TNS1
Basic information
Region (hg38): 2:217799587-218033982
Previous symbols: [ "TNS", "MXRA6" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 16 | 23 | 39 | |||
missense | 129 | 12 | 23 | 164 | ||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 4 | 4 | ||||
non coding ? | 2 | |||||
Total | 0 | 0 | 129 | 30 | 48 |
Variants in TNS1
This is a list of pathogenic ClinVar variants found in the TNS1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-217804450-G-A | TNS1-related disorder | Likely benign (Mar 01, 2019) | ||
2-217804473-C-T | TNS1-related disorder | Likely benign (May 22, 2023) | ||
2-217804493-G-C | not specified | Uncertain significance (May 09, 2024) | ||
2-217804495-G-A | TNS1-related disorder | Likely benign (Sep 10, 2019) | ||
2-217804502-T-C | TNS1-related disorder | Benign (Mar 06, 2019) | ||
2-217804556-G-T | not specified | Uncertain significance (Mar 24, 2023) | ||
2-217804558-G-A | TNS1-related disorder | Benign (Dec 31, 2019) | ||
2-217804565-G-A | TNS1-related disorder | Likely benign (Jul 14, 2022) | ||
2-217804591-G-A | Likely benign (Dec 31, 2019) | |||
2-217804603-C-T | not specified | Likely benign (Apr 23, 2024) | ||
2-217804611-C-A | TNS1-related disorder | Likely benign (Jun 18, 2019) | ||
2-217804611-C-T | TNS1-related disorder | Likely benign (Jul 23, 2019) | ||
2-217804612-G-A | TNS1-related disorder | Likely benign (May 06, 2019) | ||
2-217808657-C-T | not specified | Uncertain significance (Sep 16, 2021) | ||
2-217808675-C-A | TNS1-related disorder | Likely benign (Aug 01, 2019) | ||
2-217809875-C-T | not specified | Uncertain significance (Nov 01, 2022) | ||
2-217809892-G-A | not specified | Uncertain significance (Dec 13, 2022) | ||
2-217809974-C-T | TNS1-related disorder | Benign (Oct 17, 2019) | ||
2-217812415-G-A | not specified | Uncertain significance (Nov 17, 2022) | ||
2-217813229-T-C | not specified | Uncertain significance (Oct 17, 2023) | ||
2-217813266-T-C | not specified | Uncertain significance (Feb 06, 2023) | ||
2-217813267-C-A | not specified | Uncertain significance (Nov 09, 2021) | ||
2-217813699-T-C | not specified | Uncertain significance (Dec 18, 2023) | ||
2-217813699-T-G | not specified | Uncertain significance (Feb 28, 2023) | ||
2-217813702-A-T | not specified | Uncertain significance (Jan 30, 2024) |
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