GYS2 (glycogen synthase 2)

Gene

• Entrez ID: 2998
• Gene name: Glycogen synthase 2
• Gene symbol: GYS2
• Synonyms (NCBI Gene): -
• Chromosome: 12
• Chromosome location: 12p12.1
• Summary: The protein encoded by this gene, liver glycogen synthase, catalyzes the rate-limiting step in the synthesis of glycogen - the transfer of a glucose molecule from UDP-glucose to a terminal branch of the glycogen molecule. Mutations in this gene cause glyc

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs117639846	C>G	Conflicting-interpretations-of-pathogenicity, benign	Coding sequence variant, genic downstream transcript variant, missense variant
rs121918419	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained
rs121918421	C>G	Pathogenic	Coding sequence variant, missense variant
rs121918423	T>C	Pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs121918424	A>G	Pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant
rs121918425	G>C,T	Pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant
rs146195866	G>A,T	Pathogenic	Synonymous variant, stop gained, coding sequence variant
rs150382575	G>A,T	Pathogenic, likely-pathogenic	Synonymous variant, stop gained, coding sequence variant
rs201157731	G>A	Pathogenic	Stop gained, coding sequence variant
rs267603422	G>A,C	Pathogenic	Missense variant, stop gained, coding sequence variant
rs372079212	C>A	Pathogenic	Splice donor variant
rs587776831	C>G,T	Pathogenic	Splice donor variant
rs746120293	CACAGTATAGATGCCTCCAACTGTTAAA>-	Pathogenic	Coding sequence variant, genic upstream transcript variant, intron variant, upstream transcript variant, splice acceptor variant
rs764539267	C>T	Likely-pathogenic	Downstream transcript variant, splice donor variant, genic downstream transcript variant
rs766733439	C>T	Likely-pathogenic	Splice acceptor variant, genic downstream transcript variant
rs771205749	T>-	Pathogenic, likely-pathogenic	Coding sequence variant, frameshift variant
rs781511110	C>A	Likely-pathogenic	Splice donor variant
rs863224039	A>G,T	Likely-pathogenic	Genic downstream transcript variant, missense variant, coding sequence variant
rs1064793142	T>A	Likely-pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant
rs1064793143	A>C	Likely-pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant
rs1307281520	G>-	Pathogenic	Coding sequence variant, stop gained
rs1555156695	AAGTCTTTTCAAGATCAAAGTCGAGATGACTAAAACAAAACAAAACCAAACAGTTTCAAATGAAATACAGCAACA>-	Pathogenic	Intron variant, coding sequence variant, splice acceptor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT032359	hsa-let-7b-5p	Proteomics	18668040
MIRT649853	hsa-miR-4423-3p	HITS-CLIP	23824327
MIRT649852	hsa-miR-6794-3p	HITS-CLIP	23824327
MIRT649851	hsa-miR-6509-3p	HITS-CLIP	23824327
MIRT649850	hsa-miR-4436b-5p	HITS-CLIP	23824327
MIRT649849	hsa-miR-6875-3p	HITS-CLIP	23824327
MIRT649848	hsa-miR-4659a-3p	HITS-CLIP	23824327
MIRT649847	hsa-miR-4659b-3p	HITS-CLIP	23824327
MIRT649853	hsa-miR-4423-3p	HITS-CLIP	23824327
MIRT649852	hsa-miR-6794-3p	HITS-CLIP	23824327
MIRT649851	hsa-miR-6509-3p	HITS-CLIP	23824327
MIRT649850	hsa-miR-4436b-5p	HITS-CLIP	23824327
MIRT649849	hsa-miR-6875-3p	HITS-CLIP	23824327
MIRT649848	hsa-miR-4659a-3p	HITS-CLIP	23824327
MIRT649847	hsa-miR-4659b-3p	HITS-CLIP	23824327
MIRT1039029	hsa-miR-130a	CLIP-seq
MIRT1039030	hsa-miR-130b	CLIP-seq
MIRT1039031	hsa-miR-181a	CLIP-seq
MIRT1039032	hsa-miR-181b	CLIP-seq
MIRT1039033	hsa-miR-181c	CLIP-seq
MIRT1039034	hsa-miR-181d	CLIP-seq
MIRT1039035	hsa-miR-196a	CLIP-seq
MIRT1039036	hsa-miR-196b	CLIP-seq
MIRT1039037	hsa-miR-301a	CLIP-seq
MIRT1039038	hsa-miR-301b	CLIP-seq
MIRT1039039	hsa-miR-3666	CLIP-seq
MIRT1039040	hsa-miR-3927	CLIP-seq
MIRT1039041	hsa-miR-4262	CLIP-seq
MIRT1039042	hsa-miR-4295	CLIP-seq
MIRT1039043	hsa-miR-454	CLIP-seq
MIRT1039044	hsa-miR-4671-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004373	Function	Glycogen (starch) synthase activity	EXP	9691087
GO:0004373	Function	Glycogen (starch) synthase activity	IBA	21873635
GO:0004373	Function	Glycogen (starch) synthase activity	IDA	1731614
GO:0004373	Function	Glycogen (starch) synthase activity	ISS
GO:0005737	Component	Cytoplasm	IBA	21873635
GO:0005737	Component	Cytoplasm	ISS
GO:0005829	Component	Cytosol	ISS
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	ISS
GO:0005938	Component	Cell cortex	ISS
GO:0005978	Process	Glycogen biosynthetic process	IBA	21873635
GO:0005978	Process	Glycogen biosynthetic process	IDA	1731614
GO:0005978	Process	Glycogen biosynthetic process	IEA
GO:0005978	Process	Glycogen biosynthetic process	ISS
GO:0005978	Process	Glycogen biosynthetic process	TAS
GO:0006091	Process	Generation of precursor metabolites and energy	TAS	9691087
GO:0009749	Process	Response to glucose	ISS
GO:0030864	Component	Cortical actin cytoskeleton	ISS
GO:0043265	Component	Ectoplasm	ISS
GO:0061547	Function	Glycogen synthase activity, transferring glucose-1-phosphate	TAS

