Gene Gene information from NCBI Gene database. Download as csv Download as pdf
Entrez ID	27040
Gene name	Linker for activation of T cells
Gene symbol	LAT
Synonyms (NCBI Gene)	IMD52LAT1pp36
Chromosome	16
Chromosome location	16p11.2
Summary	The protein encoded by this gene is phosphorylated by ZAP-70/Syk protein tyrosine kinases following activation of the T-cell antigen receptor (TCR) signal transduction pathway. This transmembrane protein localizes to lipid rafts and acts as a docking site

SNP ID	Visualize variation	Clinical significance	Consequence
rs781410769	GGG>-,G	Pathogenic	Coding sequence variant, inframe deletion, frameshift variant
rs1363494222	TGTG>-,TGTGTGTG	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1555524788	->T	Pathogenic	Frameshift variant, coding sequence variant

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miRTarBase ID	miRNA	Experiments
MIRT1105128	hsa-miR-1225-3p	CLIP-seq
MIRT1105129	hsa-miR-1233	CLIP-seq
MIRT1105130	hsa-miR-2392	CLIP-seq
MIRT1105131	hsa-miR-3605-5p	CLIP-seq
MIRT1105132	hsa-miR-3943	CLIP-seq
MIRT1105133	hsa-miR-4534	CLIP-seq
MIRT1105134	hsa-miR-4663	CLIP-seq
MIRT1105135	hsa-miR-4802-5p	CLIP-seq
MIRT1105136	hsa-miR-765	CLIP-seq
MIRT2029019	hsa-miR-1234	CLIP-seq
MIRT2029020	hsa-miR-3135b	CLIP-seq
MIRT2029021	hsa-miR-3155	CLIP-seq
MIRT2029022	hsa-miR-3155b	CLIP-seq
MIRT2029023	hsa-miR-3652	CLIP-seq
MIRT2029024	hsa-miR-4430	CLIP-seq
MIRT2029025	hsa-miR-4436a	CLIP-seq
MIRT2029026	hsa-miR-4687-3p	CLIP-seq
MIRT2029027	hsa-miR-484	CLIP-seq
MIRT2259997	hsa-miR-146a	CLIP-seq
MIRT2259998	hsa-miR-146b-5p	CLIP-seq
MIRT2259999	hsa-miR-1915	CLIP-seq
MIRT2260000	hsa-miR-4269	CLIP-seq
MIRT2260001	hsa-miR-4461	CLIP-seq
MIRT2260002	hsa-miR-4652-3p	CLIP-seq
MIRT2260003	hsa-miR-4726-3p	CLIP-seq
MIRT2260004	hsa-miR-580	CLIP-seq
MIRT2260005	hsa-miR-589	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0001772	Component	Immunological synapse	IBA
GO:0001772	Component	Immunological synapse	IDA	12646565
GO:0001772	Component	Immunological synapse	IEA
GO:0002250	Process	Adaptive immune response	IEA
GO:0002260	Process	Lymphocyte homeostasis	IEA
GO:0002376	Process	Immune system process	IEA
GO:0005515	Function	Protein binding	IPI	9489702, 10811803, 12186560, 12646565, 12857726, 14722116, 16467851, 16906159, 16938345, 24642916, 24658140, 25416956, 31980649, 32296183
GO:0005794	Component	Golgi apparatus	IDA
GO:0005886	Component	Plasma membrane	IDA	9729044, 11368773
GO:0005886	Component	Plasma membrane	IDA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0005911	Component	Cell-cell junction	IEA
GO:0006954	Process	Inflammatory response	IBA
GO:0006954	Process	Inflammatory response	IEA
GO:0006955	Process	Immune response	IBA
GO:0006955	Process	Immune response	IDA	15100278
GO:0007165	Process	Signal transduction	IEA
GO:0007229	Process	Integrin-mediated signaling pathway	IDA	15100278
GO:0007265	Process	Ras protein signal transduction	IMP	12646565
GO:0008180	Component	COP9 signalosome	IEA
GO:0008180	Component	COP9 signalosome	ISS
GO:0010467	Process	Gene expression	IEA
GO:0016020	Component	Membrane	IDA	12646565
GO:0016020	Component	Membrane	IEA
GO:0019722	Process	Calcium-mediated signaling	IMP	12646565
GO:0019901	Function	Protein kinase binding	IBA
GO:0019901	Function	Protein kinase binding	IPI	12186560
GO:0030159	Function	Signaling receptor complex adaptor activity	IDA	9489702
GO:0031580	Process	Membrane raft distribution	IDA	33080222
GO:0035556	Process	Intracellular signal transduction	IBA
GO:0035556	Process	Intracellular signal transduction	IDA	12646565
GO:0035591	Function	Signaling adaptor activity	IDA	9489702
GO:0036398	Component	TCR signalosome	IDA	33080222
GO:0042110	Process	T cell activation	TAS	12186560
GO:0043303	Process	Mast cell degranulation	IEA
GO:0043410	Process	Positive regulation of MAPK cascade	IDA	11368773
GO:0045121	Component	Membrane raft	TAS	12496963, 14722116
GO:0045860	Process	Positive regulation of protein kinase activity	IEP	14624253
GO:0048872	Process	Homeostasis of number of cells	IEA
GO:0050852	Process	T cell receptor signaling pathway	IDA	23514740
GO:0050852	Process	T cell receptor signaling pathway	IDA	11368773, 25907557
GO:0050863	Process	Regulation of T cell activation	IBA
GO:0050863	Process	Regulation of T cell activation	IMP	12646565
GO:0140693	Function	Molecular condensate scaffold activity	IDA	33080222

MIM	HGNC	e!Ensembl
602354	18874	ENSG00000213658

O43561

Protein name

Linker for activation of T-cells family member 1 (36 kDa phosphotyrosine adapter protein) (pp36) (p36-38)

Protein function

Required for TCR (T-cell antigen receptor)- and pre-TCR-mediated signaling, both in mature T-cells and during their development (PubMed:23514740, PubMed:25907557). Involved in FCGR3 (low affinity immunoglobulin gamma Fc region receptor III)-medi

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF15234	LAT	1 → 262	Linker for activation of T-cells	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in thymus, T-cells, NK cells, mast cells and, at lower levels, in spleen. Present in T-cells but not B-cells (at protein level). {ECO:0000269|PubMed:16160011, ECO:0000269|PubMed:9489702}.

