Acroosteolysis-keloid-like lesions-premature aging syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome | Benign (Dec 31, 2023) | ||
| 5-150115820-C-CT | Inborn genetic diseases | Uncertain significance (Jan 16, 2022) | ||
| 5-150115827-A-AGCTCCG | Acroosteolysis-keloid-like lesions-premature aging syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome | Uncertain significance (Sep 13, 2023) | ||
| 5-150115832-T-C | not specified • Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Acroosteolysis-keloid-like lesions-premature aging syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis • Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome • Basal ganglia calcification, idiopathic, 4 • Acroosteolysis-keloid-like lesions-premature aging syndrome • Myeloproliferative disorder, chronic, with eosinophilia | Benign (Jan 31, 2024) | ||
| 5-150115838-C-T | PDGFRB-related disorder | Likely benign (May 30, 2019) | ||
| 5-150115843-C-T | Parkinsonian disorder • Basal ganglia calcification, idiopathic, 4 | Uncertain significance (Jan 01, 2017) | ||
| 5-150115879-C-T | Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Infantile myofibromatosis;Basal ganglia calcification, idiopathic, 4 | Likely benign (Nov 27, 2023) | ||
| 5-150115880-G-A | Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4;Infantile myofibromatosis | Likely benign (May 01, 2022) | ||
| 5-150115888-G-T | Uncertain significance (Sep 24, 2019) | |||
| 5-150115897-G-T | Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Infantile myofibromatosis;Basal ganglia calcification, idiopathic, 4;Acroosteolysis-keloid-like lesions-premature aging syndrome | Likely benign (Aug 23, 2023) | ||
| 5-150115903-C-T | Infantile myofibromatosis;Acroosteolysis-keloid-like lesions-premature aging syndrome;Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome;Basal ganglia calcification, idiopathic, 4 • Inborn genetic diseases | Conflicting classifications of pathogenicity (Aug 04, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PDGFRB | protein_coding | protein_coding | ENST00000261799 | 22 | 42036 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.904 | 0.0959 | 125721 | 0 | 27 | 125748 | 0.000107 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.84 | 563 | 700 | 0.804 | 0.0000450 | 7173 |
| Missense in Polyphen | 125 | 230.49 | 0.54231 | 2494 | ||
| Synonymous | -1.09 | 328 | 304 | 1.08 | 0.0000213 | 2252 |
| Loss of Function | 5.58 | 11 | 56.1 | 0.196 | 0.00000309 | 587 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000869 | 0.0000869 |
| Ashkenazi Jewish | 0.000698 | 0.000695 |
| East Asian | 0.000164 | 0.000163 |
| Finnish | 0.0000944 | 0.0000924 |
| European (Non-Finnish) | 0.0000620 | 0.0000615 |
| Middle Eastern | 0.000164 | 0.000163 |
| South Asian | 0.000163 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Tyrosine-protein kinase that acts as cell-surface receptor for homodimeric PDGFB and PDGFD and for heterodimers formed by PDGFA and PDGFB, and plays an essential role in the regulation of embryonic development, cell proliferation, survival, differentiation, chemotaxis and migration. Plays an essential role in blood vessel development by promoting proliferation, migration and recruitment of pericytes and smooth muscle cells to endothelial cells. Plays a role in the migration of vascular smooth muscle cells and the formation of neointima at vascular injury sites. Required for normal development of the cardiovascular system. Required for normal recruitment of pericytes (mesangial cells) in the kidney glomerulus, and for normal formation of a branched network of capillaries in kidney glomeruli. Promotes rearrangement of the actin cytoskeleton and the formation of membrane ruffles. Binding of its cognate ligands - homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB or homodimeric PDGFD -leads to the activation of several signaling cascades; the response depends on the nature of the bound ligand and is modulated by the formation of heterodimers between PDGFRA and PDGFRB. Phosphorylates PLCG1, PIK3R1, PTPN11, RASA1/GAP, CBL, SHC1 and NCK1. