TNS1
Basic information
Region (hg38): 2:217799588-218033982
Previous symbols: [ "TNS", "MXRA6" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 16 | 13 | 29 | |||
missense | 258 | 16 | 15 | 289 | ||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 258 | 32 | 28 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TNS1 | protein_coding | protein_coding | ENST00000171887 | 28 | 203207 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0599 | 0.940 | 125645 | 0 | 103 | 125748 | 0.000410 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.552 | 979 | 1.03e+3 | 0.952 | 0.0000627 | 11147 |
Missense in Polyphen | 373 | 423.75 | 0.88024 | 4544 | ||
Synonymous | 0.222 | 419 | 425 | 0.986 | 0.0000275 | 3634 |
Loss of Function | 6.00 | 18 | 73.6 | 0.245 | 0.00000410 | 797 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000442 | 0.000442 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.00402 | 0.00398 |
Finnish | 0.0000924 | 0.0000924 |
European (Non-Finnish) | 0.0000908 | 0.0000879 |
Middle Eastern | 0.00402 | 0.00398 |
South Asian | 0.000167 | 0.000163 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
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