NPRL3 (NPR3 like, GATOR1 complex subunit)

Gene

• Entrez ID: 8131
• Gene name: NPR3 like, GATOR1 complex subunit
• Gene symbol: NPRL3
• Synonyms (NCBI Gene): C16orf35, CGTHBA, FFEVF3, HS-40, MARE, NPR3, RMD11
• Disease Acronyms (UniProt): FFEVF3
• Chromosome: 16
• Chromosome location: 16p13.3
• Summary: The function of the encoded protein is not known. [provided by RefSeq, Aug 2011]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs886037958	->A	Pathogenic	Frameshift variant, coding sequence variant
rs886037959	CTGT>GGATGGGTCA	Pathogenic	Splice acceptor variant, intron variant
rs886037960	->TG	Pathogenic	Frameshift variant, coding sequence variant
rs886037961	G>A,T	Pathogenic	Synonymous variant, stop gained, coding sequence variant
rs886037962	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1021001959	G>A,C	Pathogenic	5 prime UTR variant, coding sequence variant, stop gained, synonymous variant
rs1064795838	C>A	Likely-pathogenic	Intron variant, splice acceptor variant
rs1431914212	T>A,C	Likely-pathogenic	Splice acceptor variant
rs1555441032	->TG	Pathogenic	Frameshift variant, coding sequence variant
rs1555443191	C>-	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1555444207	G>C	Pathogenic	Stop gained, intron variant, 5 prime UTR variant, coding sequence variant
rs1567129567	->G	Pathogenic	Frameshift variant, coding sequence variant
rs1567129739	G>A	Pathogenic	Stop gained, coding sequence variant
rs1567134495	C>A	Likely-pathogenic	Splice donor variant
rs1567139896	ACAG>-	Pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1567142752	T>A	Likely-pathogenic	Intron variant, splice acceptor variant
rs1567152003	G>A	Pathogenic	Stop gained, 5 prime UTR variant, coding sequence variant
rs1596500172	G>C	Pathogenic	Coding sequence variant, stop gained
rs1596522300	C>A	Pathogenic	Stop gained, coding sequence variant, 5 prime UTR variant
rs1596522356	C>A	Likely-pathogenic	Stop gained, coding sequence variant, 5 prime UTR variant
rs1596526915	A>-	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1596526976	G>-	Pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1596528731	G>A	Likely-pathogenic	Intron variant, coding sequence variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT051275	hsa-miR-16-5p	CLASH	23622248
MIRT039648	hsa-miR-615-3p	CLASH	23622248
MIRT639720	hsa-miR-501-5p	HITS-CLIP	23824327
MIRT639719	hsa-miR-1248	HITS-CLIP	23824327
MIRT639718	hsa-miR-4778-3p	HITS-CLIP	23824327
MIRT639717	hsa-miR-4297	HITS-CLIP	23824327
MIRT639716	hsa-miR-5581-5p	HITS-CLIP	23824327
MIRT639715	hsa-miR-6505-5p	HITS-CLIP	23824327
MIRT639714	hsa-miR-6875-3p	HITS-CLIP	23824327
MIRT639713	hsa-miR-4659a-3p	HITS-CLIP	23824327
MIRT639712	hsa-miR-4659b-3p	HITS-CLIP	23824327
MIRT639711	hsa-miR-7850-5p	HITS-CLIP	23824327
MIRT495293	hsa-miR-6785-3p	PAR-CLIP	23708386
MIRT495294	hsa-miR-205-5p	PAR-CLIP	23708386
MIRT495292	hsa-miR-6788-3p	PAR-CLIP	23708386
MIRT639720	hsa-miR-501-5p	HITS-CLIP	23824327
MIRT639719	hsa-miR-1248	HITS-CLIP	23824327
MIRT639718	hsa-miR-4778-3p	HITS-CLIP	23824327
MIRT639717	hsa-miR-4297	HITS-CLIP	23824327
MIRT639716	hsa-miR-5581-5p	HITS-CLIP	23824327
MIRT639715	hsa-miR-6505-5p	HITS-CLIP	23824327
MIRT639714	hsa-miR-6875-3p	HITS-CLIP	23824327
MIRT639713	hsa-miR-4659a-3p	HITS-CLIP	23824327
MIRT639712	hsa-miR-4659b-3p	HITS-CLIP	23824327
MIRT639711	hsa-miR-7850-5p	HITS-CLIP	23824327
MIRT495293	hsa-miR-6785-3p	PAR-CLIP	23708386
MIRT495294	hsa-miR-205-5p	PAR-CLIP	23708386
MIRT495292	hsa-miR-6788-3p	PAR-CLIP	23708386
MIRT1191273	hsa-miR-1184	CLIP-seq
