PDGFB

platelet derived growth factor subunit B

Basic information

Region (hg38): 22:39223359-39244982

Previous symbols: [ "SIS" ]

Links

ENSG00000100311 ∙ NCBI:5155 ∙ OMIM:190040 ∙ HGNC:8800 ∙ Uniprot:P01127 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• basal ganglia calcification, idiopathic, 5 (Strong), mode of inheritance: AD
• basal ganglia calcification, idiopathic, 5 (Strong), mode of inheritance: AD
• basal ganglia calcification, idiopathic, 5 (Moderate), mode of inheritance: AD
• familial meningioma (Limited), mode of inheritance: AD
• bilateral striopallidodentate calcinosis (Supportive), mode of inheritance: AD
• basal ganglia calcification, idiopathic, 5 (Strong), mode of inheritance: AD
• familial meningioma (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Basal ganglia calcification, idiopathic, 5	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	23913003

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDGFB gene.

• not provided (8 variants)
• Basal ganglia calcification, idiopathic, 5 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDGFB 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				15	2	17
missense	1	2	52	5	2	62
nonsense	3					3
start loss	1	1				2
frameshift	2					2
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	1				2
splice region			3		1	4
non coding		2	1	18	32	53
Total	8	6	54	38	36

Highest pathogenic variant AF is 0.00000657

Variants in PDGFB

This is a list of pathogenic ClinVar variants found in the PDGFB region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-39225540-A-G			Benign (Jun 01, 2019)
22-39225574-G-A			Benign (Jun 01, 2019)
22-39225699-CCA-C			Benign (Jun 01, 2019)
22-39225716-G-A		PDGFB-related disorder	Likely benign (Nov 21, 2022)
22-39225723-C-G		Basal ganglia calcification, idiopathic, 5	Pathogenic (Aug 14, 2017)
22-39225724-T-C			Uncertain significance (Oct 05, 2023)
22-39225725-A-G			Likely pathogenic (Dec 16, 2022)
22-39225727-G-C		Inborn genetic diseases	Uncertain significance (Jun 04, 2024)
22-39225733-A-G		Familial meningioma	Uncertain significance (Dec 24, 2018)
22-39225734-G-C			Uncertain significance (Oct 13, 2023)
22-39225746-G-C		Inborn genetic diseases	Uncertain significance (Mar 18, 2024)
22-39225749-C-T			Uncertain significance (Jan 09, 2023)
22-39225750-C-T			Benign (Aug 04, 2023)
22-39225758-C-A			Uncertain significance (Oct 10, 2023)
22-39225762-C-T			Likely benign (Nov 08, 2022)
22-39225763-G-A		Inborn genetic diseases	Uncertain significance (Sep 17, 2021)
22-39225764-TGTGCTTGAATTTCCG-T			Uncertain significance (Oct 29, 2019)
22-39225767-G-T			Uncertain significance (Jul 23, 2022)
22-39225779-G-A		Dermatofibrosarcoma protuberans	Benign/Likely benign (Jan 18, 2024)
22-39225788-C-T		Inborn genetic diseases	Uncertain significance (Jun 16, 2024)
22-39225791-T-G			Uncertain significance (Feb 14, 2024)
22-39225792-G-A			Likely benign (Jan 06, 2024)
22-39225792-G-T			Benign (Jan 26, 2024)
22-39225793-G-A			Uncertain significance (Jan 06, 2024)
22-39225793-G-C		Inborn genetic diseases	Uncertain significance (Dec 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDGFB	protein_coding	protein_coding	ENST00000331163	6	21393

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.770	0.230	125730	0	6	125736	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	129	168	0.766	0.0000118	1529
Missense in Polyphen		42	68.566	0.61255		601
Synonymous	-0.319	74	70.6	1.05	0.00000485	501
Loss of Function	2.92	2	13.6	0.147	8.36e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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 (PubMed:26599395). Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity). {ECO:0000250|UniProtKB:P31240, ECO:0000269|PubMed:26599395}.
• Disease: DISEASE: Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB. {ECO:0000269|PubMed:12660034}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Renal cell carcinoma - 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);Cytokine-cytokine receptor interaction - Homo sapiens (human);Osteoclast Signaling;Angiogenesis;PDGF Pathway;Differentiation Pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;Focal Adhesion;Osteoblast Signaling;Lung fibrosis;MAPK Signaling Pathway;ESC Pluripotency Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Pathways in clear cell renal cell carcinoma;PI3K-Akt Signaling Pathway;Type 2 papillary renal cell carcinoma;Regulation of Actin Cytoskeleton;Disease;Signal Transduction;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;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;GPCR signaling-G alpha s PKA and ERK;Beta3 integrin cell surface interactions;PDGF receptor signaling network;SHP2 signaling;Hemostasis;transcriptional activation of dbpb from mrna;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Signaling events mediated by TCPTP;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;Nectin adhesion pathway;Diseases of signal transduction;S1P1 pathway;S1P3 pathway;PDGFR-beta signaling pathway;Signaling events mediated by PTP1B (Consensus)

