TNS4

protein-coding

tensin 4, the group of SH2 domain containing

Gene summary

Predicted to enable actin binding activity. Involved in intracellular protein localization. Located in cytosol and focal adhesion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_032865.6

Inheritance

—

ClinVar variants

U:119B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr17:40,475,828-40,501,623

External References & Databases

Ensembl (ENSG00000131746)

Transcript & Mutation Effects

hg38 • Region Span ~25.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TNS4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 118

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032865.6. 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			1 clinvar			1
missense			112 clinvar	11 clinvar	2 clinvar	125
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	119	11	2	132

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032865.6	RefSeq	NP_116254.4	12	MANE Select
ENST00000254051.11	Ensembl	ENSP00000254051.6	12	MANE Select
ENST00000582747.1	Ensembl	ENSP00000463456.1	2	Standard
ENST00000876606.1	Ensembl	ENSP00000546665.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glucocorticoid Receptor Pathway
Nuclear Receptors Meta-Pathway
Signal Transduction
MET interacts with TNS proteins
EGFR1

Biological Process

apoptotic process
protein localization

Molecular Function

actin binding
protein binding

Cellular Component

cytosol
cytoskeleton
focal adhesion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000254051
Coding exons: 12
Length: 25770
Individuals with no LoFs: 125684
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 125748
p: 0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.683	372	411	0.905	0.0000222	4615
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00058	0.00055	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00018	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00037	0.00035	rare
South Asian	0.000098	0.000098	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.653
RVIS EVS: -0.24
RVIS percentile EVS: 36.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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