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

• nephrotic syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TNS2 gene.

• not_provided (267 variants)
• not_specified (225 variants)
• TNS2-related_disorder (58 variants)
• Nephrotic_syndrome (1 variants)

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. These statistics are base on transcript: NM_000170754.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	75	11	88
missense			289	20	3	312
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	295	95	14

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