TNR (tenascin R)

Gene

• Entrez ID: 7143
• Gene name: Tenascin R
• Gene symbol: TNR
• Synonyms (NCBI Gene): NEDSTO, TN-R
• Chromosome: 1
• Chromosome location: 1q25.1
• Summary: This gene encodes a member of the tenascin family of extracellular matrix glycoproteins. The encoded protein is restricted to the central nervous system. The protein may play a role in neurite outgrowth, neural cell adhesion and modulation of sodium chann

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs750577544	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs892080402	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1287757170	G>A	Pathogenic	Stop gained, coding sequence variant
rs1389178206	G>C,T	Pathogenic	Stop gained, 5 prime UTR variant, coding sequence variant
rs1571339601	CA>-	Pathogenic	Coding sequence variant, frameshift variant
rs1571360953	A>-	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT652313	hsa-miR-6734-3p	HITS-CLIP	23824327
MIRT652314	hsa-miR-3667-3p	HITS-CLIP	23824327
MIRT625956	hsa-miR-6867-5p	HITS-CLIP	23824327
MIRT625955	hsa-miR-4455	HITS-CLIP	23824327
MIRT625954	hsa-miR-574-5p	HITS-CLIP	23824327
MIRT621728	hsa-miR-3145-5p	HITS-CLIP	23824327
MIRT621727	hsa-miR-508-5p	HITS-CLIP	23824327
MIRT621726	hsa-miR-1250-3p	HITS-CLIP	23824327
MIRT621725	hsa-miR-6830-3p	HITS-CLIP	23824327
MIRT621724	hsa-miR-145-5p	HITS-CLIP	23824327
MIRT621723	hsa-miR-5195-3p	HITS-CLIP	23824327
MIRT625954	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT625954	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT652313	hsa-miR-6734-3p	HITS-CLIP	23824327
MIRT652314	hsa-miR-3667-3p	HITS-CLIP	23824327
MIRT625956	hsa-miR-6867-5p	HITS-CLIP	23824327
MIRT625955	hsa-miR-4455	HITS-CLIP	23824327
MIRT625954	hsa-miR-574-5p	HITS-CLIP	23824327
MIRT621728	hsa-miR-3145-5p	HITS-CLIP	23824327
MIRT621727	hsa-miR-508-5p	HITS-CLIP	23824327
MIRT621726	hsa-miR-1250-3p	HITS-CLIP	23824327
MIRT621725	hsa-miR-6830-3p	HITS-CLIP	23824327
MIRT621724	hsa-miR-145-5p	HITS-CLIP	23824327
MIRT621723	hsa-miR-5195-3p	HITS-CLIP	23824327
MIRT1444556	hsa-miR-1285	CLIP-seq
MIRT1444557	hsa-miR-2467-5p	CLIP-seq
MIRT1444558	hsa-miR-3153	CLIP-seq
MIRT1444559	hsa-miR-3173-3p	CLIP-seq
MIRT1444560	hsa-miR-3187-5p	CLIP-seq
MIRT1444561	hsa-miR-3188	CLIP-seq
MIRT1444562	hsa-miR-3189-3p	CLIP-seq
MIRT1444563	hsa-miR-326	CLIP-seq
MIRT1444564	hsa-miR-330-5p	CLIP-seq
MIRT1444565	hsa-miR-3689d	CLIP-seq
MIRT1444566	hsa-miR-378g	CLIP-seq
MIRT1444567	hsa-miR-3975	CLIP-seq
MIRT1444568	hsa-miR-4279	CLIP-seq
MIRT1444569	hsa-miR-4486	CLIP-seq
MIRT1444570	hsa-miR-4640-5p	CLIP-seq
MIRT1444571	hsa-miR-4649-3p	CLIP-seq
MIRT1444572	hsa-miR-4663	CLIP-seq
MIRT1444573	hsa-miR-4668-5p	CLIP-seq
MIRT1444574	hsa-miR-4726-5p	CLIP-seq
MIRT1444575	hsa-miR-4768-5p	CLIP-seq
MIRT1444576	hsa-miR-485-5p	CLIP-seq
MIRT1444577	hsa-miR-541	CLIP-seq
MIRT1444578	hsa-miR-612	CLIP-seq
MIRT1444579	hsa-miR-628-5p	CLIP-seq
MIRT1444580	hsa-miR-654-5p	CLIP-seq
MIRT2133044	hsa-miR-4517	CLIP-seq
MIRT2133045	hsa-miR-4781-3p	CLIP-seq
MIRT2133046	hsa-miR-889	CLIP-seq
MIRT2354092	hsa-miR-3155	CLIP-seq
MIRT2354093	hsa-miR-3155b	CLIP-seq
MIRT2354094	hsa-miR-4436b-3p	CLIP-seq
MIRT2354095	hsa-miR-4685-5p	CLIP-seq
MIRT2354096	hsa-miR-484	CLIP-seq
MIRT2354097	hsa-miR-922	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IBA
GO:0007155	Process	Cell adhesion	IEA
GO:0007155	Process	Cell adhesion	NAS	8940128
GO:0007158	Process	Neuron cell-cell adhesion	IEA
GO:0007399	Process	Nervous system development	IBA
GO:0007411	Process	Axon guidance	NAS	8940128
GO:0008306	Process	Associative learning	IEA
GO:0009986	Component	Cell surface	IEA
GO:0010977	Process	Negative regulation of neuron projection development	IEA
GO:0010977	Process	Negative regulation of neuron projection development	ISO
GO:0022029	Process	Telencephalon cell migration	IEA
GO:0022408	Process	Negative regulation of cell-cell adhesion	IEA
GO:0030155	Process	Regulation of cell adhesion	IEA
GO:0030155	Process	Regulation of cell adhesion	ISO
GO:0030198	Process	Extracellular matrix organization	IEA
GO:0030334	Process	Regulation of cell migration	IEA
GO:0030334	Process	Regulation of cell migration	ISO
GO:0030517	Process	Negative regulation of axon extension	IEA
GO:0031012	Component	Extracellular matrix	IBA
GO:0031012	Component	Extracellular matrix	IEA
GO:0035249	Process	Synaptic transmission, glutamatergic	IEA
GO:0035641	Process	Locomotory exploration behavior	IEA
GO:0045121	Component	Membrane raft	IEA
GO:0045595	Process	Regulation of cell differentiation	IEA
GO:0045595	Process	Regulation of cell differentiation	ISO
GO:0048675	Process	Axon extension	IEA
GO:0048677	Process	Axon extension involved in regeneration	IEA
GO:0048692	Process	Negative regulation of axon extension involved in regeneration	IEA
GO:0050804	Process	Modulation of chemical synaptic transmission	IEA
GO:0050805	Process	Negative regulation of synaptic transmission	IEA
GO:0050808	Process	Synapse organization	IEA
GO:0050885	Process	Neuromuscular process controlling balance	IEA
GO:0051968	Process	Positive regulation of synaptic transmission, glutamatergic	IEA
GO:0051971	Process	Positive regulation of transmission of nerve impulse	IEA
GO:0060291	Process	Long-term synaptic potentiation	IEA
GO:0072534	Component	Perineuronal net	IEA
GO:0072534	Component	Perineuronal net	ISO
GO:0090733	Component	Tenascin complex	IEA
GO:0090733	Component	Tenascin complex	ISO
GO:0097402	Process	Neuroblast migration	IEA
GO:0098685	Component	Schaffer collateral - CA1 synapse	IEA
GO:0098978	Component	Glutamatergic synapse	IEA