MIRT1191274	hsa-miR-1205	CLIP-seq
MIRT1191275	hsa-miR-1273d	CLIP-seq
MIRT1191276	hsa-miR-2277-3p	CLIP-seq
MIRT1191277	hsa-miR-3158-5p	CLIP-seq
MIRT1191278	hsa-miR-3194-3p	CLIP-seq
MIRT1191279	hsa-miR-3194-5p	CLIP-seq
MIRT1191280	hsa-miR-3914	CLIP-seq
MIRT1191281	hsa-miR-4268	CLIP-seq
MIRT1191282	hsa-miR-4283	CLIP-seq
MIRT1191283	hsa-miR-4307	CLIP-seq
MIRT1191284	hsa-miR-4420	CLIP-seq
MIRT1191285	hsa-miR-4508	CLIP-seq
MIRT1191286	hsa-miR-4640-5p	CLIP-seq
MIRT1191287	hsa-miR-4662a-5p	CLIP-seq
MIRT1191288	hsa-miR-4676-5p	CLIP-seq
MIRT1191289	hsa-miR-4688	CLIP-seq
MIRT1191290	hsa-miR-4726-5p	CLIP-seq
MIRT1191291	hsa-miR-4733-3p	CLIP-seq
MIRT1191292	hsa-miR-4777-5p	CLIP-seq
MIRT1191293	hsa-miR-4781-5p	CLIP-seq
MIRT1191294	hsa-miR-518d-5p	CLIP-seq
MIRT1191295	hsa-miR-519b-5p	CLIP-seq
MIRT1191296	hsa-miR-519c-5p	CLIP-seq
MIRT1191297	hsa-miR-520c-5p	CLIP-seq
MIRT1191298	hsa-miR-526a	CLIP-seq
MIRT1191299	hsa-miR-548a-3p	CLIP-seq
MIRT1191300	hsa-miR-548e	CLIP-seq
MIRT1191301	hsa-miR-548f	CLIP-seq
MIRT1191302	hsa-miR-548g	CLIP-seq
MIRT1191303	hsa-miR-550a	CLIP-seq
MIRT1191304	hsa-miR-575	CLIP-seq
MIRT1191305	hsa-miR-744	CLIP-seq
MIRT1191306	hsa-miR-760	CLIP-seq
MIRT1191276	hsa-miR-2277-3p	CLIP-seq
MIRT1191278	hsa-miR-3194-3p	CLIP-seq
MIRT1191307	hsa-miR-3616-3p	CLIP-seq
MIRT1191282	hsa-miR-4283	CLIP-seq
MIRT1191308	hsa-miR-4323	CLIP-seq
MIRT1191309	hsa-miR-4436b-3p	CLIP-seq
MIRT1191285	hsa-miR-4508	CLIP-seq
MIRT1191289	hsa-miR-4688	CLIP-seq
MIRT1191291	hsa-miR-4733-3p	CLIP-seq
MIRT1191310	hsa-miR-4758-3p	CLIP-seq
MIRT1191293	hsa-miR-4781-5p	CLIP-seq
MIRT1191305	hsa-miR-744	CLIP-seq
MIRT1191306	hsa-miR-760	CLIP-seq
MIRT2055402	hsa-miR-125a-3p	CLIP-seq
MIRT2055403	hsa-miR-3121-3p	CLIP-seq
MIRT2055404	hsa-miR-3127-5p	CLIP-seq
MIRT2055405	hsa-miR-3130-3p	CLIP-seq
MIRT2055406	hsa-miR-3158-3p	CLIP-seq
MIRT2055407	hsa-miR-3189-5p	CLIP-seq
MIRT1191279	hsa-miR-3194-5p	CLIP-seq
MIRT2055408	hsa-miR-3918	CLIP-seq
MIRT2055409	hsa-miR-3925-3p	CLIP-seq
MIRT2055410	hsa-miR-4436a	CLIP-seq
MIRT1191286	hsa-miR-4640-5p	CLIP-seq
MIRT2055411	hsa-miR-4655-3p	CLIP-seq
MIRT2055412	hsa-miR-4690-3p	CLIP-seq
MIRT2055413	hsa-miR-4690-5p	CLIP-seq
MIRT1191290	hsa-miR-4726-5p	CLIP-seq
MIRT1191310	hsa-miR-4758-3p	CLIP-seq
MIRT2055414	hsa-miR-4793-3p	CLIP-seq
MIRT2055415	hsa-miR-515-5p	CLIP-seq
MIRT2055416	hsa-miR-544	CLIP-seq
MIRT2055417	hsa-miR-766	CLIP-seq
MIRT2284393	hsa-miR-3185	CLIP-seq
MIRT2284394	hsa-miR-3192	CLIP-seq
MIRT2284395	hsa-miR-3689a-3p	CLIP-seq
MIRT2284396	hsa-miR-3689c	CLIP-seq
MIRT2284397	hsa-miR-4728-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003281	Process	Ventricular septum development	IEA
GO:0005096	Function	GTPase activator activity	IDA	23723238
GO:0005515	Function	Protein binding	IPI	19521502, 28199315, 28514442
GO:0005765	Component	Lysosomal membrane	IDA	28199306
GO:0032007	Process	Negative regulation of TOR signaling	IBA	21873635
GO:0032007	Process	Negative regulation of TOR signaling	IMP	23723238
GO:0034198	Process	Cellular response to amino acid starvation	IBA	21873635
GO:0034198	Process	Cellular response to amino acid starvation	IMP	23723238
GO:0035909	Process	Aorta morphogenesis	IEA
GO:0038202	Process	TORC1 signaling	IBA	21873635
GO:0043547	Process	Positive regulation of GTPase activity	IEA
GO:0048738	Process	Cardiac muscle tissue development	IEA
GO:0060021	Process	Roof of mouth development	IEA
GO:1990130	Component	GATOR1 complex	IBA	21873635
GO:1990130	Component	GATOR1 complex	IDA	23723238
GO:2000785	Process	Regulation of autophagosome assembly	IBA	21873635