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5- trisphosphate, mobilization of cytosolic Ca(2+) and the activation of protein kinase C. Phosphorylation of PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, leads to the activation of the AKT1 signaling pathway. Phosphorylation of SHC1, or of the C-terminus of PTPN11, creates a binding site for GRB2, resulting in the activation of HRAS, RAF1 and down-stream MAP kinases, including MAPK1/ERK2 and/or MAPK3/ERK1. Promotes phosphorylation and activation of SRC family kinases. Promotes phosphorylation of PDCD6IP/ALIX and STAM. Receptor signaling is down-regulated by protein phosphatases that dephosphorylate the receptor and its down-stream effectors, and by rapid internalization of the activated receptor. {ECO:0000269|PubMed:11297552, ECO:0000269|PubMed:11331881, ECO:0000269|PubMed:1314164, ECO:0000269|PubMed:1396585, ECO:0000269|PubMed:1653029, ECO:0000269|PubMed:1709159, ECO:0000269|PubMed:1846866, ECO:0000269|PubMed:20494825, ECO:0000269|PubMed:20529858, ECO:0000269|PubMed:21098708, ECO:0000269|PubMed:21679854, ECO:0000269|PubMed:21733313, ECO:0000269|PubMed:2554309, ECO:0000269|PubMed:26599395, ECO:0000269|PubMed:2835772, ECO:0000269|PubMed:2850496, ECO:0000269|PubMed:7685273, ECO:0000269|PubMed:7691811, ECO:0000269|PubMed:7692233, ECO:0000269|PubMed:8195171}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving PDGFRB is found in a form of chronic myelomonocytic leukemia (CMML). Translocation t(5;12)(q33;p13) with EVT6/TEL. It is characterized by abnormal clonal myeloid proliferation and by progression to acute myelogenous leukemia (AML).; DISEASE: Myeloproliferative disorder chronic with eosinophilia (MPE) [MIM:131440]: A hematologic disorder characterized by malignant eosinophils proliferation. Note=The gene represented in this entry may be involved in disease pathogenesis. Chromosomal aberrations involving PDGFRB have been found in many instances of chronic myeloproliferative disorder with eosinophilia. Translocation t(5;12) with ETV6 on chromosome 12 creating an PDGFRB-ETV6 fusion protein (PubMed:12181402). Translocation t(5;15)(q33;q22) with TP53BP1 creating a PDGFRB-TP53BP1 fusion protein (PubMed:15492236). Translocation t(1;5)(q23;q33) that forms a PDE4DIP-PDGFRB fusion protein (PubMed:12907457). Translocation t(5;6)(q33-34;q23) with CEP85L that fuses the 5'-end of CEP85L (isoform 4) to the 3'-end of PDGFRB (PubMed:21938754). {ECO:0000269|PubMed:12181402, ECO:0000269|PubMed:12907457, ECO:0000269|PubMed:15492236, ECO:0000269|PubMed:21938754}.; DISEASE: Leukemia, acute myelogenous (AML) [MIM:601626]: A subtype of acute leukemia, a cancer of the white blood cells. AML is a malignant disease of bone marrow characterized by maturational arrest of hematopoietic precursors at an early stage of development. Clonal expansion of myeloid blasts occurs in bone marrow, blood, and other tissue. Myelogenous leukemias develop from changes in cells that normally produce neutrophils, basophils, eosinophils and monocytes. Note=The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving PDGFRB has been found in a patient with AML. Translocation t(5;14)(q33;q32) with TRIP11 (PubMed:9373237). {ECO:0000269|PubMed:9373237}.; DISEASE: Leukemia, juvenile myelomonocytic (JMML) [MIM:607785]: An aggressive pediatric myelodysplastic syndrome/myeloproliferative disorder characterized by malignant transformation in the hematopoietic stem cell compartment with proliferation of differentiated progeny. Patients have splenomegaly, enlarged lymph nodes, rashes, and hemorrhages. Note=The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving PDGFRB has been found in a patient with JMML. Translocation t(5;17)(q33;p11.2) with SPECC1 (PubMed:15087372). {ECO:0000269|PubMed:15087372}.; DISEASE: Basal ganglia calcification, idiopathic, 4 (IBGC4) [MIM:615007]: A form of basal ganglia calcification, an autosomal dominant condition characterized by symmetric calcification in the basal ganglia and