Other IDs

• MIM: 601995
• HGNC: 11953
• e!Ensembl: ENSG00000116147

Protein

• UniProt ID: Q92752
• Protein name: Tenascin-R (TN-R) (Janusin) (Restrictin)
• Protein function: Neural extracellular matrix (ECM) protein involved in interactions with different cells and matrix components. These interactions can influence cellular behavior by either evoking a stable adhesion and differentiation, or repulsion and inhibitio
• PDB: 8FN9, 8FNA
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF18720	EGF_Tenascin	203 → 231	Tenascin EGF domain	Domain
  PF18720	EGF_Tenascin	234 → 262	Tenascin EGF domain	Domain
  PF07974	EGF_2	297 → 323	EGF-like domain	Domain
  PF00041	fn3	327 → 404	Fibronectin type III domain	Domain
  PF00041	fn3	416 → 496	Fibronectin type III domain	Domain
  PF00041	fn3	505 → 585	Fibronectin type III domain	Domain
  PF00041	fn3	595 → 677	Fibronectin type III domain	Domain
  PF00041	fn3	687 → 766	Fibronectin type III domain	Domain
  PF00041	fn3	775 → 855	Fibronectin type III domain	Domain
  PF00041	fn3	865 → 944	Fibronectin type III domain	Domain
  PF00041	fn3	954 → 1033	Fibronectin type III domain	Domain
  PF00041	fn3	1042 → 1121	Fibronectin type III domain	Domain
  PF00147	Fibrinogen_C	1134 → 1343	Fibrinogen beta and gamma chains, C-terminal globular domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Brain specific. {ECO:0000269|PubMed:8626505}.
• Sequence:

  MGADGETVVLKNMLIGINLILLGSMIKPSECQLEVTTERVQRQSVEEEGGIANYNTSSKE
  QPVVFNHVYNINVPLDNLCSSGLEASAEQEVSAEDETLAEYMGQTSDHESQVTFTHRINF
  PKKACPCASSAQVLQELLSRIEMLEREVSVLRDQCNANCCQESAATGQLDYIPHCSGHGN
  FSFESCGCICNEGWFGKNCSEPYCPLGCSSRGVCVDGQCICDSEYSGDDCSELRCPTDCS
  SRGLCVDGECVCEEPYTGEDCRELRCPGDCSGKGRCANGTCLCEEGYVGEDCGQRQCLNA
  CSGRGQCEEGLCVCEEGYQGPDCSAVAPPEDLRVAGISDRSIELEWDGPMAVTEYVISYQ
  PTALGGLQLQQRVPGDWSGVTITELEPGLTYNISVYAVISNILSLPITAKVATHLSTPQG
  LQFKTITETTVEVQWEPFSFSFDGWEISFIPKNNEGGVIAQVPSDVTSFNQTGLKPGEEY
  IVNVVALKEQARSPPTSASVSTVIDGPTQILVRDVSDTVAFVEWIPPRAKVDFILLKYGL
  VGGEGGRTTFRLQPPLSQYSVQALRPGSRYEVSVSAVRGTNESDSATTQFTTEIDAPKNL
  RVGSRTATSLDLEWDNSEAEVQEYKVVYSTLAGEQYHEVLVPRGIGPTTRATLTDLVPGT
  EYGVGISAVMNSQQSVPATMNARTELDSPRDLMVTASSETSISLIWTKASGPIDHYRITF
  TPSSGIASEVTVPKDRTSYTLTDLEPGAEYIISVTAERGRQQSLESTVDAFTGFRPISHL
  HFSHVTSSSVNITWSDPSPPADRLILNYSPRDEEEEMMEVSLDATKRHAVLMGLQPATEY
  IVNLVAVHGTVTSEPIVGSITTGIDPPKDITISNVTKDSVMVSWSPPVASFDYYRVSYRP
  TQVGRLDSSVVPNTVTEFTITRLNPATEYEISLNSVRGREESERICTLVHTAMDNPVDLI
  ATNITPTEALLQWKAPVGEVENYVIVLTHFAVAGETILVDGVSEEFRLVDLLPSTHYTAT
  MYATNGPLTSGTISTNFSTLLDPPANLTASEVTRQSALISWQPPRAEIENYVLTYKSTDG
  SRKELIVDAEDTWIRLEGLLENTDYTVLLQAAQDTTWSSITSTAFTTGGRVFPHPQDCAQ
  HLMNGDTLSGVYPIFLNGELSQKLQVYCDMTTDGGGWIVFQRRQNGQTDFFRKWADYRVG
  FGNVEDEFWLGLDNIHRITSQGRYELRVDMRDGQEAAFASYDRFSVEDSRNLYKLRIGSY
  NGTAGDSLSYHQGRPFSTEDRDNDVAVTNCAMSYKGAWWYKNCHRTNLNGKYGESRHSQG
  INWYHWKGHEFSIPFVEMKMRPYNHRLMAGRKRQSLQF

• Sequence length: 1358

Pathways

KEGG:

PI3K-Akt signaling pathway
Focal adhesion
ECM-receptor interaction
Human papillomavirus infection
MicroRNAs in cancer

Reactome:

