LAT (linker for activation of T cells)

Gene

• Entrez ID: 27040
• Gene name: Linker for activation of T cells
• Gene symbol: LAT
• Synonyms: IMD52, LAT1, pp36
• 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

SNPs

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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000165	Process	MAPK cascade	TAS
GO:0001772	Component	Immunological synapse	IBA	21873635
GO:0001772	Component	Immunological synapse	IDA	12646565
GO:0002250	Process	Adaptive immune response	IEA
GO:0005515	Function	Protein binding	IPI	9489702, 10811803, 12186560, 12646565, 12857726, 14722116, 16938345, 24642916, 24658140, 25416956, 31980649
GO:0005794	Component	Golgi apparatus	IDA
GO:0005886	Component	Plasma membrane	IDA
GO:0005886	Component	Plasma membrane	TAS
GO:0006954	Process	Inflammatory response	IBA	21873635
GO:0006955	Process	Immune response	IBA	21873635
GO:0006955	Process	Immune response	IDA	15100278
GO:0007229	Process	Integrin-mediated signaling pathway	IDA	15100278
GO:0007265	Process	Ras protein signal transduction	IMP	12646565
GO:0008180	Component	COP9 signalosome	ISS
GO:0016021	Component	Integral component of membrane	IDA	12646565
GO:0019722	Process	Calcium-mediated signaling	IMP	12646565
GO:0019901	Function	Protein kinase binding	IBA	21873635
GO:0019901	Function	Protein kinase binding	IPI	12186560
GO:0030159	Function	Signaling receptor complex adaptor activity	IDA	9489702
GO:0035556	Process	Intracellular signal transduction	IBA	21873635
GO:0035556	Process	Intracellular signal transduction	IDA	12646565
GO:0038095	Process	Fc-epsilon receptor signaling pathway	TAS
GO:0042110	Process	T cell activation	TAS	12186560
GO:0043303	Process	Mast cell degranulation	IEA
GO:0045121	Component	Membrane raft	TAS	12496963, 14722116
GO:0045860	Process	Positive regulation of protein kinase activity	IBA	21873635
GO:0045860	Process	Positive regulation of protein kinase activity	IEP	14624253
GO:0050852	Process	T cell receptor signaling pathway	TAS
GO:0050863	Process	Regulation of T cell activation	IBA	21873635
GO:0050863	Process	Regulation of T cell activation	IMP	12646565

Other IDs

• MIM: 602354
• HGNC: 18874
• e!Ensembl: ENSG00000213658

Protein

• UniProt ID: 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

• Sequence:

  MEEAILVPCVLGLLLLPILAMLMALCVHCHRLPGSYDSTSSDSLYPRGIQFKRPHTVAPW
  PPAYPPVTSYPPLSQPDLLPIPRSPQPLGGSHRTPSSRRDSDGANSVASYENEGASGIRG
  AQAGWGVWGPSWTRLTPVSLPPEPACEDADEDEDDYHNPGYLVVLPDSTPATSTAAPSAP
  ALSTPGIRDSAFSMESIDDYVNVPESGESAEASLDGSREYVNVSQELHPGAAKTEPAALS
  SQEAEEVEEEGAPDYENLQELN

• Sequence length: 262

Pathways

KEGG:

Ras signaling pathway
Rap1 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
Fc epsilon RI signaling pathway
Fc gamma R-mediated phagocytosis
Yersinia infection
PD-L1 expression and PD-1 checkpoint pathway in cancer

Reactome:

GPVI-mediated activation cascade
Generation of second messenger molecules
DAP12 signaling
Fc epsilon receptor (FCERI) signaling
FCERI mediated MAPK activation
FCERI mediated Ca+2 mobilization
RAF/MAP kinase cascade

