Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
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

Show/Hide all (22)

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

Show/Hide all (31)

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

Show/Hide all (26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003824	Function	Catalytic activity	IEA
GO:0004373	Function	Alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity	EXP	9691087
GO:0004373	Function	Alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity	IBA
GO:0004373	Function	Alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity	IDA	1731614
GO:0004373	Function	Alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity	IEA
GO:0004373	Function	Alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity	IMP	9691087
GO:0004373	Function	Alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity	ISS
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	ISS
GO:0005829	Component	Cytosol	IEA
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
GO:0005978	Process	Glycogen biosynthetic process	IDA	1731614
GO:0005978	Process	Glycogen biosynthetic process	IEA
GO:0005978	Process	Glycogen biosynthetic process	IMP	9691087
GO:0005978	Process	Glycogen biosynthetic process	ISS
GO:0005978	Process	Glycogen biosynthetic process	TAS
GO:0009749	Process	Response to glucose	ISS
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0030864	Component	Cortical actin cytoskeleton	ISS
GO:0061547	Function	Glycogen synthase activity, transferring glucose-1-phosphate	IEA
GO:0061547	Function	Glycogen synthase activity, transferring glucose-1-phosphate	TAS

MIM	HGNC	e!Ensembl
138571	4707	ENSG00000111713

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

Interactions

View interactions

	KEGG		Reactome
	Starch and sucrose metabolism Metabolic pathways PI3K-Akt signaling pathway AMPK signaling pathway Insulin signaling pathway Glucagon signaling pathway Insulin resistance Diabetic cardiomyopathy		Glycogen synthesis Glycogen storage disease type 0 (liver GYS2) Glycogen storage disease type IV (GBE1)

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)

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Glycogen storage disease	Likely pathogenic; Pathogenic	rs121918419, rs771205749	RCV000605157 RCV000826208	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glycogen storage disorder due to hepatic glycogen synthase deficiency	Likely pathogenic; Pathogenic	rs2136913413, rs2136877292, rs763671258, rs1199090828, rs756685797, rs150382575, rs201157731, rs2540534282, rs752819982, rs121918419, rs587776831, rs121918420, rs121918421, rs121918422, rs121918423 View all (10 more)	RCV005005983 RCV001783411 RCV002470458 RCV003085721 RCV003078418 View all (20 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
GYS2-related disorder	Likely pathogenic; Pathogenic	rs764833435, rs121918419, rs781511110	RCV003408810 RCV003944826 RCV003892530	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Thymoma	Likely pathogenic; Pathogenic	rs121918419	RCV005887533	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (10)

Phenotype Name	Clinical Significance	Source	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.
Acute myeloid leukemia	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARCINOMA, HEPATOCELLULAR	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLYCOGEN STORAGE DISEASE 0, LIVER	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLYCOGEN STORAGE DISEASE DUE TO HEPATIC GLYCOGEN SYNTHASE DEFICIENCY	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEPATIC GLYCOGEN SYNTHASE DEFICIENCY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (43)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adult Medulloblastoma	Medulloblastoma	BEFREE	29167993		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	37247276	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	32987529	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Childhood Medulloblastoma	Medulloblastoma	BEFREE	29167993		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	Pubtator	34783271	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	20051115	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	37574425	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Familial aplasia of the vermis	Cerebellar vermis agenesis	BEFREE	29961766		★★★★★ ★☆☆☆☆ Found in Text Mining only
Gerstmann-Straussler-Scheinker Disease	Gerstmann-Straussler-Scheinker syndrome	BEFREE	29784585		★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease	Glycogen Storage Disease	CLINVAR_DG	20051115, 9691087		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glycogen Storage Disease	Glycogen Storage Disease	BEFREE	22899091, 28245189, 29167993, 29784585		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glycogen Storage Disease	Glycogen Storage Disease	GENOMICS_ENGLAND_DG	27604308		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glycogen Storage Disease	Glycogen storage disease	Pubtator	37574425	Associate	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glycogen Storage Disease 0 Muscle	Glycogen storage disease	Pubtator	20051115, 29961766, 30968641	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease 0, Liver	Glycogen Storage Disease	CLINVAR_DG	12072888, 20051115, 25070466, 28245189, 9691087		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease 0, Liver	Glycogen Storage Disease	BEFREE	18341095, 29167993		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease 0, Liver	Glycogen Storage Disease	GENOMICS_ENGLAND_DG	27604308		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease 0, Liver	Glycogen Storage Disease	UNIPROT_DG	9691087		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease 0, Liver	Glycogen Storage Disease	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease 0, Liver	Glycogen Storage Disease	ORPHANET_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen storage disease due to hepatic glycogen synthase deficiency	Glycogen Storage Disease	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease Type III	Glycogen Storage Disease	BEFREE	29784585		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperglycemia	Hyperglycemia	BEFREE	20051115, 23426827		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperglycemia	Hyperglycemia	Pubtator	20051115, 30968641	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperlipidemia	Hyperlipidemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	Pubtator	20051115, 30968641, 37574425	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Ketonuria	Ketonuria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ketosis	Ketosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	CTD_human_DG	28284560		★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	30584071, 31139015		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	34783271	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Medulloblastoma	Medulloblastoma	BEFREE	29167993		★★★★★ ★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic syndrome	Pubtator	20051115	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic Diseases	BEFREE	29167993		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neonatal hypoglycemia	Hypoglycemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	30584071		★★★★★ ★☆☆☆☆ Found in Text Mining only
Orofaciodigital Syndromes	Orofaciodigital syndrome	BEFREE	29961766		★★★★★ ★☆☆☆☆ Found in Text Mining only
Parkinsonian Disorders	Parkinson disease	Pubtator	19761607	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pediatric Obesity	Childhood obesity	BEFREE	22951595		★★★★★ ★☆☆☆☆ Found in Text Mining only
Polycystic Ovary Syndrome	Polycystic Ovary Syndrome	BEFREE	22951595		★★★★★ ★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	37574425	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

GYS2 (glycogen synthase 2)