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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	2992
Gene name Gene Name - the full gene name approved by the HGNC.	Glycogenin 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	GYG1
Synonyms (NCBI Gene) Gene synonyms aliases	GSD15, GYG
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3q24
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a member of the glycogenin family. Glycogenin is a glycosyltransferase that catalyzes the formation of a short glucose polymer from uridine diphosphate glucose in an autoglucosylation reaction. This reaction is followed by elongation and

Show/Hide all(9)

SNP ID	Visualize variation	Clinical significance	Consequence
rs143137713	G>C	Pathogenic, pathogenic-likely-pathogenic	Genic upstream transcript variant, missense variant, coding sequence variant
rs267606858	C>A,G,T	Pathogenic, uncertain-significance	Coding sequence variant, genic upstream transcript variant, missense variant
rs370652040	G>C,T	Pathogenic	Intron variant, genic upstream transcript variant
rs727502869	C>T	Pathogenic	Stop gained, coding sequence variant, synonymous variant
rs727502870	G>A	Pathogenic	Stop gained, intron variant, coding sequence variant
rs727502871	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs949456055	G>A	Likely-pathogenic	Genic upstream transcript variant, splice donor variant
rs1064795548	G>-	Likely-pathogenic	Intron variant, frameshift variant, genic upstream transcript variant, coding sequence variant
rs1559834349	G>T	Pathogenic	Genic upstream transcript variant, stop gained, 5 prime UTR variant, coding sequence variant

Show/Hide all(203)

