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

ENSG00000079308 ∙ NCBI:7145 ∙ OMIM:600076 ∙ HGNC:11973 ∙ Uniprot:Q9HBL0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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				5	7	12
missense			180	7	5	192
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	180	12	12

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 • not specified	Uncertain significance (Feb 09, 2025)
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)
2-217804520-G-A		not specified	Uncertain significance (Oct 08, 2024)
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 (Jan 01, 2025)
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 (Jan 18, 2025)
2-217809892-G-A		not specified	Uncertain significance (Dec 13, 2022)
2-217809902-C-A		not specified	Uncertain significance (Dec 06, 2024)
2-217809974-C-T		TNS1-related disorder	Benign (Oct 17, 2019)
2-217810283-G-T		not specified	Uncertain significance (Feb 05, 2025)
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)

GnomAD

Source: gnomAD

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: 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

	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