TNS3

protein-coding

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

Gene summary

Predicted to enable guanyl-nucleotide exchange factor adaptor activity. Predicted to be involved in positive regulation of Rac protein signal transduction. Predicted to act upstream of or within several processes, including bone resorption; negative regulation of Rho protein signal transduction; and podosome assembly. Located in focal adhesion. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

TENS1

MANE transcript

NM_022748.12

Inheritance

—

ClinVar variants

U:233B:51

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr7:47,275,154-47,582,558

External References & Databases

Ensembl (ENSG00000136205)

Transcript & Mutation Effects

hg38 • Region Span ~307.4 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 TNS3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 231

not providedTotal: 45

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022748.12. 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	16 clinvar	5 clinvar	27
missense			220 clinvar	21 clinvar	9 clinvar	250
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	233	37	14	284

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 60 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022748.12	RefSeq	NP_073585.8	26	MANE Select
ENST00000311160.14	Ensembl	ENSP00000312143.9	26	MANE Select
NM_001410877.1	RefSeq	NP_001397806.1	31	Standard
NM_001410878.1	RefSeq	NP_001397807.1	31	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
MET interacts with TNS proteins
Fibroblast growth factor-1
EGFR1
MET promotes cell motility

Biological Process

positive regulation of cell population proliferation
cell migration
lung alveolus development

Molecular Function

protein binding

Cellular Component

cytosol
focal adhesion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398879
Coding exons: 26
Length: 307405
Individuals with no LoFs: 124804
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 124820
p: 0.0000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.945	785	863	0.910	0.0000525	9346
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000084	0.000079	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.141

Intolerance Scores

LoFtool: 0.0417
RVIS EVS: 0.13
RVIS percentile EVS: 63.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.258

Gene Damage Prediction

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