miRTarBase ID	miRNA	Experiments	Reference
MIRT025494	hsa-miR-34a-5p	Proteomics	21566225
MIRT025494	hsa-miR-34a-5p	Proteomics	21566225
MIRT052247	hsa-let-7b-5p	CLASH	23622248
MIRT049896	hsa-miR-31-5p	CLASH	23622248
MIRT1038823	hsa-miR-1184	CLIP-seq
MIRT1038824	hsa-miR-1205	CLIP-seq
MIRT1038825	hsa-miR-1227	CLIP-seq
MIRT1038826	hsa-miR-1285	CLIP-seq
MIRT1038827	hsa-miR-129-5p	CLIP-seq
MIRT1038828	hsa-miR-155	CLIP-seq
MIRT1038829	hsa-miR-190	CLIP-seq
MIRT1038830	hsa-miR-190b	CLIP-seq
MIRT1038831	hsa-miR-204	CLIP-seq
MIRT1038832	hsa-miR-211	CLIP-seq
MIRT1038833	hsa-miR-297	CLIP-seq
MIRT1038834	hsa-miR-3128	CLIP-seq
MIRT1038835	hsa-miR-3149	CLIP-seq
MIRT1038836	hsa-miR-3155	CLIP-seq
MIRT1038837	hsa-miR-3155b	CLIP-seq
MIRT1038838	hsa-miR-3158-5p	CLIP-seq
MIRT1038839	hsa-miR-3163	CLIP-seq
MIRT1038840	hsa-miR-3187-5p	CLIP-seq
MIRT1038841	hsa-miR-3194-3p	CLIP-seq
MIRT1038842	hsa-miR-3662	CLIP-seq
MIRT1038843	hsa-miR-3665	CLIP-seq
MIRT1038844	hsa-miR-3680	CLIP-seq
MIRT1038845	hsa-miR-3919	CLIP-seq
MIRT1038846	hsa-miR-3925-5p	CLIP-seq
MIRT1038847	hsa-miR-4252	CLIP-seq
MIRT1038848	hsa-miR-4282	CLIP-seq
MIRT1038849	hsa-miR-4418	CLIP-seq
MIRT1038850	hsa-miR-4446-5p	CLIP-seq
MIRT1038851	hsa-miR-4506	CLIP-seq
MIRT1038852	hsa-miR-4639-3p	CLIP-seq
MIRT1038853	hsa-miR-4720-5p	CLIP-seq
MIRT1038854	hsa-miR-4755-5p	CLIP-seq
MIRT1038855	hsa-miR-4756-3p	CLIP-seq
MIRT1038856	hsa-miR-4799-3p	CLIP-seq
MIRT1038857	hsa-miR-4799-5p	CLIP-seq
MIRT1038858	hsa-miR-484	CLIP-seq
MIRT1038859	hsa-miR-509-3-5p	CLIP-seq
MIRT1038860	hsa-miR-509-5p	CLIP-seq
MIRT1038861	hsa-miR-526b	CLIP-seq
MIRT1038862	hsa-miR-563	CLIP-seq
MIRT1038863	hsa-miR-567	CLIP-seq
MIRT1038864	hsa-miR-569	CLIP-seq
MIRT1038865	hsa-miR-603	CLIP-seq
MIRT1038866	hsa-miR-612	CLIP-seq
MIRT1038867	hsa-miR-623	CLIP-seq
MIRT1038868	hsa-miR-657	CLIP-seq
MIRT1038869	hsa-miR-760	CLIP-seq
MIRT1038870	hsa-miR-885-3p	CLIP-seq
MIRT1038871	hsa-miR-889	CLIP-seq
MIRT2007975	hsa-miR-3117-5p	CLIP-seq
MIRT1038834	hsa-miR-3128	CLIP-seq
MIRT2007976	hsa-miR-34b	CLIP-seq
MIRT2007977	hsa-miR-3609	CLIP-seq
MIRT2007978	hsa-miR-4521	CLIP-seq
MIRT1038852	hsa-miR-4639-3p	CLIP-seq
MIRT1038853	hsa-miR-4720-5p	CLIP-seq
MIRT1038856	hsa-miR-4799-3p	CLIP-seq
MIRT2007979	hsa-miR-548ah	CLIP-seq
MIRT1038824	hsa-miR-1205	CLIP-seq
MIRT1038825	hsa-miR-1227	CLIP-seq
MIRT1038827	hsa-miR-129-5p	CLIP-seq
MIRT2240678	hsa-miR-1324	CLIP-seq
