TNS3

tensin 3, the group of SH2 domain containing|C2 tensin-type domain containing

Basic information

Region (hg38): 7:47275154-47582558

Previous symbols: [ "TENS1" ]

Links

ENSG00000136205 ∙ NCBI:64759 ∙ OMIM:606825 ∙ HGNC:21616 ∙ Uniprot:Q68CZ2 ∙ 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 TNS3 gene.

• not_specified (209 variants)
• not_provided (43 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNS3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022748.12. 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				15	5	20
missense			194	21	9	224
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	194	36	14

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNS3	protein_coding	protein_coding	ENST00000398879	26	307405

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000331	124804	0	16	124820	0.0000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.945	785	863	0.910	0.0000525	9346
Missense in Polyphen		232	306.9	0.75595		3403
Synonymous	-1.22	409	379	1.08	0.0000266	2962
Loss of Function	6.57	6	61.7	0.0972	0.00000307	723

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000835	0.0000794
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in actin remodeling. Involved in the dissociation of the integrin-tensin-actin complex. EGF activates TNS4 and down-regulates TNS3 which results in capping the tail of ITGB1. Seems to be involved in mammary cell migration. May be involved in cell migration and bone development (By similarity). {ECO:0000250, ECO:0000269|PubMed:17643115}.
• Pathway: Signal Transduction;MET interacts with TNS proteins;Fibroblast growth factor-1;EGFR1;MET promotes cell motility;Signaling by MET;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.0417
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.293
• hipred: Y
• hipred_score: 0.663
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.258

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tns3
• Phenotype: hematopoietic 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); respiratory system phenotype; skeleton phenotype; immune system phenotype; digestive/alimentary phenotype; growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: positive regulation of cell population proliferation;cell migration;lung alveolus development
• Cellular component: cytosol;focal adhesion
• Molecular function: protein binding