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Amyotrophic lateral sclerosis	Amyotrophic Lateral Sclerosis, Familial	rs267607084, rs312262720, rs312262752, rs121908287, rs121908288, rs29001584, rs28941475, rs121434378, rs386134173, rs386134174, rs80356730, rs80356727, rs4884357, rs80356717, rs80356733, rs80356731, rs80356726, rs267606928, rs267606929, rs1885090126, rs121434591, rs121912431, rs121912432, rs121912433, rs121912434, rs121912435, rs121912440, rs121912436, rs121912437, rs121912438, rs121912439, rs74315452, rs121912442, rs121912443, rs121912444, rs121912446, rs121912447, rs1197141604, rs121912448, rs121912449, rs121912450, rs121912451, rs121912452, rs121912453, rs121912454, rs369600566, rs121912455, rs121912456, rs121912457, rs121912458, rs1555836889, rs121909667, rs121909668, rs121909669, rs121909671, rs121909535, rs121909537, rs121909538, rs121909539, rs121909540, rs121909542, rs121909544, rs80356734, rs367543041, rs80356740, rs80356719, rs80356721, rs80356723, rs80356725, rs387906627, rs387906628, rs387906709, rs387906710, rs387906711, rs387906829, rs387907264, rs387907265, rs387907266, rs312262739, rs312262709, rs312262749, rs200793464, rs147713329, rs312262788, rs397514262, rs63751180, rs587777132, rs730880025, rs730880026, rs730880027, rs368743618, rs730880029, rs730882255, rs730882256, rs786205611, rs121912441, rs199947197, rs780136067, rs772731615, rs879253926, rs879254294, rs764717219, rs886041390, rs750159428, rs753207473, rs267607087, rs767350733, rs778305085, rs1554707680, rs1554707622, rs1393363759, rs750959420, rs1555509569, rs1554716504, rs11556620, rs1247392012, rs142083484, rs140385286, rs749428135, rs371575563, rs1402429085, rs1218712729, rs1555179091, rs1555179087, rs746971952, rs1555836950, rs368276916, rs140376902, rs747220413, rs76731700, rs770684782, rs1200906022, rs1804449, rs1482760341, rs769898852, rs140599944, rs757972700, rs1555451521, rs1592362719, rs1555836803, rs763455928, rs1378590183, rs1583695322, rs1362178149, rs1197928094, rs368751524, rs1555509609, rs1574787779, rs1601157750, rs1301635320, rs1341055534, rs1402092579, rs1568809172, rs1555836170, rs1315541036, rs1339283341, rs1643659556, rs1644506661, rs1435710212, rs1553122918, rs1689580631, rs374047961, rs775935265, rs2076486420, rs1820836522, rs757260058, rs1844420892, rs1833371664, rs1833438306, rs1833451208, rs2083790483, rs1303294230, rs1226110412, rs2053207945, rs2053208751, rs2053501632, rs2053539304, rs1567479067, rs544088874, rs1228194239, rs1568807400, rs1169198442, rs2049594204, rs2049594311, rs1568810641, rs1568811372, rs2049618449, rs1476760624, rs2079347087	11796754
Anemia	Anemia, Hemolytic	rs118204044, rs118204045, rs118204046, rs121918330, rs869320719, rs869312029, rs121918332, rs869320724, rs767094129, rs786205058, rs786205059, rs137853119, rs137853120, rs137853121, rs1384933966, rs137853122, rs137853123, rs786205060, rs267607121, rs121908584, rs80338697, rs80338699, rs120074166, rs120074167, rs1050828, rs74575103, rs137852314, rs5030868, rs137852316, rs137852317, rs137852318, rs137852319, rs137852320, rs137852321, rs137852322, rs137852323, rs137852324, rs72554665, rs387906468, rs5030872, rs137852326, rs137852333, rs137852327, rs137852328, rs137852329, rs137852330, rs137852331, rs137852332, rs137852334, rs137852335, rs137852336, rs137852339, rs76645461, rs137852340, rs137852341, rs78478128, rs137852343, rs137852344, rs137852345, rs587776730, rs137852346, rs137852347, rs137852349, rs2070404412, rs2070350038, rs2070350009, rs137852303, rs137852304, rs33946267, rs34378160, rs33933298, rs11549407, rs35724775, rs34598529, rs41469945, rs267607201, rs80338694, rs80338696, rs387907018, rs398123546, rs78365220, rs587777100, rs587777101, rs483352840, rs869312752, rs765487627, rs1557229599, rs1557230040, rs1555524842, rs782090947, rs1358275550, rs1557229736, rs1557230573, rs1556323334, rs1233124208, rs1293528130, rs146864395, rs1595503440, rs1603411214, rs137852325, rs1575247302, rs1603411177, rs1336651679, rs782322505