ECM proteoglycans

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
Gastric cancer	Likely pathogenic	rs1245352495	RCV005930373	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder, nonprogressive, with spasticity and transient opisthotonus	Pathogenic; Likely pathogenic	rs2102034857, rs199853947, rs2102011470, rs1571308125, rs1571339601, rs1287757170, rs1571360953, rs892080402, rs750577544, rs1389178206	RCV001796949 RCV002246777 RCV002246778 RCV001796799 RCV001796798 RCV001796797 RCV001849450 RCV001849453 RCV001849454 RCV001849451	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Non-progressive neurodevelopmental disorder with spasticity and transient opisthotonus	Pathogenic; Likely pathogenic	rs1571308125, rs1571339601, rs1287757170, rs1571360953, rs892080402, rs750577544, rs1389178206	RCV000853187 RCV000853186 RCV000853185 RCV000853188 RCV000853191 RCV000853192 RCV000853189	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORNEAL ASTIGMATISM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPEN-ANGLE GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Parkinson disease	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
SARCOIDOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TNR-related disorder	Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WET MACULAR DEGENERATION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Attention Deficit Disorder with Hyperactivity	Attention deficit hyperactivity disorder	Pubtator	30563984	Associate	★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	BEFREE	30563984		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	BEFREE	9359972		★☆☆☆☆ Found in Text Mining only
Brain Injuries	Brain injuries	Pubtator	30980710	Stimulate	★☆☆☆☆ Found in Text Mining only
Brain Injuries Traumatic	Brain injuries	Pubtator	30980710	Associate	★☆☆☆☆ Found in Text Mining only
Cerebrovascular accident	Stroke	BEFREE	29367009		★☆☆☆☆ Found in Text Mining only
Choreoathetosis Hypothyroidism And Neonatal Respiratory Distress	Choreoathetosis	Pubtator	22730557	Associate	★☆☆☆☆ Found in Text Mining only
Choroidal Neovascularization	Choroidal neovascularization	Pubtator	29346644	Associate	★☆☆☆☆ Found in Text Mining only
Chronic leukemia (category)	Leukemia	BEFREE	15225161		★☆☆☆☆ Found in Text Mining only
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	15225161		★☆☆☆☆ Found in Text Mining only
Deuteranomaly	Deuteranomaly	BEFREE	16766924		★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	32099069	Associate	★☆☆☆☆ Found in Text Mining only
Dysequilibrium syndrome	Dysequilibrium syndrome	Pubtator	32099069	Associate	★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	25231141	Stimulate	★☆☆☆☆ Found in Text Mining only
Exudative age-related macular degeneration	Exudative Macular Degeneration	GWASCAT_DG	29346644		★☆☆☆☆ Found in Text Mining only
exudative macular degeneration	Exudative macular degeneration	GWASCAT_DG	29346644		★☆☆☆☆ Found in Text Mining only
Frontotemporal Dementia	Frontotemporal dementia	Pubtator	32576262	Associate	★☆☆☆☆ Found in Text Mining only
Fuchs Endothelial Dystrophy	Fuchs Endothelial Dystrophy	BEFREE	30682148		★☆☆☆☆ Found in Text Mining only
Ganglioglioma	Ganglioglioma	BEFREE	20202125		★☆☆☆☆ Found in Text Mining only
Geographic Atrophy	Geographic Atrophy	BEFREE	29346644		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	20202125		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	32987560	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	22730557		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	22730557	Associate	★☆☆☆☆ Found in Text Mining only
leukemia	Leukemia	BEFREE	15225161		★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	15225161, 20202125		★☆☆☆☆ Found in Text Mining only
Medulloblastoma	Medulloblastoma	BEFREE	12959442		★☆☆☆☆ Found in Text Mining only
Miscarriage	Miscarriage	CTD_human_DG	18539642		★☆☆☆☆ Found in Text Mining only
Mucinous Adenocarcinoma	Mucinous Adenocarcinoma	BEFREE	30008837		★☆☆☆☆ Found in Text Mining only
Myeloproliferative Syndrome Transient	Transient myeloproliferative disorder	Pubtator	32099069	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	15225161		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	22634605		★☆☆☆☆ Found in Text Mining only
oligodendroglioma	Oligodendroglioma	BEFREE	20202125		★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	Pubtator	26595808, 33818904	Associate	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Pilocytic Astrocytoma	Astrocytoma	BEFREE	20202125		★☆☆☆☆ Found in Text Mining only
Well Differentiated Oligodendroglioma	Oligodendroglioma	BEFREE	20202125		★☆☆☆☆ Found in Text Mining only