Sequence

MEEAILVPCVLGLLLLPILAMLMALCVHCHRLPGSYDSTSSDSLYPRGIQFKRPHTVAPW
PPAYPPVTSYPPLSQPDLLPIPRSPQPLGGSHRTPSSRRDSDGANSVASYENEGASGIRG
AQAGWGVWGPSWTRLTPVSLPPEPACEDADEDEDDYHNPGYLVVLPDSTPATSTAAPSAP
ALSTPGIRDSAFSMESIDDYVNVPESGESAEASLDGSREYVNVSQELHPGAAKTEPAALS
SQEAEEVEEEGAPDYENLQELN

Sequence length

262

Interactions

View interactions

KEGG Pathway	Reactome Pathway
Ras signaling pathway	GPVI-mediated activation cascade
Rap1 signaling pathway	Generation of second messenger molecules
NF-kappa B signaling pathway	DAP12 signaling
Natural killer cell mediated cytotoxicity	Fc epsilon receptor (FCERI) signaling
Th1 and Th2 cell differentiation	FCERI mediated MAPK activation
Th17 cell differentiation	FCERI mediated Ca+2 mobilization
T cell receptor signaling pathway	RAF/MAP kinase cascade
Fc epsilon RI signaling pathway
Fc gamma R-mediated phagocytosis
Yersinia infection
PD-L1 expression and PD-1 checkpoint pathway in cancer

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Severe combined immunodeficiency due to LAT deficiency	Pathogenic	rs749637413, rs781410769, rs1555524788	RCV001333641 RCV000490648 RCV000490650	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal. Show/Hide Unknown Diseases (15)
ALZHEIMER DISEASE	—	GWAS catalog	39998322	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AMYOTROPHIC LATERAL SCLEROSIS 1	—	CTD, Disgenet CTD, Disgenet	11796754	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION	—	GWAS catalog	40050429	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIFFUSE GASTRIC ADENOCARCINOMA	—	GWAS catalog	39862296	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTRIC CANCER	—	GWAS catalog	39862296	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTRIC CARCINOMA	—	GWAS catalog	39862296	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IMMUNODEFICIENCY 52	—	Disgenet, HPO Disgenet, HPO	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LAT-related disorder	Benign; Likely benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIVER DISEASES	—	CTD, Disgenet CTD, Disgenet	19784758	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MOTOR NEURON DISEASE	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SARCOIDOSIS	—	GWAS catalog	40075078	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
ZAP70	3	["Immunodeficiency","Sarcoidosis","Severe combined immunodeficiency"]	9	["Ras signaling pathway","NF-kappa B signaling pathway","Natural killer cell mediated cytotoxicity","Th1 and Th2 cell differentiation","Th17 cell differentiation","T cell receptor signaling pathway","Yersinia infection","PD-L1 expression and PD-1 checkpoint pathway in cancer","Generation of second messenger molecules"]	3	["HPO (Immunodeficiency)","Disgenet (Immunodeficiency)","GWAS catalog (Sarcoidosis)"]
LCK	2	["Immunodeficiency","Severe combined immunodeficiency"]	10	["NF-kappa B signaling pathway","Natural killer cell mediated cytotoxicity","Th1 and Th2 cell differentiation","Th17 cell differentiation","T cell receptor signaling pathway","Yersinia infection","PD-L1 expression and PD-1 checkpoint pathway in cancer","DAP12 signaling","GPVI-mediated activation cascade","Generation of second messenger molecules"]	4	["HPO (Immunodeficiency)","Disgenet (Immunodeficiency)","ClinGen (Severe combined immunodeficiency)","ClinVar (Severe combined immunodeficiency)"]
CD3D	3	["Immunodeficiency","Liver disease","Severe combined immunodeficiency"]	5	["Th1 and Th2 cell differentiation","Th17 cell differentiation","T cell receptor signaling pathway","PD-L1 expression and PD-1 checkpoint pathway in cancer","Generation of second messenger molecules"]	4	["HPO (Immunodeficiency)","Disgenet (Immunodeficiency)","Disgenet (Liver disease)","CTD (Liver disease)"]
CTPS1	2	["Immunodeficiency","Severe combined immunodeficiency"]	0	[]	5	["HPO (Immunodeficiency)","Disgenet (Immunodeficiency)","ClinGen (Severe combined immunodeficiency)","Orphanet (Severe combined immunodeficiency)","ClinVar (Severe combined immunodeficiency)"]
PRKDC	2	["Immunodeficiency","Severe combined immunodeficiency"]	0	[]	6	["HPO (Immunodeficiency)","Disgenet (Immunodeficiency)","ClinGen (Severe combined immunodeficiency)","GWAS catalog (Severe combined immunodeficiency)","Orphanet (Severe combined immunodeficiency)","ClinVar (Severe combined immunodeficiency)"]

LAT (linker for activation of T cells)

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