Immunodeficiency	IMMUNODEFICIENCY 52	rs1565678077, rs121908002, rs1421444086, rs1565688667, rs944235493, rs121918314, rs587776713, rs137852678, rs587776714, rs128620188, rs2147483647, rs1569556522, rs137853331, rs137853332, rs179363866, rs483352928, rs121918659, rs111033580, rs111033581, rs74315290, rs193922740, rs193922741, rs104894199, rs483352927, rs104894286, rs1571865049, rs886041032, rs2069709, rs587776822, rs74315444, rs587776823, rs1315265916, rs104893893, rs104893894, rs121434560, rs387906572, rs587776853, rs104893973, rs587776854, rs587776855, rs587776857, rs104893974, rs121912715, rs1393707607, rs113994136, rs387906593, rs587776870, rs387906763, rs387906913, rs199469663, rs199469662, rs199469664, rs193922640, rs193922641, rs193922645, rs398122890, rs387907316, rs397514710, rs398122383, rs397515453, rs397514332, rs398123058, rs397518423, rs587777075, rs199676861, rs77563738, rs587777337, rs28730670, rs587777389, rs587777390, rs587777413, rs587777414, rs587777415, rs587777416, rs267608260, rs267608261, rs587778405, rs587777446, rs587777562, rs587777564, rs587777565, rs869320745, rs587777709, rs606231305, rs672601318, rs727503779, rs727503780, rs730880296, rs786200953, rs375323253, rs794729666, rs886041037, rs886041038, rs796051887, rs796051888, rs749956849, rs199641706, rs775739391, rs869312886, rs869312857, rs879253731, rs879253732, rs201025290, rs770927552, rs878853275, rs878853276, rs878853277, rs878853278, rs1567506566, rs886037920, rs886037921, rs750610248, rs200044623, rs886043118, rs886060531, rs1057519074, rs1057519075, rs1057518744, rs1057519079, rs1057518745, rs1057518746, rs1057518747, rs782178147, rs55729925, rs1064795762, rs1064794957, rs1085307649, rs745463649, rs773694113, rs1192554889, rs779575307, rs1554051075, rs1554051067, rs1554051033, rs1554067182, rs1555167566, rs1555169270, rs1555908409, rs1555719963, rs1554064929, rs768091235, rs1404084330, rs144104577, rs1553238837, rs1553243550, rs1554020278, rs1554066684, rs762678772, rs570768621, rs1443126481, rs1553721236, rs121434258, rs888230251, rs1759915032, rs1759514836, rs138156467, rs1560914625, rs755373718, rs1561423197, rs1560938296, rs200803157, rs766555082, rs201543770, rs114951157, rs775578531, rs201128237, rs778624945, rs1563340753, rs1561772403, rs1484948342, rs777878144, rs1562364898, rs1561254290, rs1569296295, rs1568815169, rs1568822574, rs1571880832, rs934523851, rs1922072844, rs1266114717, rs137869655, rs869320689, rs1571880941, rs1580875488, rs1581303476, rs1448018291, rs1390410878, rs774803573, rs1591278347, rs1602300615, rs1601340933, rs757598952, rs1181595292, rs1408683294, rs1595843113, rs1595848141, rs779560450, rs1595816926, rs1601861196, rs1601861199, rs756541321, rs1594389703, rs1594390415, rs1581401865, rs1236009877, rs753213766, rs778993919, rs1602878106, rs141698985, rs1264504989, rs1580974401, rs2093571190, rs530286781, rs2086875746, rs2089298923, rs1206185362, rs1581573705, rs1596718225, rs1004337827, rs1573613529, rs1574636674, rs1574657735, rs1574657762, rs1574672718, rs1581573640, rs1553657429, rs200666300, rs1578735747, rs1578771211, rs1578793312, rs1578795536, rs1578809101, rs1578811073, rs1578811245, rs1171694504, rs1578971328, rs140800288, rs374333820, rs1584926133, rs1585040113, rs1584409386, rs1379376784, rs1586940273, rs1587143342, rs748910652, rs1592117677, rs758555433, rs1596712783, rs34019455, rs147766868, rs751386365, rs1600631294, rs1489114116, rs1057520578, rs1603007888, rs1603008329, rs1574450161, rs1578735709, rs1403833564, rs1580262965, rs570910902, rs1589866171, rs1578999313, rs1582635229, rs1582637044, rs1580851910, rs1750760771, rs745453685, rs1249197356, rs201840561, rs1940921909, rs1941410085, rs1941465194, rs1321690789, rs1302362911, rs1730552437, rs2052705192, rs1941856970	27242165, 27522155
