THBS3

thrombospondin 3, the group of Thrombospondin family

Basic information

Region (hg38): 1:155195588-155209051

Links

ENSG00000169231

∙ NCBI:7059 ∙ OMIM:188062 ∙ HGNC:11787 ∙ Uniprot:P49746 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the THBS3 gene.

not_specified (107 variants)
not_provided (2 variants)
Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THBS3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007112.5. 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				1 clinvar		1
missense			109 clinvar			109
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	109	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THBS3	protein_coding	protein_coding	ENST00000368378	23	13464

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.58e-21	0.514	125573	0	175	125748	0.000696

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	455	575	0.791	0.0000337	6341
Missense in Polyphen		175	235.92	0.74178		2688
Synonymous	1.60	196	227	0.865	0.0000136	1864
Loss of Function	2.00	41	57.4	0.715	0.00000351	528

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000901	0.000901
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.000925	0.000925
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000776	0.000774
Middle Eastern	0.000925	0.000925
South Asian	0.00114	0.00114
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Can bind to fibrinogen, fibronectin, laminin and type V collagen.;
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);Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Inflammatory Response Pathway;Signal Transduction;Signaling by PDGF;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

pRec: 0.233

Intolerance Scores

loftool: 0.337
rvis_EVS: -1.48
rvis_percentile_EVS: 3.66

Haploinsufficiency Scores

pHI: 0.197
hipred: Y
hipred_score: 0.603
ghis: 0.586

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.324

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Thbs3
Phenotype: skeleton phenotype; limbs/digits/tail phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: cell-matrix adhesion;ossification involved in bone maturation;bone trabecula formation
Cellular component: extracellular region;perinuclear region of cytoplasm;collagen-containing extracellular matrix
Molecular function: extracellular matrix structural constituent;calcium ion binding;heparin binding