TNS1

tensin 1, the group of MicroRNA protein coding host genes|Protein phosphatase 1 regulatory subunits|SH2 domain containing|C2 tensin-type domain containing|PTEN protein phosphatases

Basic information

Region (hg38): 2:217799588-218033982

Previous symbols: [ "TNS", "MXRA6" ]

Links

ENSG00000079308NCBI:7145OMIM:600076HGNC:11973Uniprot:Q9HBL0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TNS1 gene.

  • not_specified (267 variants)
  • TNS1-related_disorder (56 variants)
  • not_provided (23 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001387777.1. 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
16
clinvar
13
clinvar
29
missense
258
clinvar
16
clinvar
15
clinvar
289
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 258 32 28
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TNS1protein_codingprotein_codingENST00000171887 28203207
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.05990.94012564501031257480.000410
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5529791.03e+30.9520.000062711147
Missense in Polyphen373423.750.880244544
Synonymous0.2224194250.9860.00002753634
Loss of Function6.001873.60.2450.00000410797

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004420.000442
Ashkenazi Jewish0.00009920.0000992
East Asian0.004020.00398
Finnish0.00009240.0000924
European (Non-Finnish)0.00009080.0000879
Middle Eastern0.004020.00398
South Asian0.0001670.000163
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in fibrillar adhesion formation. May be involved in cell migration, cartilage development and in linking signal transduction pathways to the cytoskeleton. {ECO:0000269|PubMed:21768292}.;
Pathway
Integrin-mediated Cell Adhesion;erk and pi-3 kinase are necessary for collagen binding in corneal epithelia;integrin signaling pathway;EGFR1;Integrin-linked kinase signaling (Consensus)

Recessive Scores

pRec
0.156

Intolerance Scores

loftool
0.0123
rvis_EVS
1.59
rvis_percentile_EVS
95.81

Haploinsufficiency Scores

pHI
0.493
hipred
Y
hipred_score
0.680
ghis
0.540

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.662

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Tns1
Phenotype
reproductive system phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; cellular phenotype;

Zebrafish Information Network

Gene name
tns1b
Affected structure
endothelial cell
Phenotype tag
abnormal
Phenotype quality
decreased accumulation

Gene ontology

Biological process
cell-substrate junction assembly;fibroblast migration
Cellular component
cytoplasm;cytoskeleton;focal adhesion;cell surface
Molecular function
RNA binding;actin binding;protein binding