Lateral sclerosis	AMYOTROPHIC LATERAL SCLEROSIS 1, Amyotrophic Lateral Sclerosis, Sporadic	rs386134181, rs386134176, rs386134174, rs386134184, rs386134178, rs1693780539, rs1574698048	11796754
Severe combined immunodeficiency disease	Severe combined immunodeficiency due to LAT deficiency	rs886037607, rs118203993, rs121908714, rs121908739, rs121908740, rs121908735, rs121908721, rs121908722, rs121908156, rs1564414523, rs1564418254, rs1564446526, rs786205074, rs121908157, rs121908159, rs786200884, rs397515357, rs104894562, rs137852624, rs137852625, rs137852626, rs137852627, rs137852507, rs137852509, rs111033619, rs111033620, rs1569480018, rs111033621, rs137852510, rs587776729, rs111033622, rs111033617, rs111033618, rs121917894, rs121917896, rs2133313409, rs121917897, rs28933392, rs104894282, rs104894283, rs104894285, rs121918570, rs121918572, rs730880318, rs104893674, rs730880319, rs104894453, rs104894454, rs104894451, rs137853206, rs777503956, rs267606645, rs267606648, rs397515390, rs193922346, rs193922347, rs193922348, rs193922349, rs193922350, rs137852508, rs193922640, rs193922641, rs193922643, rs193922645, rs193922361, rs193922364, rs193922464, rs148508754, rs193922574, rs113994174, rs606231246, rs397514671, rs397514686, rs397514755, rs199474679, rs199474685, rs199474686, rs199474681, rs150739647, rs267605358, rs886041036, rs587777335, rs587778405, rs145092287, rs587777562, rs606231256, rs200296680, rs786205456, rs786205517, rs774202259, rs786205615, rs878853261, rs786205890, rs782753385, rs746052951, rs869025224, rs869312857, rs869320660, rs869320659, rs869320658, rs879253742, rs886037924, rs886037925, rs750610248, rs886039394, rs761242509, rs886039387, rs886041043, rs886041044, rs886042051, rs886041333, rs749481781, rs1057517747, rs1057519506, rs1057523762, rs1057521062, rs1057520644, rs761583890, rs751635016, rs55729925, rs1064793248, rs1064793347, rs1064794027, rs781410769, rs1555524788, rs1486760100, rs769633203, rs1556330713, rs1555322558, rs1556330234, rs1556330755, rs1556329779, rs1556330552, rs1556329822, rs1556330286, rs1556331272, rs2146178281, rs376610445, rs757797994, rs775704953, rs1555743321, rs1564995660, rs1564995662, rs1556330249, rs144104577, rs886041796, rs1026474882, rs570768621, rs1556330562, rs1556330568, rs780014431, rs778343059, rs1555844617, rs1567629968, rs1567628757, rs1567629943, rs1567632864, rs1567632829, rs1567626023, rs1559328006, rs1561423197, rs1452483770, rs1568400897, rs1569479913, rs1568404443, rs1569480047, rs1563340753, rs368303189, rs1568431262, rs1568431102, rs1561424886, rs1602289943, rs1241698978, rs1569479994, rs1569480082, rs1602289649, rs1573261820, rs770985198, rs1589050343, rs1340132582, rs1589064324, rs1589070600, rs1213680890, rs149316157, rs1599873591, rs755706305, rs1602288051, rs1602289411, rs1602289183, rs1583513256, rs1589136659, rs1380154594, rs1011307501, rs1599876167, rs1569967422, rs1602289631, rs1573262398, rs760191638, rs1592117677, rs1640406042, rs372597855, rs1839558393, rs1839622622, rs1839957089, rs777008519, rs1233957241, rs2092261618, rs1839255008, rs1677695565, rs936493226, rs1162344514, rs991089005

Unknown
Disease name	Disease term	dbSNP ID	References
Immunologic deficiency syndromes	Immunologic Deficiency Syndromes
Lung diseases	Chronic lung disease