Other IDs

• MIM: 600928
• HGNC: 14124
• e!Ensembl: ENSG00000103148

Protein

• UniProt ID: Q12980
• Protein name: GATOR1 complex protein NPRL3 (-14 gene protein) (Alpha-globin regulatory element-containing gene protein) (Nitrogen permease regulator 3-like protein) (Protein CGTHBA)
• Protein function: As a component of the GATOR1 complex functions as an inhibitor of the amino acid-sensing branch of the mTORC1 pathway (PubMed:23723238, PubMed:29590090, PubMed:35338845). In response to amino acid depletion, the GATOR1 complex has GTPase activat
• PDB: 6CES, 6CET, 7T3A, 7T3B, 7T3C, 8FW5
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF03666	NPR3	63 → 112	Nitrogen Permease regulator of amino acid transport activity 3	Family
  PF03666	NPR3	101 → 418	Nitrogen Permease regulator of amino acid transport activity 3	Family

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed. Expressed in the frontal lobe cortex as well as in the temporal, parietal, and occipital lobes (PubMed:26505888, PubMed:27173016). {ECO:0000269|PubMed:26505888, ECO:0000269|PubMed:27173016}.
• Sequence:

  MRDNTSPISVILVSSGSRGNKLLFRYPFQRSQEHPASQTSKPRSRYAASNTGDHADEQDG
  DSRFSDVILATILATKSEMCGQKFELKIDNVRFVGHPTLLQHALGQISKTDPSPKREAPT
  MILFNVVFALRANADPSVINCLHNLSRRIATVLQHEERRCQYLTREAKLILALQDEVSAM
  ADGNEGPQSPFHHILPKCKLARDLKEAYDSLCTSGVVRLHINSWLEVSFCLPHKIHYAAS
  SLIPPEAIERSLKAIRPYHALLLLSDEKSLLGELPIDCSPALVRVIKTTSAVKNLQQLAQ
  DADLALLQVFQLAAHLVYWGKAIIIYPLCENNVYMLSPNASVCLYSPLAEQFSHQFPSHD
  LPSVLAKFSLPVSLSEFRNPLAPAVQETQLIQMVVWMLQRRLLIQLHTYVCLMASPSEEE
  PRPREDDVPFTARVGGRSLSTPNALSFGSPTSSDDMTLTSPSMDNSSAELLPSGDSPLNQ
  RMTENLLASLSEHERAAILSVPAAQNPEDLRMFARLLHYFRGRHHLEEIMYNENTRRSQL
  LMLFDKFRSVLVVTTHEDPVIAVFQALLP

• Sequence length: 569

Pathways

KEGG:

mTOR signaling pathway

Reactome:

