THSD1 (thrombospondin type 1 domain containing 1)

Gene

• Entrez ID: 55901
• Gene name: Thrombospondin type 1 domain containing 1
• Gene symbol: THSD1
• Synonyms (NCBI Gene): ANIB12, LMPHM13, TMTSP, UNQ3010
• Chromosome: 13
• Chromosome location: 13q14.3
• Summary: The protein encoded by this gene contains a type 1 thrombospondin domain, which is found in a number of proteins involved in the complement pathway, as well as in extracellular matrix proteins. Alternatively spliced transcript variants encoding different

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs9536062	G>A,C	Likely-pathogenic	Missense variant, stop gained, coding sequence variant
rs786205669	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1594095223	G>A	Pathogenic	Stop gained, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1423726	hsa-miR-4289	CLIP-seq
MIRT1423727	hsa-miR-556-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	27895300
GO:0005576	Component	Extracellular region	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005768	Component	Endosome	IDA	29069646
GO:0005768	Component	Endosome	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005925	Component	Focal adhesion	IEA
GO:0005925	Component	Focal adhesion	IMP	27895300
GO:0010008	Component	Endosome membrane	IEA
GO:0016020	Component	Membrane	IEA
GO:0048041	Process	Focal adhesion assembly	IDA	29069646
GO:0050840	Function	Extracellular matrix binding	IMP	27895300
GO:0070161	Component	Anchoring junction	IEA
GO:0071944	Component	Cell periphery	IBA

Other IDs

• MIM: 616821
• HGNC: 17754
• e!Ensembl: ENSG00000136114

Protein

• UniProt ID: Q9NS62
• Protein name: Thrombospondin type-1 domain-containing protein 1 (Transmembrane molecule with thrombospondin module)
• Protein function: Is a positive regulator of nascent focal adhesion assembly, involved in the modulation of endothelial cell attachment to the extracellular matrix.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00090	TSP_1	344 → 392	Thrombospondin type 1 domain	Domain

• Sequence:

  MKPMLKDFSNLLLVVLCDYVLGEAEYLLLREPGHVALSNDTVYVDFQYFDGANGTLRNVS
  VLLLEANTNQTVTTKYLLTNQSQGTLKFECFYFKEAGDYWFTMTPEATDNSTPFPWWEKS
  AFLKVEWPVFHVDLNRSAKAAEGTFQVGLFTSQPLCPFPVDKPNIVVDVIFTNSLPEARR
  NSRQPLEIRTSKRTELAQGQWVEFGCAPLGPEAYVTVVLKLLGRDSVITSTGPIDLAQKF
  GYKLVMVPELTCESGVEVTVLPPPCTFVQGVVTVFKEAPRYPGKRTIHLAENSLPLGERR
  TIFNCTLFDMGKNKYCFDFGISSRSHFSAKEECMLIQRNTETWGLWQPWSQCSATCGDGV
  RERRRVCLTSFPSSPVCPGMSLEASLCSLEECAAFQPSSPSPLQPQGPVKSNNIVTVTGI
  SLCLFIIIATVLITLWRRFGRPAKCSTPARHNSIHSPSFRKNSDEENICELSEQRGSFSD
  GGDGPTGSPGDTGIPLTYRRSGPVPPEDDASGSESFQSNAQKIIPPLFSYRLAQQQLKEM
  KKKGLTETTKVYHVSQSPLTDTAIDAAPSAPLDLESPEEAAANKFRIKSPFPEQPAVSAG
  ERPPSRLDLNVTQASCAISPSQTLIRKSQARHVGSRGGPSERSHARNAHFRRTASFHEAR
  QARPFRERSMSTLTPRQAPAYSSRTRTCEQAEDRFRPQSRGAHLFPEKLEHFQEASGTRG
  PLNPLPKSYTLGQPLRKPDLGDHQAGLVAGIERTEPHRARRGPSPSHKSVSRKQSSPISP
  KDNYQRVSSLSPSQCRKDKCQSFPTHPEFAFYDNTSFGLTEAEQRMLDLPGYFGSNEEDE
  TTSTLSVEKLVI

• Sequence length: 852

Pathways

Reactome:

Defective B3GALTL causes Peters-plus syndrome (PpS)
O-glycosylation of TSR domain-containing proteins

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Aneurysm, intracranial berry, 12	Pathogenic	rs1594095223	RCV000991274	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Lymphatic malformation 13	Likely pathogenic; Pathogenic	rs786205669, rs2547596958, rs2547597183, rs2547604512	RCV003224867 RCV003152352 RCV003152353 RCV003333901	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Non-immune hydrops fetalis	Likely pathogenic	rs786205669	RCV000170576	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Aortic aneurysm	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Cervical cancer	-	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA, VASCULAR	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL CEREBRAL SACCULAR ANEURYSM	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYDROPS FETALIS, NON-IMMUNE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTRACRANIAL BERRY ANEURYSM	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
THSD1-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Vascular dementia	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Aneurysm	Aneurysm	Pubtator	29069646	Associate	★☆☆☆☆ Found in Text Mining only
Cerebrovascular Disorders	Cerebrovascular disorder	Pubtator	32367296	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	22664866		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	BEFREE	22664866		★☆☆☆☆ Found in Text Mining only
Depression Postpartum	Major depressive disorder	Pubtator	26036949	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal carcinoma	Esophageal Carcinoma	BEFREE	18403638		★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophageal neoplasm	Pubtator	18403638	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	18403638	Inhibit	★☆☆☆☆ Found in Text Mining only
Familial cerebral saccular aneurysm	Cerebral Saccular Aneurysm	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hemangioma	Hemangioma	BEFREE	30055085		★☆☆☆☆ Found in Text Mining only
Hydrops Fetalis	Hydrops fetalis	Pubtator	26036949	Associate	★☆☆☆☆ Found in Text Mining only
Hydrops Fetalis, Non-Immune	Hydrops Fetalis	CLINVAR_DG	26036949		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hydrops Fetalis, Non-Immune	Hydrops Fetalis	BEFREE	30055085		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hydrops Fetalis, Non-Immune	Hydrops Fetalis	ORPHANET_DG	30055085		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Infertility	Infertility	Pubtator	38274228	Associate	★☆☆☆☆ Found in Text Mining only
Infertility Female	Female infertility	Pubtator	38274228	Inhibit	★☆☆☆☆ Found in Text Mining only
Intracranial Aneurysm	Intracranial Aneurysm	BEFREE	27895300, 29069646, 31055715		★☆☆☆☆ Found in Text Mining only
Intracranial Aneurysm	Intracranial aneurysm	Pubtator	29069646	Associate	★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	18403638		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	18403638		★☆☆☆☆ Found in Text Mining only
Non-immune hydrops fetalis	Nonimmune Hydrops Fetalis	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	18403638		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	27270314	Associate	★☆☆☆☆ Found in Text Mining only
Subarachnoid Hemorrhage	Subarachnoid hemorrhage	BEFREE	27895300, 29069646		★☆☆☆☆ Found in Text Mining only
Subarachnoid Hemorrhage	Subarachnoid hemorrhage	GENOMICS_ENGLAND_DG	27895300		★☆☆☆☆ Found in Text Mining only