THBS2

thrombospondin 2, the group of Thrombospondin family

Basic information

Region (hg38): 6:169215779-169254050

Links

ENSG00000186340 ∙ NCBI:7058 ∙ OMIM:188061 ∙ HGNC:11786 ∙ Uniprot:P35442 ∙ 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 THBS2 gene.

• Inborn genetic diseases (39 variants)
• not provided (20 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.

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				2	10	12
missense			36	6	4	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	36	8	15

Variants in THBS2

This is a list of pathogenic ClinVar variants found in the THBS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-169217820-G-A		THBS2-related disorder	Likely benign (Jun 27, 2019)
6-169217827-T-C		not specified	Likely benign (Oct 12, 2021)
6-169220268-G-A		THBS2-related disorder	Benign (Dec 31, 2019)
6-169221441-A-G		THBS2-related disorder	Benign (Oct 22, 2019)
6-169221447-G-C			Benign (Dec 31, 2019)
6-169221505-G-A			Benign (Dec 31, 2019)
6-169221515-A-C		not specified	Uncertain significance (Sep 12, 2023)
6-169222204-G-A		THBS2-related disorder	Benign (Jan 21, 2020)
6-169222227-C-T			Likely benign (Dec 01, 2022)
6-169222230-G-A			Benign (Dec 31, 2019)
6-169222254-C-T			Benign (Dec 31, 2019)
6-169222287-G-A		THBS2-related disorder	Likely benign (Apr 01, 2019)
6-169222304-G-A		not specified	Uncertain significance (Jul 06, 2021)
6-169222306-G-A		not specified	Uncertain significance (Dec 21, 2023)
6-169222388-C-T		not specified	Uncertain significance (Sep 22, 2022)
6-169222395-G-A		THBS2-related disorder	Benign (Oct 23, 2019)
6-169222396-G-A		THBS2-related disorder	Benign (May 24, 2019)
6-169222460-C-T		not specified	Uncertain significance (Mar 24, 2023)
6-169223255-G-A			Benign (Dec 31, 2019)
6-169223271-T-C		not specified	Uncertain significance (Apr 12, 2023)
6-169225200-G-A		THBS2-related disorder	Benign (Apr 05, 2019)
6-169225205-C-T		not specified	Likely benign (Sep 26, 2023)
6-169225212-G-A			Benign (Oct 25, 2018)
6-169225232-A-G		Ehlers-Danlos syndrome	Pathogenic (Mar 08, 2024)
6-169225235-C-T			Likely benign (Nov 06, 2018)

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
0.556	0.444	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

Haploinsufficiency Scores

• pHI: 0.745
• hipred: Y
• hipred_score: 0.603
• ghis: 0.523

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

Mouse Genome Informatics

• Gene name: Thbs2
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype; immune system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); 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); hematopoietic system phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype

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