THBS3

thrombospondin 3, the group of Thrombospondin family

Basic information

Region (hg38): 1:155195587-155209051

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.

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.

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				1		1
missense			46			46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	49	1	0

Variants in THBS3

This is a list of pathogenic ClinVar variants found in the THBS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155195869-C-T		not specified	Uncertain significance (May 27, 2022)
1-155195870-G-A		not specified	Uncertain significance (May 20, 2024)
1-155196000-C-G		not specified	Uncertain significance (Aug 04, 2021)
1-155196076-A-G		not specified	Uncertain significance (Jul 11, 2023)
1-155196125-C-T		not specified	Uncertain significance (May 01, 2023)
1-155197081-G-A		not specified	Uncertain significance (Apr 13, 2022)
1-155197098-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-155197126-A-G		not specified	Uncertain significance (Jun 11, 2024)
1-155197134-C-T		not specified	Uncertain significance (Mar 07, 2023)
1-155197210-C-G		not specified	Uncertain significance (Oct 17, 2023)
1-155197485-G-A		not specified	Uncertain significance (Nov 10, 2022)
1-155197546-C-T		not specified	Uncertain significance (Jan 03, 2022)
1-155197555-G-T		not specified	Uncertain significance (Jul 25, 2023)
1-155198055-A-G		not specified	Uncertain significance (Jun 18, 2024)
1-155198065-G-C		not specified	Uncertain significance (Jan 09, 2024)
1-155198098-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-155198113-C-A		not specified	Uncertain significance (May 04, 2022)
1-155198167-C-G		not specified	Uncertain significance (May 05, 2023)
1-155198212-C-T		not specified	Uncertain significance (Sep 07, 2022)
1-155198220-C-T		not specified	Uncertain significance (Feb 06, 2024)
1-155198444-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-155198538-C-T		not specified	Uncertain significance (Feb 07, 2023)
1-155200007-G-T		not specified	Uncertain significance (Dec 13, 2023)
1-155200064-C-G		not specified	Uncertain significance (Nov 09, 2023)
1-155200104-T-C		not specified	Uncertain significance (Dec 14, 2023)

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