TNS2

protein-coding

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

Gene summary

The protein encoded by this gene belongs to the tensin family. Tensin is a focal adhesion molecule that binds to actin filaments and participates in signaling pathways. This protein plays a role in regulating cell migration. Alternative splicing occurs at this locus and three transcript variants encoding three distinct isoforms have been identified. [provided by RefSeq, Jul 2008]

Previous symbols:

TENC1

MANE transcript

NM_170754.4

Inheritance

ClinVar variants

U:351B:130

Top phenotype

nephrotic syndrome

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr12:53,046,969-53,064,379

External References & Databases

Ensembl (ENSG00000111077)

Transcript & Mutation Effects

hg38 • Region Span ~17.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

nephrotic syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0005377

Submitter: PanelApp Australia

nephrotic syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0005377

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TNS2 variants in ClinVar

4 Conditions Cataloged

not providedTotal: 320

not specifiedTotal: 249

TNS2-related disorderTotal: 64

Nephrotic syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_170754.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	96 clinvar	9 clinvar	111
missense			329 clinvar	22 clinvar	3 clinvar	354
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			13 clinvar			13
Total	0	0	351	118	12	481

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_170754.4	RefSeq	NP_736610.2	29	MANE Select
ENST00000314250.11	Ensembl	ENSP00000319684.7	29	MANE Select
NM_001416202.1	RefSeq	NP_001403131.1	29	Standard
NM_001416203.1	RefSeq	NP_001403132.1	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

EGFR1

Biological Process

kidney development
protein dephosphorylation
negative regulation of cell population proliferation
response to muscle activity
cellular homeostasis

Molecular Function

phosphoprotein phosphatase activity
protein binding
kinase binding
metal ion binding

Cellular Component

plasma membrane
focal adhesion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000314276
Coding exons: 29
Length: 17404
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 70
Defined: 125748
p: 0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.06	751	837	0.897	0.0000490	9007
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00039	0.00037	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00056	0.00054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00027	0.00026	rare
South Asian	0.00029	0.00029	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.163

Intolerance Scores

RVIS EVS: -1.31
RVIS percentile EVS: 4.82

Essentials

Essential (gene trap): N