TNR

tenascin R, the group of Tenascins

Basic information

Region (hg38): 1:175315194-175743595

Links

ENSG00000116147NCBI:7143OMIM:601995HGNC:11953Uniprot:Q92752AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • neurodevelopmental disorder, nonprogressive, with spasticity and transient opisthotonus (Strong), mode of inheritance: AR

ClinVar

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

  • Inborn_genetic_diseases (177 variants)
  • not_provided (55 variants)
  • Neurodevelopmental_disorder,_nonprogressive,_with_spasticity_and_transient_opisthotonus (23 variants)
  • Non-progressive_neurodevelopmental_disorder_with_spasticity_and_transient_opisthotonus (8 variants)
  • Parkinson_disease (5 variants)
  • TNR-related_disorder (4 variants)
  • not_specified (1 variants)
  • Autoimmune_enteropathy_and_endocrinopathy_-_susceptibility_to_chronic_infections_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNR gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003285.3. 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.

EffectPLPVUSLBBSum
synonymous
22
clinvar
9
clinvar
31
missense
2
clinvar
2
clinvar
187
clinvar
11
clinvar
3
clinvar
205
nonsense
2
clinvar
1
clinvar
1
clinvar
4
start loss
0
frameshift
4
clinvar
4
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 8 4 188 33 12

Highest pathogenic variant AF is 0.0000272594

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TNRprotein_codingprotein_codingENST00000367674 21428577
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.5240.4761257180301257480.000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.606858130.8430.00004808851
Missense in Polyphen253353.430.715853767
Synonymous-0.5083413291.040.00002142717
Loss of Function6.141672.40.2210.00000436700

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001770.000177
Ashkenazi Jewish0.0001990.000198
East Asian0.0002210.000217
Finnish0.0001390.000139
European (Non-Finnish)0.0001060.000105
Middle Eastern0.0002210.000217
South Asian0.00003270.0000327
Other0.0006530.000489

dbNSFP

Source: dbNSFP

Function
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 inhibition of neurite growth. Binding to cell surface gangliosides inhibits RGD-dependent integrin-mediated cell adhesion and results in an inhibition of PTK2/FAK1 (FAK) phosphorylation and cell detachment. Binding to membrane surface sulfatides results in a oligodendrocyte adhesion and differentiation. Interaction with CNTN1 induces a repulsion of neurons and an inhibition of neurite outgrowth. Interacts with SCN2B may play a crucial role in clustering and regulation of activity of sodium channels at nodes of Ranvier. TNR-linked chondroitin sulfate glycosaminoglycans are involved in the interaction with FN1 and mediate inhibition of cell adhesion and neurite outgrowth. The highly regulated addition of sulfated carbohydrate structure may modulate the adhesive properties of TNR over the course of development and during synapse maintenance (By similarity). {ECO:0000250}.;
Pathway
PI3K-Akt signaling pathway - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Extracellular matrix organization;ECM proteoglycans (Consensus)

Recessive Scores

pRec
0.373

Intolerance Scores

loftool
0.502
rvis_EVS
-0.54
rvis_percentile_EVS
20.04

Haploinsufficiency Scores

pHI
0.140
hipred
Y
hipred_score
0.663
ghis
0.554

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.832

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Tnr
Phenotype
nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
tnr
Affected structure
optic tract
Phenotype tag
abnormal
Phenotype quality
branchiness

Gene ontology

Biological process
cell adhesion;neuron cell-cell adhesion;axon guidance;associative learning;telencephalon cell migration;negative regulation of cell-cell adhesion;extracellular matrix organization;locomotory exploration behavior;negative regulation of axon extension involved in regeneration;negative regulation of synaptic transmission;synapse organization;neuromuscular process controlling balance;positive regulation of synaptic transmission, glutamatergic;positive regulation of transmission of nerve impulse;long-term synaptic potentiation
Cellular component
extracellular region;cell surface;membrane raft;perineuronal net;Schaffer collateral - CA1 synapse;glutamatergic synapse
Molecular function