Other IDs

• MIM: 138571
• HGNC: 4707
• e!Ensembl: ENSG00000111713

Protein

• UniProt ID: P54840
• Protein name: Glycogen [starch] synthase, liver (EC 2.4.1.11) (Glycogen synthase 2)
• Protein function: Glycogen synthase participates in the glycogen biosynthetic process along with glycogenin and glycogen branching enzyme. Extends the primer composed of a few glucose units formed by glycogenin by adding new glucose units to it. In this context,
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05693	Glycogen_syn	32 → 667	Glycogen synthase	Family

• Tissue specificity: TISSUE SPECIFICITY: Specifically expressed in liver (at protein level). {ECO:0000269|PubMed:1731614}.
• Sequence:

  MLRGRSLSVTSLGGLPQWEVEELPVEELLLFEVAWEVTNKVGGIYTVIQTKAKTTADEWG
  ENYFLIGPYFEHNMKTQVEQCEPVNDAVRRAVDAMNKHGCQVHFGRWLIEGSPYVVLFDI
  GYSAWNLDRWKGDLWEACSVGIPYHDREANDMLIFGSLTAWFLKEVTDHADGKYVVAQFH
  EWQAGIGLILSRARKLPIATIFTTHATLLGRYLCAANIDFYNHLDKFNIDKEAGERQIYH
  RYCMERASVHCAHVFTTVSEITAIEAEHMLKRKPDVVTPNGLNVKKFSAVHEFQNLHAMY
  KARIQDFVRGHFYGHLDFDLEKTLFLFIAGRYEFSNKGADIFLESLSRLNFLLRMHKSDI
  TVMVFFIMPAKTNNFNVETLKGQAVRKQLWDVAHSVKEKFGKKLYDALLRGEIPDLNDIL
  DRDDLTIMKRAIFSTQRQSLPPVTTHNMIDDSTDPILSTIRRIGLFNNRTDRVKVILHPE
  FLSSTSPLLPMDYEEFVRGCHLGVFPSYYEPWGYTPAECTVMGIPSVTTNLSGFGCFMQE
  HVADPTAYGIYIVDRRFRSPDDSCNQLTKFLYGFCKQSRRQRIIQRNRTERLSDLLDWRY
  LGRYYQHARHLTLSRAFPDKFHVELTSPPTTEGFKYPRPSSVPPSPSGSQASSPQSSDVE
  DEVEDERYDEEEEAERDRLNIKSPFSLSHVPHGKKKLHGEYKN

• Sequence length: 703

Pathways

KEGG:

Starch and sucrose metabolism
Metabolic pathways
PI3K-Akt signaling pathway
AMPK signaling pathway
Insulin signaling pathway
Glucagon signaling pathway
Insulin resistance
Diabetic cardiomyopathy

Reactome:

Glycogen synthesis
Glycogen storage disease type 0 (liver GYS2)
Glycogen storage disease type IV (GBE1)