other brain regions. Affected individuals can either be asymptomatic or show a wide spectrum of neuropsychiatric symptoms, including parkinsonism, dystonia, tremor, ataxia, dementia, psychosis, seizures, and chronic headache. Serum levels of calcium, phosphate, alkaline phosphatase and parathyroid hormone are normal. The neuropathological hallmark of the disease is vascular and pericapillary calcification, mainly of calcium phosphate, in the affected brain areas. {ECO:0000269|PubMed:23255827, ECO:0000269|PubMed:24065723, ECO:0000269|PubMed:26599395}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myofibromatosis, infantile 1 (IMF1) [MIM:228550]: A rare mesenchymal disorder characterized by the development of benign tumors in the skin, striated muscles, bones, and, more rarely, visceral organs. Subcutaneous or soft tissue nodules commonly involve the skin of the head, neck, and trunk. Skeletal and muscular lesions occur in about half of the patients. Lesions may be solitary or multicentric, and they may be present at birth or become apparent in early infancy or occasionally in adult life. Visceral lesions are associated with high morbidity and mortality. {ECO:0000269|PubMed:23731537, ECO:0000269|PubMed:23731542}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Kosaki overgrowth syndrome (KOGS) [MIM:616592]: A syndrome characterized by somatic overgrowth, distinctive facial features, hyperelastic and fragile skin, and progressive neurologic deterioration with white matter lesions on brain imaging. {ECO:0000269|PubMed:25454926}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Premature aging syndrome, Penttinen type (PENTT) [MIM:601812]: A syndrome characterized by a prematurely aged appearance with lipoatrophy, epidermal and dermal atrophy along with hypertrophic lesions that resemble scars, thin hair, proptosis, underdeveloped cheekbones, and marked acro-osteolysis. {ECO:0000269|PubMed:26279204}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Central carbon metabolism in cancer - 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);Calcium signaling pathway - 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);Cytokine-cytokine receptor interaction - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Pathway_PA165959425;Sorafenib Pharmacodynamics;Vemurafenib Pathway, Pharmacodynamics;update your name in edit mode;Signaling Pathways in Glioblastoma;PDGF Pathway;Focal Adhesion;Osteoblast Signaling;Imatinib and Chronic Myeloid Leukemia;MAPK Signaling Pathway;ESC Pluripotency Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PDGFR-beta pathway;Protein alkylation leading to liver fibrosis;miRNA regulation of prostate cancer signaling pathways;Pathways in clear cell renal cell carcinoma;PI3K-Akt Signaling Pathway;Ras Signaling;Regulation of Actin Cytoskeleton;Disease;Signal Transduction;Signaling by PDGF;IL-7 signaling;Beta3 integrin cell surface interactions;PDGF receptor signaling network;EGFR1;SHP2 signaling;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Signaling events mediated by TCPTP;PIP3 activates AKT signaling;JAK STAT pathway and regulation;PDGF;EPO signaling;Downstream signal transduction;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Constitutive Signaling by Aberrant PI3K in Cancer;PI3K/AKT Signaling in Cancer;Signaling by Receptor Tyrosine Kinases;VEGF;Intracellular signaling by second messengers;Nectin adhesion pathway;Diseases of signal transduction;Validated targets of C-MYC transcriptional repression;S1P1 pathway;S1P3 pathway;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling;PDGFR-beta signaling pathway;Signaling events mediated by PTP1B
(Consensus)
Recessive Scores
- pRec
- 0.815
Intolerance Scores
- loftool
- 0.123
- rvis_EVS
- -0.72
- rvis_percentile_EVS
- 14.3
Haploinsufficiency Scores
- pHI
- 0.830
- hipred
- Y
- hipred_score
- 0.790
- ghis
- 0.611
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.962
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pdgfrb
- Phenotype
- endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; craniofacial 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); limbs/digits/tail phenotype; digestive/alimentary phenotype; muscle phenotype; 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); normal phenotype; hematopoietic system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; vision/eye phenotype;
Zebrafish Information Network
- Gene name
- pdgfrb
- Affected structure
- cerebellar central artery
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- MAPK cascade;hematopoietic progenitor cell differentiation;glycosaminoglycan biosynthetic process;signal transduction;transmembrane receptor protein tyrosine kinase signaling pathway;G protein-coupled receptor signaling pathway;aging;positive regulation of cell population proliferation;male gonad development;positive regulation of phospholipase C activity;positive regulation of phosphatidylinositol 3-kinase signaling;positive regulation of smooth muscle cell migration;cell migration;peptidyl-tyrosine phosphorylation;positive regulation of cell migration;response to estradiol;positive regulation of phosphoprotein phosphatase activity;response to retinoic acid;regulation of actin cytoskeleton organization;positive regulation of collagen biosynthetic process;response to fluid shear stress;positive regulation of Rho protein signal transduction;cell migration involved in vasculogenesis;metanephric mesenchymal cell migration;platelet-derived growth factor receptor-beta signaling pathway;positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway;aorta morphogenesis;cellular response to platelet-derived growth factor stimulus;positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway;wound healing;response to hydrogen peroxide;positive regulation of apoptotic process;positive regulation of MAP kinase activity;positive regulation of MAPK cascade;positive regulation of phosphatidylinositol 3-kinase activity;response to estrogen;positive regulation of mitotic nuclear division;phosphatidylinositol metabolic process;protein autophosphorylation;phosphatidylinositol phosphorylation;platelet-derived growth factor receptor signaling pathway;phosphatidylinositol-mediated signaling;positive regulation of fibroblast proliferation;positive regulation of smooth muscle cell proliferation;inner ear development;positive regulation of chemotaxis;positive regulation of protein kinase B signaling;cardiac myofibril assembly;response to hyperoxia;cell chemotaxis;lung growth;cell migration involved in coronary angiogenesis;retina vasculature development in camera-type eye;positive regulation of ERK1 and ERK2 cascade;smooth muscle cell chemotaxis;metanephric mesenchyme development;metanephric glomerular mesangial cell proliferation involved in metanephros development;metanephric glomerular capillary formation;metanephric comma-shaped body morphogenesis;metanephric S-shaped body morphogenesis;positive regulation of calcium ion import;positive regulation of reactive oxygen species metabolic process;positive regulation of hepatic stellate cell activation;positive regulation of DNA biosynthetic process
- Cellular component
- nucleus;cytoplasm;Golgi apparatus;plasma membrane;integral component of plasma membrane;focal adhesion;cell surface;membrane;apical plasma membrane;intrinsic component of plasma membrane;cytoplasmic vesicle;lysosomal lumen;intracellular membrane-bounded organelle;receptor complex
- Molecular function
- protein tyrosine kinase activity;transmembrane receptor protein tyrosine kinase activity;platelet activating factor receptor activity;platelet-derived growth factor-activated receptor activity;platelet-derived growth factor beta-receptor activity;Ras guanyl-nucleotide exchange factor activity;signaling receptor binding;platelet-derived growth factor receptor binding;protein binding;ATP binding;enzyme binding;protein kinase binding;vascular endothelial growth factor binding;phosphatidylinositol 3-kinase binding;phosphatidylinositol-4,5-bisphosphate 3-kinase activity;platelet-derived growth factor binding