TNS3

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

Basic information

Region (hg38): 7:47275153-47582558

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.

• Inborn genetic diseases (67 variants)
• not provided (41 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.

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				14	5	19
missense			61	10	10	81
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding					2	2
Total	0	0	61	24	17

Variants in TNS3

This is a list of pathogenic ClinVar variants found in the TNS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-47278106-C-T			Benign (Dec 31, 2019)
7-47278126-T-C		not specified	Uncertain significance (Feb 05, 2024)
7-47278132-T-C		not specified	Uncertain significance (Mar 24, 2023)
7-47280176-C-T			Likely benign (May 01, 2023)
7-47280299-G-A		not specified	Uncertain significance (May 31, 2023)
7-47280323-T-C		not specified	Uncertain significance (Jan 09, 2024)
7-47280330-G-A			Benign (May 01, 2023)
7-47283818-C-T		not specified	Uncertain significance (Jul 14, 2021)
7-47291996-G-A			Benign (Dec 31, 2019)
7-47292853-C-A			Likely benign (Oct 10, 2018)
7-47292869-G-A		not specified	Uncertain significance (May 04, 2023)
7-47292896-G-A		not specified	Uncertain significance (Jan 26, 2023)
7-47293806-G-A			Likely benign (May 17, 2018)
7-47297113-G-A			Likely benign (Feb 17, 2018)
7-47297145-C-A		not specified	Uncertain significance (Feb 02, 2024)
7-47297185-C-T			Likely benign (May 14, 2018)
7-47297208-C-T		not specified	Uncertain significance (Aug 13, 2021)
7-47302955-A-T		not specified	Uncertain significance (Dec 02, 2022)
7-47302958-G-A		not specified	Uncertain significance (Dec 01, 2022)
7-47302989-C-T		not specified	Uncertain significance (Dec 28, 2023)
7-47303013-T-A			Benign (Oct 10, 2018)
7-47303029-G-A			Likely benign (Jul 01, 2022)
7-47303039-C-A		not specified	Uncertain significance (Feb 27, 2024)
7-47303093-G-A		not specified	Uncertain significance (Jul 25, 2023)
7-47303115-G-C			Benign/Likely benign (Apr 01, 2023)

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