MIRT1038829	hsa-miR-190	CLIP-seq
MIRT1038830	hsa-miR-190b	CLIP-seq
MIRT2007975	hsa-miR-3117-5p	CLIP-seq
MIRT2240679	hsa-miR-3653	CLIP-seq
MIRT2240680	hsa-miR-3658	CLIP-seq
MIRT1038843	hsa-miR-3665	CLIP-seq
MIRT1038847	hsa-miR-4252	CLIP-seq
MIRT2240681	hsa-miR-4307	CLIP-seq
MIRT1038849	hsa-miR-4418	CLIP-seq
MIRT2240682	hsa-miR-4511	CLIP-seq
MIRT2007978	hsa-miR-4521	CLIP-seq
MIRT2240683	hsa-miR-488	CLIP-seq
MIRT1038859	hsa-miR-509-3-5p	CLIP-seq
MIRT1038860	hsa-miR-509-5p	CLIP-seq
MIRT2240684	hsa-miR-548b-3p	CLIP-seq
MIRT1038868	hsa-miR-657	CLIP-seq
MIRT2544143	hsa-miR-1229	CLIP-seq
MIRT2544144	hsa-miR-1251	CLIP-seq
MIRT1038826	hsa-miR-1285	CLIP-seq
MIRT2544145	hsa-miR-134	CLIP-seq
MIRT2544146	hsa-miR-141	CLIP-seq
MIRT2544147	hsa-miR-194	CLIP-seq
MIRT2544148	hsa-miR-200a	CLIP-seq
MIRT1038831	hsa-miR-204	CLIP-seq
MIRT1038832	hsa-miR-211	CLIP-seq
MIRT2544149	hsa-miR-2964a-3p	CLIP-seq
MIRT1038833	hsa-miR-297	CLIP-seq
MIRT2544150	hsa-miR-302f	CLIP-seq
MIRT2544151	hsa-miR-3065-5p	CLIP-seq
MIRT2544152	hsa-miR-3118	CLIP-seq
MIRT2544153	hsa-miR-3121-3p	CLIP-seq
MIRT2544154	hsa-miR-3136-5p	CLIP-seq
MIRT1038835	hsa-miR-3149	CLIP-seq
MIRT2544155	hsa-miR-3159	CLIP-seq
MIRT2544156	hsa-miR-3161	CLIP-seq
MIRT2544157	hsa-miR-3179	CLIP-seq
MIRT1038840	hsa-miR-3187-5p	CLIP-seq
MIRT2544158	hsa-miR-346	CLIP-seq
MIRT2544159	hsa-miR-34a	CLIP-seq
MIRT2544160	hsa-miR-34c-5p	CLIP-seq
MIRT2007977	hsa-miR-3609	CLIP-seq
MIRT2544161	hsa-miR-3977	CLIP-seq
MIRT2544162	hsa-miR-410	CLIP-seq
MIRT2544163	hsa-miR-4277	CLIP-seq
MIRT1038848	hsa-miR-4282	CLIP-seq
MIRT2544164	hsa-miR-4288	CLIP-seq
MIRT2544165	hsa-miR-4439	CLIP-seq
MIRT1038850	hsa-miR-4446-5p	CLIP-seq
MIRT2544166	hsa-miR-449a	CLIP-seq
MIRT2544167	hsa-miR-449b	CLIP-seq
MIRT2544168	hsa-miR-4513	CLIP-seq
MIRT2544169	hsa-miR-4659a-5p	CLIP-seq
MIRT2544170	hsa-miR-4659b-5p	CLIP-seq
MIRT2544171	hsa-miR-4731-3p	CLIP-seq
MIRT1038854	hsa-miR-4755-5p	CLIP-seq
MIRT2544172	hsa-miR-4762-3p	CLIP-seq
MIRT2544173	hsa-miR-4766-5p	CLIP-seq
MIRT2544174	hsa-miR-4781-3p	CLIP-seq
MIRT1038857	hsa-miR-4799-5p	CLIP-seq
MIRT2544175	hsa-miR-4801	CLIP-seq
MIRT2240683	hsa-miR-488	CLIP-seq
MIRT2544176	hsa-miR-494	CLIP-seq
MIRT2544177	hsa-miR-505	CLIP-seq
MIRT2544178	hsa-miR-513b	CLIP-seq
MIRT2007979	hsa-miR-548ah	CLIP-seq
MIRT2544179	hsa-miR-548m	CLIP-seq
MIRT2544180	hsa-miR-548t	CLIP-seq
MIRT1038863	hsa-miR-567	CLIP-seq
MIRT2544181	hsa-miR-570	CLIP-seq
