TGFBR3

transforming growth factor beta receptor 3, the group of Proteoglycans

Basic information

Region (hg38): 1:91680343-91906335

Links

ENSG00000069702 ∙ NCBI:7049 ∙ OMIM:600742 ∙ HGNC:11774 ∙ Uniprot:Q03167 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TGFBR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TGFBR3 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				8	7	15
missense			41	9	2	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding				1		1
Total	0	0	41	18	9

Variants in TGFBR3

This is a list of pathogenic ClinVar variants found in the TGFBR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-91683746-G-A		not specified	Uncertain significance (Dec 15, 2023)
1-91683748-G-T		not specified	Uncertain significance (Dec 15, 2022)
1-91683776-G-A		Malignant tumor of prostate • Infertility disorder • not specified	Uncertain significance (May 16, 2022)
1-91683783-C-T		not specified	Uncertain significance (Mar 07, 2023)
1-91683834-C-G		not specified	Uncertain significance (Apr 07, 2022)
1-91695741-T-A		TGFBR3-related disorder	Likely benign (Feb 23, 2022)
1-91695749-A-G		not specified	Uncertain significance (May 20, 2024)
1-91695782-A-G		TGFBR3-related disorder	Likely benign (Jul 10, 2019)
1-91698089-G-A		Familial thoracic aortic aneurysm and aortic dissection • TGFBR3-related disorder	Benign/Likely benign (Aug 01, 2024)
1-91698125-C-G		TGFBR3-related disorder	Benign (Dec 31, 2019)
1-91708684-G-A		not specified	Uncertain significance (Apr 11, 2023)
1-91708703-A-G		TGFBR3-related disorder	Benign (Oct 17, 2019)
1-91708709-C-T		TGFBR3-related disorder	Likely benign (Jun 04, 2019)
1-91708741-T-G		not specified	Uncertain significance (Mar 28, 2024)
1-91708747-C-T		not specified	Uncertain significance (Jan 31, 2024)
1-91708748-G-A			Likely benign (Nov 01, 2023)
1-91708764-G-A		not specified	Uncertain significance (Aug 30, 2021)
1-91712277-G-A		not specified	Uncertain significance (Feb 10, 2023)
1-91712286-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-91712381-A-G		TGFBR3-related disorder	Benign (Oct 21, 2019)
1-91712382-A-G		Connective tissue disorder	Uncertain significance (Jun 01, 2018)
1-91712391-C-G		not specified	Uncertain significance (Apr 17, 2024)
1-91712395-T-C		not specified	Uncertain significance (Aug 06, 2021)
1-91712490-A-C		not specified	Uncertain significance (Jan 10, 2023)
1-91716230-T-A		TGFBR3-related disorder	Likely benign (Dec 11, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TGFBR3	protein_coding	protein_coding	ENST00000212355	16	225991

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00306	0.997	125724	1	23	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	381	453	0.840	0.0000245	5582
Missense in Polyphen		90	143.3	0.62807		1864
Synonymous	-0.523	188	179	1.05	0.0000107	1677
Loss of Function	4.01	12	39.0	0.308	0.00000217	452

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000147	0.000147
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000898	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.000163	0.000131
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to TGF-beta. Could be involved in capturing and retaining TGF-beta for presentation to the signaling receptors.
• Pathway: Extracellular vesicle-mediated signaling in recipient cells;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;TGF-beta Signaling Pathway;Hypothesized Pathways in Pathogenesis of Cardiovascular Disease;TGF-beta Receptor Signaling;TGF_beta_Receptor;TGF-beta receptor signaling (Consensus)

Recessive Scores

• pRec: 0.359

Intolerance Scores

• loftool: 0.283
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.24

Haploinsufficiency Scores

• pHI: 0.600
• hipred: Y
• hipred_score: 0.680
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.643

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tgfbr3
• Phenotype: cellular phenotype; muscle phenotype; skeleton phenotype; immune system phenotype; limbs/digits/tail 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); 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); liver/biliary system phenotype

Zebrafish Information Network

• Gene name: tgfbr3
• Affected structure: dorsal longitudinal anastomotic vessel
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: response to hypoxia;epithelial to mesenchymal transition;liver development;heart morphogenesis;muscular septum morphogenesis;outflow tract morphogenesis;ventricular compact myocardium morphogenesis;immune response;transforming growth factor beta receptor signaling pathway;transforming growth factor beta receptor complex assembly;cell migration;BMP signaling pathway;positive regulation of transforming growth factor beta receptor signaling pathway;negative regulation of transforming growth factor beta receptor signaling pathway;animal organ regeneration;response to follicle-stimulating hormone;response to prostaglandin E;response to luteinizing hormone;intracellular signal transduction;regulation of protein binding;regulation of JNK cascade;negative regulation of epithelial cell proliferation;negative regulation of cellular component movement;ventricular cardiac muscle tissue morphogenesis;cardiac muscle cell proliferation;positive regulation of cardiac muscle cell proliferation;definitive hemopoiesis;cardiac epithelial to mesenchymal transition;definitive erythrocyte differentiation;heart trabecula formation;pathway-restricted SMAD protein phosphorylation;ventricular septum morphogenesis;epicardium-derived cardiac fibroblast cell development;vasculogenesis involved in coronary vascular morphogenesis;heart trabecula morphogenesis;secondary palate development;regulation of ERK1 and ERK2 cascade
• Cellular component: extracellular space;cytoplasm;integral component of plasma membrane;external side of plasma membrane;cell surface;extracellular matrix;inhibin-betaglycan-ActRII complex;receptor complex;extracellular exosome
• Molecular function: transforming growth factor beta-activated receptor activity;type II transforming growth factor beta receptor binding;transforming growth factor beta receptor binding;protein binding;glycosaminoglycan binding;heparin binding;coreceptor activity;fibroblast growth factor binding;PDZ domain binding;SMAD binding;activin binding;transforming growth factor beta binding;transforming growth factor beta receptor activity, type III