TNS2

tensin 2, the group of SH2 domain containing|C2 tensin-type domain containing|PTEN protein phosphatases|MicroRNA protein coding host genes

Basic information

Region (hg38): 12:53046969-53064379

Previous symbols: [ "TENC1" ]

Links

ENSG00000111077 ∙ NCBI:23371 ∙ OMIM:607717 ∙ HGNC:19737 ∙ Uniprot:Q63HR2 ∙ 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 TNS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNS2 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			3	70	9	82
missense			174	15	6	195
nonsense			1			1
start loss						0
frameshift						0
inframe indel			3			3
splice donor/acceptor (+/-2bp)			2			2
splice region			4	3	1	8
non coding			3	23	22	48
Total	0	0	186	108	37

Variants in TNS2

This is a list of pathogenic ClinVar variants found in the TNS2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-53049172-G-C			Benign (Jan 30, 2024)
12-53049215-G-A			Likely benign (Oct 31, 2022)
12-53049257-C-T		TNS2-related disorder	Likely benign (Aug 30, 2023)
12-53049263-T-C			Likely benign (Jul 12, 2022)
12-53049265-G-C			Benign (Jan 28, 2024)
12-53050220-G-A		TNS2-related disorder	Uncertain significance (Dec 29, 2023)
12-53050223-C-T		TNS2-related disorder	Likely benign (Dec 20, 2022)
12-53050251-C-G			Likely benign (Feb 01, 2023)
12-53051866-T-G			Likely benign (Jun 11, 2022)
12-53051883-G-A		not specified	Uncertain significance (Apr 07, 2022)
12-53051893-T-C		TNS2-related disorder	Benign/Likely benign (Dec 27, 2023)
12-53051905-A-T			Uncertain significance (May 31, 2022)
12-53051920-A-G			Conflicting classifications of pathogenicity (Oct 01, 2023)
12-53051939-G-A		not specified	Uncertain significance (Apr 17, 2024)
12-53051970-C-T		TNS2-related disorder	Likely benign (Feb 08, 2024)
12-53052175-T-C			Benign (May 15, 2021)
12-53052468-G-A		TNS2-related disorder	Likely benign (Jan 27, 2023)
12-53052471-G-A		TNS2-related disorder	Likely benign (Nov 30, 2022)
12-53052495-G-A			Uncertain significance (Nov 04, 2023)
12-53053398-G-A			Uncertain significance (Apr 07, 2023)
12-53053401-C-T		TNS2-related disorder	Benign (Jan 19, 2024)
12-53053404-C-T			Likely benign (Jan 12, 2024)
12-53053420-G-T			Uncertain significance (Aug 21, 2022)
12-53053431-C-G			Likely benign (Dec 20, 2021)
12-53053441-G-A			Uncertain significance (Feb 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNS2	protein_coding	protein_coding	ENST00000314276	29	17404

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.70e-7	1.00	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	751	837	0.897	0.0000490	9007
Missense in Polyphen		311	358.29	0.868		3976
Synonymous	0.616	334	349	0.958	0.0000211	3013
Loss of Function	4.93	24	67.8	0.354	0.00000324	775

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000733	0.000718
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000561	0.000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000266	0.000264
Middle Eastern	0.000561	0.000544
South Asian	0.000295	0.000294
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates cell motility and proliferation. May have phosphatase activity. Reduces AKT1 phosphorylation. Lowers AKT1 kinase activity and interferes with AKT1 signaling. {ECO:0000269|PubMed:15817639}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• rvis_EVS: -1.31
• rvis_percentile_EVS: 4.82

Haploinsufficiency Scores

• pHI: 0.214
• hipred: N
• hipred_score: 0.415
• ghis: 0.578

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tns2
• Phenotype: hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: kidney development;protein dephosphorylation;negative regulation of cell population proliferation;response to muscle activity;cellular homeostasis;collagen metabolic process;multicellular organism growth;intracellular signal transduction;multicellular organismal homeostasis
• Cellular component: plasma membrane;focal adhesion
• Molecular function: phosphoprotein phosphatase activity;protein binding;kinase binding;metal ion binding