MIRT2544182	hsa-miR-580	CLIP-seq
MIRT1038866	hsa-miR-612	CLIP-seq
MIRT1038867	hsa-miR-623	CLIP-seq
MIRT2544183	hsa-miR-632	CLIP-seq
MIRT2544184	hsa-miR-654-3p	CLIP-seq
MIRT2544143	hsa-miR-1229	CLIP-seq
MIRT1038826	hsa-miR-1285	CLIP-seq
MIRT2544146	hsa-miR-141	CLIP-seq
MIRT2544147	hsa-miR-194	CLIP-seq
MIRT2544148	hsa-miR-200a	CLIP-seq
MIRT1038831	hsa-miR-204	CLIP-seq
MIRT1038832	hsa-miR-211	CLIP-seq
MIRT2544149	hsa-miR-2964a-3p	CLIP-seq
MIRT1038833	hsa-miR-297	CLIP-seq
MIRT2544150	hsa-miR-302f	CLIP-seq
MIRT2544151	hsa-miR-3065-5p	CLIP-seq
MIRT2544153	hsa-miR-3121-3p	CLIP-seq
MIRT1038834	hsa-miR-3128	CLIP-seq
MIRT1038835	hsa-miR-3149	CLIP-seq
MIRT2544155	hsa-miR-3159	CLIP-seq
MIRT2544156	hsa-miR-3161	CLIP-seq
MIRT2544157	hsa-miR-3179	CLIP-seq
MIRT1038840	hsa-miR-3187-5p	CLIP-seq
MIRT2544158	hsa-miR-346	CLIP-seq
MIRT2544159	hsa-miR-34a	CLIP-seq
MIRT2544160	hsa-miR-34c-5p	CLIP-seq
MIRT2007977	hsa-miR-3609	CLIP-seq
MIRT1038844	hsa-miR-3680	CLIP-seq
MIRT2544161	hsa-miR-3977	CLIP-seq
MIRT2544162	hsa-miR-410	CLIP-seq
MIRT2682209	hsa-miR-4267	CLIP-seq
MIRT2544163	hsa-miR-4277	CLIP-seq
MIRT1038848	hsa-miR-4282	CLIP-seq
MIRT2544164	hsa-miR-4288	CLIP-seq
MIRT1038850	hsa-miR-4446-5p	CLIP-seq
MIRT2544166	hsa-miR-449a	CLIP-seq
MIRT2544167	hsa-miR-449b	CLIP-seq
MIRT1038852	hsa-miR-4639-3p	CLIP-seq
MIRT2544169	hsa-miR-4659a-5p	CLIP-seq
MIRT2544170	hsa-miR-4659b-5p	CLIP-seq
MIRT1038853	hsa-miR-4720-5p	CLIP-seq
MIRT2544171	hsa-miR-4731-3p	CLIP-seq
MIRT1038854	hsa-miR-4755-5p	CLIP-seq
MIRT2544172	hsa-miR-4762-3p	CLIP-seq
MIRT2544173	hsa-miR-4766-5p	CLIP-seq
MIRT2544174	hsa-miR-4781-3p	CLIP-seq
MIRT1038856	hsa-miR-4799-3p	CLIP-seq
MIRT1038857	hsa-miR-4799-5p	CLIP-seq
MIRT2544175	hsa-miR-4801	CLIP-seq
MIRT2240683	hsa-miR-488	CLIP-seq
MIRT2544176	hsa-miR-494	CLIP-seq
MIRT2682210	hsa-miR-499a-5p	CLIP-seq
MIRT2544177	hsa-miR-505	CLIP-seq
MIRT2544178	hsa-miR-513b	CLIP-seq
MIRT2682211	hsa-miR-513c	CLIP-seq
MIRT2682212	hsa-miR-514b-5p	CLIP-seq
MIRT1038861	hsa-miR-526b	CLIP-seq
MIRT2007979	hsa-miR-548ah	CLIP-seq
MIRT2544179	hsa-miR-548m	CLIP-seq
MIRT2544180	hsa-miR-548t	CLIP-seq
MIRT1038863	hsa-miR-567	CLIP-seq
MIRT2544182	hsa-miR-580	CLIP-seq
MIRT1038866	hsa-miR-612	CLIP-seq
MIRT1038867	hsa-miR-623	CLIP-seq
MIRT2544183	hsa-miR-632	CLIP-seq
MIRT2544184	hsa-miR-654-3p	CLIP-seq
MIRT1038870	hsa-miR-885-3p	CLIP-seq
MIRT1038871	hsa-miR-889	CLIP-seq

