PDGFD

platelet derived growth factor D

Basic information

Region (hg38): 11:103907188-104164379

Links

ENSG00000170962 ∙ NCBI:80310 ∙ OMIM:609673 ∙ HGNC:30620 ∙ Uniprot:Q9GZP0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pulmonary arterial hypertension (Limited), mode of inheritance: AD

ClinVar

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

• Inborn genetic diseases (39 variants)
• not provided (5 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.

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						0
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			26	2	4	32
Total	0	0	38	2	4

Variants in PDGFD

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

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

Position	Type	Phenotype	Significance	ClinVar
11-103927088-T-G		not specified	Uncertain significance (Feb 28, 2023)
11-103927100-C-T		not specified	Uncertain significance (Oct 10, 2023)
11-103943454-T-C		not specified	Uncertain significance (Dec 17, 2021)
11-103943463-C-T		not specified	Uncertain significance (Jun 29, 2023)
11-103943464-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-103943475-G-A		not specified	Uncertain significance (May 25, 2022)
11-103943476-A-G		not specified	Uncertain significance (May 25, 2022)
11-103943518-G-C		not specified	Uncertain significance (Mar 24, 2023)
11-103943535-T-C		not specified	Uncertain significance (Mar 03, 2022)
11-103947682-A-G		not specified	Uncertain significance (Dec 08, 2023)
11-103996085-T-G		not specified	Uncertain significance (Nov 08, 2022)
11-103996163-G-A		not specified	Uncertain significance (Oct 05, 2021)
11-104000057-A-G		not specified	Uncertain significance (Dec 16, 2022)
11-104000097-A-C		not specified	Uncertain significance (Aug 13, 2021)
11-104036890-C-G		not specified	Uncertain significance (Nov 17, 2022)
11-104036945-C-T			Benign (Aug 05, 2018)
11-104036946-G-A		not specified	Uncertain significance (Feb 10, 2022)
11-104037001-C-T		not specified	Uncertain significance (Dec 20, 2021)
11-104037022-A-G		not specified	Uncertain significance (Jul 20, 2021)
11-104037033-A-G		not specified	Likely benign (Jun 22, 2021)
11-104037036-G-C		not specified	Uncertain significance (Mar 07, 2023)
11-104037073-C-T		not specified	Uncertain significance (Aug 14, 2023)
11-104037106-A-G		not specified	Uncertain significance (Feb 22, 2023)
11-104037121-C-T		not specified	Uncertain significance (Nov 08, 2022)
11-104037157-C-T		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

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: 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. 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

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