Associated diseases

Causal
Disease term	Disease name	dbSNP ID	References
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291, rs886041382, rs1057518991, rs1057518699, rs753254213, rs748294403, rs762552974, rs1135401795, rs1553121073, rs1553122926, rs1364690005, rs1554086554, rs1554210415, rs1554168326, rs1554776342, rs1553873247, rs1567860112, rs779009256, rs1557447255, rs1564568350, rs780011005, rs1597464953, rs1200336864, rs1569513017, rs1587459606, rs1570332505, rs748888652, rs1575155995, rs2087029320, rs1589669105, rs1601769604, rs1184981709, rs749201074
Glycogen storage disease	Glycogen Storage Disease, Glycogen Storage Disease 0, Liver, Glycogen storage disease due to hepatic glycogen synthase deficiency	rs10250779, rs387906244, rs113994126, rs113994129, rs113994134, rs369973784, rs199922945, rs118203964, rs113994132, rs387906246, rs113994128, rs267606639, rs267606640, rs755419857, rs895690691, rs121918193, rs121918195, rs121918196, rs116987552, rs119103251, rs119103252, rs119103253, rs119103254, rs144081869, rs119103255, rs786200874, rs267606993, rs119103257, rs119103258, rs119103259, rs119103260, rs1474863903, rs764313717, rs397515342, rs80338671, rs137852886, rs80338672, rs137852888, rs80338673, rs397515343, rs137852889, rs137852890, rs137852891, rs1575782181, rs137852892, rs397515344, rs137852894, rs121907936, rs121907937, rs28937909, rs121907938, rs121907940, rs121907941, rs386834236, rs121907939, rs28940868, rs1555603048, rs121907942, rs386834235, rs121907943, rs121907945, rs121908987, rs121908991, rs267606977, rs137852546, rs137852547, rs1603266754, rs137852548, rs137852528, rs137852529, rs431905501, rs137852531, rs137852532, rs137852533, rs137852535, rs137852536, rs137852537, rs137852538, rs431905503, rs137852539, rs137852285, rs137852286, rs587776731, rs137852287, rs137852288, rs587776732, rs137852293, rs137852289, rs137852290, rs137852291, rs137852292, rs137852294, rs587776733, rs2147483647, rs137852295, rs113993982, rs113993974, rs113993977, rs113993981, rs80356488, rs1801175, rs104894563, rs80356487, rs104894566, rs587776757, rs80356484, rs104894565, rs104894567, rs104894568, rs104894569, rs80356482, rs1801176, rs104894571, rs34667348, rs797044442, rs121918021, rs137853588, rs137853589, rs137853590, rs1596680941, rs137853591, rs137853592, rs121918419, rs587776831, rs121918420, rs121918421, rs121918422, rs121918423, rs121918424, rs121434584, rs80356485, rs80356479, rs80356483, rs113994130, rs113994131, rs113993978, rs113993979, rs113993986, rs113993973, rs113993975, rs387906505, rs113993976, rs199948078, rs193922697, rs397514631, rs1325298827, rs140869027, rs398123169, rs398123171, rs398123172, rs369532274, rs398123173, rs398123174, rs398124208, rs398124209, rs398124210, rs587777375, rs527236146, rs527236147, rs370652040, rs143137713, rs727502871, rs369531647, rs730880022, rs730880372, rs201958741, rs730882148, rs796051877, rs752921215, rs786204489, rs781580050, rs771961377, rs370792293, rs786204678, rs786204616, rs786204481, rs786204490, rs776977863, rs786204595, rs786204655, rs769960481, rs767739769, rs786204723, rs755117847, rs764920787, rs780226142, rs367727229, rs786204467, rs201185475, rs786204614, rs786204661, rs767882689, rs528367092, rs370950728, rs757700700, rs786204532, rs201896815, rs543300039, rs786204507, rs786204646, rs786204517, rs770610356, rs770276275, rs147804176, rs772883420, rs140826989, rs786204720, rs786204727, rs781088002, rs549029029, rs368438393, rs536906561, rs374143224, rs757111744, rs786204621, rs786204645, rs786204549, rs780321415, rs786204561, rs202143236, rs786204785, rs374470794, rs771427957, rs150547274, rs113994127, rs193186112, rs794727706, rs794729208, rs797045008, rs192044702, rs797044877, rs150382575, rs201157731, rs863224023, rs869312919, rs764622267, rs878855017, rs1800312, rs886039883, rs886041476, rs779556619, rs757617999, rs143523371, rs886042086, rs201201443, rs886042358, rs761317813, rs142752477, rs142967546, rs766074609, rs770590394, rs144016984, rs886043148, rs778032599, rs886043343, rs886043399, rs886043920, rs775450536, rs755253527, rs758004953, rs766935302, rs886058900, rs1057516189, rs1057516870, rs1057517057, rs1057516567, rs1057517347, rs1057517243, rs777857395, rs1057516868, rs757967016, rs1057516308, rs1057517344, rs1057516397, rs1057516471, rs748789700, rs763554006, rs1057516741, rs1057516948, rs1057516913, rs1057516570, rs1057516563, rs1057516708, rs1057516666, rs1057517136, rs1057517425, rs1057516984, rs1057516254, rs531425980, rs1057516793, rs1057516306, rs1057516952, rs1057516513, rs1057517079, rs764318570, rs1057517017, rs867341758, rs745757264, rs1057517405, rs1057516994, rs1057517315, rs1057516529, rs1057517001, rs1057517058, rs1057517067, rs1057516598, rs753181427, rs1057517442, rs747513238, rs752848974, rs1057516259, rs1057516612, rs749560316, rs1057516468, rs1057517400, rs752851284, rs1057516329, rs1057516629, rs1057517145, rs1057517361, rs1057516349, rs772194378, rs1057516367, rs1057517227, rs1057516674, rs1057517008, rs1057516630, rs749323139, rs1057516858, rs80356486, rs1055945806, rs1057516251, rs1057517165, rs1057516503, rs1057517381, rs1057517320, rs376229714, rs1057516600, rs762260678, rs1057516290, rs1057516785, rs1057516520, rs757458607, rs1057516546, rs1057517286, rs1057516215, rs560575383, rs747610090, rs892129065, rs1057517267, rs1057516426, rs377544304, rs1057516826, rs1057517105, rs753269119, rs778418246, rs1057516928, rs1057516581, rs1057516327, rs1057516328, rs1057516277, rs1057516363, rs777275355, rs1057516924, rs1057517148, rs1057516704, rs1057516341, rs763359208, rs1057518106, rs780883601, rs775685508, rs751952198, rs148842275, rs766733439, rs1064795728, rs1064795749, rs1064796703, rs1064794288, rs375470378, rs1064796706, rs1064797157, rs764567774, rs145166656, rs767409395, rs150911354, rs757681143, rs200483245, rs771069887, rs114073621, rs1553690406, rs774465102, rs758504480, rs143670942, rs1422043936, rs373517016, rs1553188832, rs771853367, rs1553185403, rs12118058, rs1553193463, rs370247862, rs1555602832, rs1555560204, rs1555603264, rs61736895, rs763016962, rs1556016365, rs1555601828, rs991082382, rs1555599713, rs1555136390, rs754134578, rs752002666, rs1553183220, rs1307281520, rs1479740763, rs1555989523, rs1555600102, rs142917638, rs1553185302, rs1553684545, rs1555601234, rs373345919, rs1553183359, rs1556014969, rs760589837, rs776733170, rs1553185474, rs1553186489, rs757987101, rs140095668, rs1188310172, rs1555467052, rs1555467557, rs748363083, rs763027848, rs1555600730, rs1555598796, rs1555988479, rs1556000892, rs1556007472, rs1556002344, rs764591009, rs769172044, rs1555328280, rs1354714214, rs1553183148, rs930434905, rs751112302, rs878959417, rs775498547, rs1443902661, rs1553192718, rs1293077915, rs1553193529, rs1553181400, rs1215043175, rs1553185418, rs1553185883, rs1553183178, rs1553186577, rs1553188559, rs750492389, rs1553188849, rs1432024176, rs1289339080, rs767346840, rs1553190751, rs1553184620, rs755747010, rs1553193486, rs1553184657, rs1327892944, rs1553187237, rs1553185905, rs1553193530, rs1553186613, rs1553187957, rs773095419, rs1553189468, rs1185321132, rs770438130, rs1553190316, rs1555133248, rs1462767117, rs1555136752, rs1163710370, rs1555136208, rs1555136540, rs750857876, rs1555136459, rs187131358, rs1555559741, rs1411037881, rs1485038937, rs1555598687, rs1555598880, rs1555599171, rs1555599586, rs1555599637, rs1555598869, rs1555599644, rs1555599594, rs1555599619, rs1555600050, rs1555599960, rs766680292, rs1555600166, rs996798292, rs1555600575, rs770780848, rs1555601780, rs765362308, rs1209887739, rs1555603216, rs1428358278, rs776948121, rs1555601662, rs1555603131, rs192679574, rs1555559279, rs1189630738, rs1555559991, rs1555560140, rs1555560185, rs1555598460, rs1555598544, rs1555598824, rs1555600111, rs778068209, rs1555600846, rs747150965, rs753505