Recessive Scores

• pRec: 0.914

Intolerance Scores

• loftool: 0.292
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.212
• hipred: Y
• hipred_score: 0.743
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.751

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pdgfb
• 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); growth/size/body region phenotype; muscle phenotype; homeostasis/metabolism phenotype; immune system phenotype; liver/biliary system phenotype; respiratory system phenotype; embryo phenotype; pigmentation 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); 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); hematopoietic system phenotype; vision/eye 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); renal/urinary system phenotype

Gene ontology

• Biological process: MAPK cascade;embryonic placenta development;positive regulation of endothelial cell proliferation;monocyte chemotaxis;platelet degranulation;positive regulation of glomerular filtration;protein phosphorylation;heart development;positive regulation of cell population proliferation;response to wounding;regulation of signaling receptor activity;negative regulation of phosphatidylinositol biosynthetic process;negative regulation of platelet activation;positive regulation of gene expression;negative regulation of gene expression;positive regulation of phosphatidylinositol 3-kinase signaling;positive regulation of smooth muscle cell migration;peptidyl-serine phosphorylation;peptidyl-tyrosine phosphorylation;hemopoiesis;extracellular matrix organization;positive regulation of cell migration;positive regulation of protein autophosphorylation;negative regulation of protein binding;activation of protein kinase activity;activation of protein kinase B activity;interleukin-18-mediated signaling pathway;positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway;paracrine signaling;positive regulation of MAP kinase activity;positive regulation of MAPK cascade;positive regulation of blood vessel endothelial cell migration;positive regulation of phosphatidylinositol 3-kinase activity;positive regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of mitotic nuclear division;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;phosphatidylinositol phosphorylation;platelet-derived growth factor receptor signaling pathway;positive regulation of fibroblast proliferation;positive regulation of smooth muscle cell proliferation;positive regulation of peptidyl-tyrosine phosphorylation;positive chemotaxis;positive regulation of chemotaxis;positive regulation of cell division;positive regulation of protein kinase B signaling;cell chemotaxis;positive regulation of protein tyrosine kinase activity;positive regulation of ERK1 and ERK2 cascade;protein kinase C signaling;cellular response to growth factor stimulus;cellular response to mycophenolic acid;positive regulation of glomerular mesangial cell proliferation;metanephric glomerular mesangial cell development;reactive oxygen species metabolic process;positive regulation of calcium ion import;positive regulation of hyaluronan biosynthetic process;negative regulation of pri-miRNA transcription by RNA polymerase II;positive regulation of pri-miRNA transcription by RNA polymerase II;positive regulation of vascular smooth muscle cell proliferation;positive regulation of vascular associated smooth muscle cell migration;negative regulation of vascular smooth muscle cell differentiation;positive regulation of vascular smooth muscle cell dedifferentiation;positive regulation of reactive oxygen species metabolic process;positive regulation of DNA biosynthetic process;positive regulation of metanephric mesenchymal cell migration
• Cellular component: Golgi membrane;extracellular region;extracellular space;cytoplasm;endoplasmic reticulum lumen;Golgi lumen;cell surface;basolateral plasma membrane;platelet alpha granule lumen;collagen-containing extracellular matrix
• Molecular function: Ras guanyl-nucleotide exchange factor activity;platelet-derived growth factor receptor binding;protein binding;collagen binding;growth factor activity;superoxide-generating NADPH oxidase activator activity;chemoattractant activity;identical protein binding;protein homodimerization activity;phosphatidylinositol-4,5-bisphosphate 3-kinase activity;protein heterodimerization activity;platelet-derived growth factor binding