TNS4

tensin 4, the group of SH2 domain containing

Basic information

Region (hg38): 17:40475828-40501623

Links

ENSG00000131746 ∙ NCBI:84951 ∙ OMIM:608385 ∙ HGNC:24352 ∙ Uniprot:Q8IZW8 ∙ 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 TNS4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNS4 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						0
missense			42	5	2	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	5	2

Variants in TNS4

This is a list of pathogenic ClinVar variants found in the TNS4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-40477667-G-A		not specified	Uncertain significance (Apr 13, 2023)
17-40477704-G-C		not specified	Uncertain significance (Nov 07, 2022)
17-40478310-G-A		not specified	Uncertain significance (Sep 07, 2022)
17-40478332-A-T		not specified	Uncertain significance (Jan 23, 2024)
17-40478583-C-T		not specified	Uncertain significance (Feb 22, 2023)
17-40478638-G-A		not specified	Uncertain significance (Oct 20, 2021)
17-40479737-G-A		not specified	Uncertain significance (Feb 03, 2022)
17-40479783-C-T		not specified	Uncertain significance (Mar 29, 2022)
17-40479795-C-T		not specified	Uncertain significance (Jan 03, 2022)
17-40479806-T-C		not specified	Uncertain significance (Dec 13, 2021)
17-40479837-G-A		not specified	Uncertain significance (May 08, 2024)
17-40480702-G-A			Benign (Apr 06, 2018)
17-40480754-C-A		not specified	Uncertain significance (Nov 29, 2023)
17-40480759-C-T		not specified	Uncertain significance (Sep 23, 2023)
17-40482189-C-T		not specified	Uncertain significance (Jun 23, 2021)
17-40482392-C-G		not specified	Uncertain significance (Oct 14, 2021)
17-40482392-C-T		not specified	Uncertain significance (Sep 27, 2022)
17-40482416-C-T		not specified	Uncertain significance (Mar 15, 2024)
17-40484535-C-T		not specified	Uncertain significance (Feb 05, 2024)
17-40484594-C-T		not specified	Uncertain significance (Sep 29, 2022)
17-40484962-G-A		not specified	Uncertain significance (Aug 02, 2021)
17-40484976-C-A		not specified	Uncertain significance (Jan 06, 2023)
17-40485002-C-A		not specified	Likely benign (May 23, 2023)
17-40485002-C-T		not specified	Likely benign (Jan 16, 2024)
17-40487152-G-T		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNS4	protein_coding	protein_coding	ENST00000254051	12	25770

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.53e-7	0.997	125684	0	64	125748	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.683	372	411	0.905	0.0000222	4615
Missense in Polyphen		125	132.31	0.94476		1565
Synonymous	1.11	153	172	0.892	0.00000986	1507
Loss of Function	2.67	16	32.4	0.494	0.00000195	331

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000667	0.000641
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.000181	0.000163
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000366	0.000352
Middle Eastern	0.000181	0.000163
South Asian	0.0000981	0.0000980
Other	0.000656	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in cell migration, cartilage development and in linking signal transduction pathways to the cytoskeleton (By similarity). May promote apoptosis, via its cleavage by caspase-3. {ECO:0000250}.
• Pathway: Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Signal Transduction;MET interacts with TNS proteins;EGFR1;MET promotes cell motility;Signaling by MET;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.653
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.28

Haploinsufficiency Scores

• pHI: 0.0857
• hipred: N
• hipred_score: 0.267
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tns4

Gene ontology

• Biological process: apoptotic process;protein localization
• Cellular component: cytosol;cytoskeleton;focal adhesion
• Molecular function: actin binding;protein binding