203, rs914396317, rs1555602692, rs1344266804, rs1555558920, rs1457925404, rs1555598800, rs1207988953, rs1555599667, rs1555600061, rs1434761678, rs759518659, rs1555601802, rs1555602703, rs1555602860, rs1555603434, rs1555995635, rs1567825175, rs1567705064, rs1567838823, rs1559637815, rs1557794150, rs756175624, rs146195866, rs781511110, rs759657964, rs1563131309, rs746120293, rs746348793, rs770037766, rs1270523244, rs1567706564, rs1567260747, rs201056962, rs764539267, rs765718882, rs1568619900, rs1569298646, rs1569344469, rs1567828977, rs561646250, rs1569297379, rs1210626722, rs1569300538, rs1256371424, rs747947171, rs1565538121, rs1565536363, rs1569297427, rs1567830317, rs764750389, rs1555603219, rs1567829962, rs1430517061, rs1205507761, rs149244943, rs748262135, rs1556299510, rs780246932, rs752961445, rs1315020035, rs767095759, rs756205397, rs149096315, rs1242540921, rs371296953, rs1303617854, rs766536350, rs1414146587, rs1567835775, rs1567835781, rs1570433472, rs1570508240, rs763216519, rs1598585402, rs1598578030, rs1598581682, rs1592412131, rs1571232214, rs1571232404, rs1571243699, rs1570433686, rs1570438459, rs765367405, rs1206517501, rs1239498701, rs774926455, rs1480850606, rs777589783, rs768604948, rs1592410003, rs1592818641, rs760187622, rs539898848, rs755612674, rs1597988331, rs775826449, rs1232001857, rs200210219, rs1598575231, rs141533320, rs1598582021, rs764670084, rs1448515860, rs886043882, rs1601685358, rs1601689006, rs1601739229, rs1601781024, rs1601781031, rs539203557, rs1212333772, rs372079212, rs765425704, rs776545903, rs1597989985, rs1598592604, rs1597989983, rs1556257317, rs1475559733, rs1598577666, rs1598580364, rs1596687577, rs1372753669, rs1601714299, rs1601747985, rs1601776276, rs1601760689, rs1601763099, rs1571232325, rs1570445130, rs370202718, rs1570487381, rs1576183537, rs1592408302, rs1592409633, rs150483902, rs1596687555, rs762089284, rs1597990895, rs1597990906, rs1597991608, rs1597991733, rs1601687244, rs1601748216, rs1601776523, rs1571243862, rs1592409631, rs1601780766, rs2039275157, rs2039287628, rs1567702823, rs756632286, rs1597990921, rs1576137368, rs1322527832, rs1596047883, rs1650040391, rs780694207, rs758182700, rs1652018859, rs1652879873, rs1654912428, rs1703086906, rs781198373, rs1703800818, rs1490328834, rs1804721948, rs1311913891, rs2058363627, rs1005687078, rs2058388882, rs2058407169, rs2058421657, rs138893744, rs758943884, rs2056023296, rs1401928680, rs764401169, rs2056091436, rs915675670, rs2039038743, rs2039117815, rs2039190879, rs2039192386, rs2039213824, rs766398206, rs2039287852, rs2047467477, rs2047492649, rs2047492720, rs765360653, rs111911126, rs1219299972, rs2047834385, rs2039261208, rs1262967083, rs2047514376, rs2048391185, rs2058357329, rs1598580407, rs2039250790, rs755305465, rs766448695	20051115, 27604308, 9691087, 12072888, 25070466, 28245189
Hyperlipidemia	Hyperlipidemia	rs118204057, rs118204060, rs118204062, rs1563569634, rs118204069, rs118204070, rs118204071, rs1566946168, rs1064797075

Unknown
Disease term	Disease name	Evidence	References	Source
Diabetes	Diabetes			GWAS

Associations from Text Mining
Disease Name	Relationship Type	References
Breast Neoplasms	Associate	37247276
Carcinoma Hepatocellular	Inhibit	32987529
Cholangiocarcinoma	Inhibit	34783271
Diabetes Mellitus Type 2	Associate	20051115
Disease	Associate	34783271
Epilepsy	Associate	37574425
Glucose Intolerance	Associate	20051115
Glycogen Storage Disease	Associate	37574425
Glycogen Storage Disease 0 Muscle	Associate	20051115, 29961766, 30968641
Hyperglycemia	Associate	20051115, 30968641
Hypoglycemia	Associate	20051115, 30968641, 37574425
Lymphatic Metastasis	Inhibit	34783271
Metabolic Diseases	Associate	20051115
Muscular dystrophy congenital with central nervous system involvement	Associate	37574425
Neoplasms	Inhibit	32987529
Neoplasms	Associate	34783271
Parkinsonian Disorders	Associate	19761607
Seizures	Associate	37574425