THBS2

thrombospondin 2, the group of Thrombospondin family

Basic information

Region (hg38): 6:169215780-169254050

Links

ENSG00000186340

∙ NCBI:7058 ∙ OMIM:188061 ∙ HGNC:11786 ∙ Uniprot:P35442 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Ehlers-Danlos syndrome, classic-like, 3 (Limited), mode of inheritance: AD
Ehlers-Danlos syndrome, classic-like, 3 (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the THBS2 gene.

not_specified (157 variants)
not_provided (21 variants)
THBS2-related_disorder (16 variants)
Ehlers-Danlos_syndrome,_classic-like,_3 (2 variants)
Ehlers-Danlos_syndrome (2 variants)
Cardiomyopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THBS2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003247.5. 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			7 clinvar	6 clinvar	11 clinvar	24
missense	1 clinvar		149 clinvar	17 clinvar	8 clinvar	175
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	0	160	23	19

Highest pathogenic variant AF is 6.841143e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THBS2	protein_coding	protein_coding	ENST00000366787	21	38265

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	587	759	0.774	0.0000501	7796
Missense in Polyphen		214	351.14	0.60945		3565
Synonymous	-0.248	334	328	1.02	0.0000263	2159
Loss of Function	5.58	13	59.5	0.219	0.00000283	625

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000304	0.000298
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000977	0.0000967
Middle Eastern	0.000163	0.000163
South Asian	0.0000653	0.0000653
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Ligand for CD36 mediating antiangiogenic properties. {ECO:0000269|PubMed:20714802}.;
Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Phagosome - Homo sapiens (human);Malaria - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);miRNA targets in ECM and membrane receptors;Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;miR-509-3p alteration of YAP1-ECM axis;PI3K-Akt Signaling Pathway;Signal Transduction;Post-translational protein modification;Metabolism of proteins;Signaling by PDGF;Signaling by Receptor Tyrosine Kinases;O-glycosylation of TSR domain-containing proteins;Beta1 integrin cell surface interactions;O-linked glycosylation;Alpha4 beta1 integrin signaling events (Consensus)

Recessive Scores

pRec: 0.521

Intolerance Scores

loftool: 0.108
rvis_EVS: -0.47
rvis_percentile_EVS: 23.05

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.883

Gene Damage Prediction

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

Gene ontology

Biological process: cell adhesion;negative regulation of angiogenesis;positive regulation of synapse assembly
Cellular component: extracellular region;basement membrane;platelet alpha granule;collagen-containing extracellular matrix
Molecular function: extracellular matrix structural constituent;calcium ion binding;protein binding;heparin binding