Show/Hide all(25)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	16189514, 17055998, 25416956, 32296183, 35271311
GO:0005576	Component	Extracellular region	TAS
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	ISS
GO:0005737	Component	Cytoplasm	ISS
GO:0005829	Component	Cytosol	TAS
GO:0005978	Process	Glycogen biosynthetic process	IBA
GO:0005978	Process	Glycogen biosynthetic process	IEA
GO:0005978	Process	Glycogen biosynthetic process	IMP	22160680
GO:0005978	Process	Glycogen biosynthetic process	TAS
GO:0008466	Function	Glycogenin glucosyltransferase activity	EXP	20357282
GO:0008466	Function	Glycogenin glucosyltransferase activity	IDA	22160680, 30356213
GO:0008466	Function	Glycogenin glucosyltransferase activity	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IBA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0030145	Function	Manganese ion binding	IDA	22160680, 30356213
GO:0034774	Component	Secretory granule lumen	TAS
GO:0042803	Function	Protein homodimerization activity	IDA	22160680, 30356213
GO:0043202	Component	Lysosomal lumen	TAS
GO:0046872	Function	Metal ion binding	IEA
GO:1904813	Component	Ficolin-1-rich granule lumen	TAS

MIM	HGNC	e!Ensembl
603942	4699	ENSG00000163754

Protein

UniProt ID

P46976

Protein name

Glycogenin-1 (GN-1) (GN1) (EC 2.4.1.186)

Protein function

Glycogenin participates in the glycogen biosynthetic process along with glycogen synthase and glycogen branching enzyme. It catalyzes the formation of a short alpha (1,4)-glucosyl chain covalently attached via a glucose 1-O-tyrosyl linkage to in

PDB

3Q4S , 3QVB , 3RMV , 3RMW , 3T7M , 3T7N , 3T7O , 3U2T , 3U2U , 3U2V , 3U2W , 3U2X , 6EQJ , 6EQL , 7OVX , 7Q0B , 7Q0S , 7Q12 , 7Q13 , 7ZBN , 8CVX , 8CVY , 8CVZ

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01501	Glyco_transf_8	6 → 224	Glycosyl transferase family 8	Family

Tissue specificity

TISSUE SPECIFICITY: Highly expressed in skeletal muscle and heart, with lower levels in brain, lung, kidney and pancreas. {ECO:0000269|PubMed:8602861}.

Sequence

MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIM
VDVLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFDREEL
SAAPDPGWPDCFNSGVFVYQPSVETYNQLLHLASEQGSFDGGDQGILNTFFSSWATTDIR
KHLPFIYNLSSISIYSYLPAFKVFGASAKVVHFLGRVKPWNYTYDPKTKSVKSEAHDPNM
THPEFLILWWNIFTTNVLPLLQQFGLVKDTCSYVNVLSDLVYTLAFSCGFCRKEDVSGAI
SHLSLGEIPAMAQPFVSSEERKERWEQGQADYMGADSFDNIKRKLDTYLQ

Sequence length

350

Interactions

View interactions

	KEGG		Reactome
	Starch and sucrose metabolism Metabolic pathways		Glycogen synthesis Myoclonic epilepsy of Lafora Glycogen storage disease type XV (GYG1) Glycogen storage disease type 0 (muscle GYS1) Glycogen storage disease type II (GAA) Neutrophil degranulation Glycogen breakdown (glycogenolysis)

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Glycogen Storage Disease	glycogen storage disease xv	rs143137713, rs727502871, rs370652040	N/A
Polyglucosan body myopathy	polyglucosan body myopathy type 2	rs727502869, rs143137713, rs727502870, rs727502871, rs949456055, rs370652040	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Atrial Fibrillation	Atrial fibrillation	N/A	N/A	GWAS
Dementia	Dementia	N/A	N/A	GWAS

Show/Hide Text Mining Associations (16)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Arrhythmias Cardiac	Associate	20357282
Cardiomyopathies	Associate	27718144, 31628455
Cardiomyopathy Dilated	Associate	27718144
Cardiovascular Diseases	Associate	38062767
Compartment Syndromes	Associate	33257366
Cytomegalovirus Infections	Associate	32838938
Genetic Diseases Inborn	Associate	26652229
Glycogen Storage Disease	Associate	22198226, 25272951
Heart Failure	Associate	27718144
Inflammation	Associate	38427757
Metabolic Diseases	Associate	33257366
Mucocutaneous Lymph Node Syndrome	Associate	36042431, 38427757
Muscle Weakness	Associate	20357282
Polyglucosan Body Disease Adult Form	Associate	26652229
Thyroid Carcinoma Anaplastic	Associate	38062767
Vacuolar myopathy	Associate	32419263

GYG1 (glycogenin 1)