Amino acids regulate mTORC1

Associated diseases

Causal
Disease term	Disease name	dbSNP ID	References
Anemia	Anemia, Sickle Cell	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	23406172
Diabetes mellitus	Diabetes Mellitus, Non-Insulin-Dependent	rs587776515, rs61730328, rs606231121, rs606231122, rs79020217, rs77625743, rs78378398, rs606231123, rs1362648752, rs104893649, rs80356624, rs80356616, rs80356625, rs80356611, rs104894237, rs80356613, rs387906407, rs151344623, rs28938469, rs28936371, rs137852672, rs80356637, rs80356642, rs80356653, rs137852673, rs137852674, rs80356634, rs80356651, rs193929360, rs137853334, rs137853335, rs137853336, rs1600731198, rs137853338, rs121964882, rs121964883, rs387906511, rs121964884, rs121964885, rs2147483647, rs387906512, rs121964887, rs121964888, rs121964889, rs121964890, rs121964891, rs28934878, rs74315383, rs121964893, rs886037620, rs886037621, rs121434593, rs121913150, rs587776825, rs137853236, rs2135842335, rs137853237, rs137853238, rs2135818776, rs1566092470, rs1463923467, rs137853243, rs137853244, rs2135839114, rs137853245, rs2135847417, rs121918407, rs104894005, rs104894006, rs80356655, rs104894008, rs104894009, rs104894010, rs104894011, rs80356654, rs104894016, rs193929376, rs193929374, rs193929375, rs193929373, rs80356669, rs80356664, rs193929366, rs1048095, rs193929355, rs193929356, rs1259467443, rs104893642, rs387906777, rs193922396, rs193922400, rs193922401, rs137852676, rs193922407, rs193922638, rs193922257, rs193922258, rs193922259, rs193922260, rs193922261, rs193922262, rs193922263, rs193922264, rs193922265, rs193922268, rs193921338, rs193922269, rs193922272, rs193922273, rs193922275, rs193922278, rs193922279, rs193922280, rs193922281, rs193922282, rs193922283, rs193922284, rs193922286, rs193922287, rs193922289, rs193922291, rs193922295, rs193922297, rs193922300, rs193922302, rs193922303, rs193922308, rs193922313, rs193922314, rs144723656, rs193922315, rs193922316, rs193922317, rs148311934, rs193922319, rs193922320, rs193922326, rs193922329, rs193922330, rs193922331, rs193922335, rs193922336, rs193922338, rs193922340, rs193922341, rs193922471, rs193922475, rs193922476, rs193922479, rs80356663, rs193922355, rs193922356, rs193922576, rs193922578, rs193922582, rs193922588, rs193922592, rs193922594, rs193922596, rs386134267, rs193922598, rs193922599, rs193922600, rs193922604, rs193922605, rs397514580, rs397515519, rs267601516, rs587780343, rs587780345, rs587780346, rs587780347, rs587780357, rs148954387, rs587783672, rs587783669, rs786204676, rs794727236, rs151344624, rs794727775, rs794727839, rs199946797, rs869320673, rs796065047, rs759072800, rs797045595, rs797045209, rs797045207, rs797045213, rs863225280, rs149703259, rs864321656, rs139964066, rs777870079, rs878853246, rs769268803, rs886039380, rs886041392, rs886041391, rs886042610, rs143064649, rs1057516192, rs746480424, rs1057516281, rs576684889, rs754728827, rs1057520291, rs1057520779, rs893256143, rs1057520504, rs1057524790, rs1057524902, rs1057524904, rs1057524905, rs764232985, rs1064793998, rs1064794268, rs769086289, rs369429452, rs1085307913, rs1131691416, rs765432081, rs1131692182, rs748749585, rs1554335441, rs762263694, rs1312678560, rs767565869, rs1375656631, rs1554335391, rs1360415315, rs1554335616, rs1554335752, rs1554909277, rs769518471, rs757171524, rs768951263, rs762703502, rs1555212248, rs1555212359, rs1555813319, rs1555816654, rs371977235, rs1415041911, rs1554334894, rs1260178539, rs1554335421, rs1555211904, rs779184183, rs1554335564, rs200670692, rs1400535021, rs1554334872, rs1555212749, rs1553876668, rs1553878211, rs954727530, rs1554924035, rs372307320, rs925231098, rs1554913069, rs1554933565, rs766431403, rs746714109, rs751279984, rs770664202, rs1008906426, rs758844607, rs1554924540, rs1566092307, rs753998395, rs1565885935, rs1167124132, rs1376796469, rs556436603, rs1562715657, rs1486280029, rs1564869850, rs755259997, rs769569410, rs1172328722, rs1286294151, rs1375557127, rs1568731279, rs1562715426, rs556581174, rs1564865302, rs1565886545, rs1568724014, rs1392795567, rs781260712, rs1562719705, rs1382448285, rs1564977373, rs750586210, rs1598842892, rs1583592247, rs780612692, rs1593060859, rs1476637197, rs751279776, rs1593060890, rs1191912908, rs1167675604, rs1583601110, rs1593058932, rs778611627, rs753296261	17463246
Epilepsy	Epilepsy, Partial, with Variable Foci, EPILEPSY, FAMILIAL FOCAL, WITH VARIABLE FOCI 3, Familial focal epilepsy with variable foci	rs113994140, rs28937874, rs1589762127, rs104894166, rs28939075, rs2134001459, rs104894167, rs119488099, rs119488100, rs387906420, rs121917752, rs121918622, rs281865564, rs387907313, rs397514670, rs768241563, rs587776973, rs587776974, rs587776975, rs879255234, rs587776976, rs587776977, rs121917993, rs398123588, rs13306758, rs587777458, rs587777459, rs541024038, rs797044545, rs730882240, rs786205703, rs794726859, rs796053126, rs796053035, rs796053216, rs796052839, rs869025201, rs797044999, rs797044998, rs797045045, rs794726762, rs869312971, rs869312972, rs879255652, rs886037938, rs886037958, rs886037959, rs886037960, rs886037961, rs886037962, rs886037965, rs886037966, rs886039245, rs886039246, rs886039251, rs886039252, rs772872014, rs886039253, rs886039256, rs757511744, rs886039261, rs886039263, rs578185749, rs886039266, rs886039268, rs886039269, rs886039273, rs368820286, rs1057518801, rs1057518688, rs1057519107, rs1057519273, rs752753379, rs767795673, rs1057519424, rs755946598, rs760609867, rs1057521066, rs1057524233, rs1060501488, rs1060501487, rs755127868, rs751533302, rs771373457, rs1475605360, rs1555401942, rs1553567864, rs200661329, rs766667249, rs1556607762, rs1555882921, rs1555882867, rs1555900914, rs1553546836, rs77216276, rs755595256, rs747661902, rs2105890565, rs1021001959, rs1555441032, rs1555439541, rs1556526609, rs1315483224, rs759952667, rs1555885023, rs1553456695, rs1555942720, rs1569083500, rs1559127505, rs1206309859, rs1567139896, rs1567134495, rs1431914212, rs1569166925, rs1569255443, rs1568955379, rs1567152003, rs374158137, rs1567129567, rs1569523728, rs1568991466, rs1569186093, rs1569254004, rs1372605067, rs1569067939, rs1568963062, rs1563959514, rs1569012755, rs1559118914, rs1602338615, rs1596522356, rs1364913665, rs1596522300, rs1596526976, rs1229740428, rs1596385588, rs1596500172, rs1596505517, rs1601925213, rs1601970168, rs1602010382, rs1602903591, rs1603014297, rs1603014708, rs1601875057, rs1601970824, rs1601755632, rs1587393982, rs1592977444, rs1575562076, rs1570998206, rs1588057922, rs1596528731, rs1602349641, rs1587401875, rs2065899210, rs1596526915, rs2093486364, rs2056165149, rs2056100951, rs781482552, rs1899868619, rs1900088045, rs1898675878, rs1898686157, rs1898837245, rs1898844513, rs2082841677, rs2085727988, rs2092933941, rs2091657024, rs1899864955, rs1898844907, rs2083056830, rs2084070588, rs1899713412, rs2082695884, rs1977106116, rs1977105425, rs1443687532	26505888, 27173016, 26285051

Unknown
Disease term	Disease name	Evidence	References	Source
Pulmonary Fibrosis	Pulmonary Fibrosis			GWAS

Associations from Text Mining
Disease Name	Relationship Type	References
alpha Thalassemia	Associate	10910890, 32720864
Anemia	Associate	32720864
Anemia Hypochromic	Associate	32720864
Anemia hypochromic microcytic	Associate	32720864
Anemia Sickle Cell	Associate	23406172, 29590102
Cerulean cataract	Associate	23406172
Cortical Dysplasia Focal Epilepsy Syndrome	Associate	26786403
Drug Resistant Epilepsy	Associate	37099548
Endometrial Neoplasms	Associate	34970268
Epilepsies Partial	Associate	36639812
Epilepsy	Associate	26786403, 30093711, 36639812
Epilepsy Nocturnal Frontal Lobe Type 1	Associate	26786403
Epilepsy Partial with Variable Foci	Associate	37099548
Fabry Disease	Associate	12614224
Hemolysis	Associate	23406172
Hemolytic Uremic Syndrome	Associate	23406172
Ichthyosis Lamellar	Associate	32720864
Psychotic Disorders	Associate	39950246
Rare Diseases	Associate	32720864
Seizures	Associate	37099548
Thalassemia	Associate	34690349
Vaginal Discharge	Associate	37099548