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	5836
Gene name	Glycogen phosphorylase L
Gene symbol	PYGL
Synonyms (NCBI Gene)	GSD6
Chromosome	14
Chromosome location	14q22.1
Summary	This gene encodes a homodimeric protein that catalyses the cleavage of alpha-1,4-glucosidic bonds to release glucose-1-phosphate from liver glycogen stores. This protein switches from inactive phosphorylase B to active phosphorylase A by phosphorylation o

Show/Hide all (26)

SNP ID	Visualize variation	Clinical significance	Consequence
rs113993973	G>A	Pathogenic	Stop gained, intron variant, coding sequence variant
rs113993974	C>G	Pathogenic	Splice acceptor variant
rs113993976	T>C	Pathogenic	Missense variant, coding sequence variant
rs113993977	G>C	Pathogenic	Missense variant, coding sequence variant
rs113993978	G>A	Pathogenic	Stop gained, coding sequence variant
rs113993979	C>T	Pathogenic	Missense variant, coding sequence variant
rs113993980	G>A	Pathogenic	Missense variant, coding sequence variant
rs113993981	C>A,G,T	Likely-pathogenic	Splice donor variant
rs113993982	C>G,T	Pathogenic	Splice donor variant
rs113993983	T>A	Pathogenic	Missense variant, coding sequence variant
rs113993984	C>T	Pathogenic	Missense variant, coding sequence variant
rs113993985	A>T	Pathogenic	Missense variant, coding sequence variant
rs113993986	G>A,C	Pathogenic	Missense variant, coding sequence variant
rs113993988	A>G	Pathogenic	Missense variant, coding sequence variant
rs147211684	G>T	Benign, conflicting-interpretations-of-pathogenicity	Intron variant
rs149096315	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, stop gained
rs150547274	G>T	Pathogenic	Coding sequence variant, stop gained
rs529502292	->G	Pathogenic	Frameshift variant, coding sequence variant
rs749922511	C>A,T	Uncertain-significance, pathogenic	Coding sequence variant, missense variant
rs755485474	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs760913598	A>-	Pathogenic	Frameshift variant, coding sequence variant
rs765425704	CA>-	Likely-pathogenic	Intron variant, splice donor variant, coding sequence variant
rs776545903	C>T	Likely-pathogenic	Splice donor variant
rs1555326546	GTAC>-	Pathogenic	Splice donor variant, intron variant
rs1555328280	TGATCATGGT>-	Pathogenic	Coding sequence variant, intron variant, frameshift variant
rs1596047883	CTT>TTA	Pathogenic	Stop gained, coding sequence variant

Show/Hide all (19)

miRTarBase ID	miRNA	Experiments	Reference
MIRT021033	hsa-miR-155-5p	Proteomics	18668040
MIRT049286	hsa-miR-92a-3p	CLASH	23622248
MIRT049286	hsa-miR-92a-3p	CLASH	23622248
MIRT048878	hsa-miR-93-5p	CLASH	23622248
MIRT047597	hsa-miR-10a-5p	CLASH	23622248
MIRT1279457	hsa-miR-1257	CLIP-seq
MIRT1279458	hsa-miR-1297	CLIP-seq
MIRT1279459	hsa-miR-26a	CLIP-seq
MIRT1279460	hsa-miR-26b	CLIP-seq
MIRT1279461	hsa-miR-3613-5p	CLIP-seq
MIRT1279462	hsa-miR-409-3p	CLIP-seq
MIRT1279463	hsa-miR-4465	CLIP-seq
MIRT1279464	hsa-miR-548c-3p	CLIP-seq
MIRT1279465	hsa-miR-1470	CLIP-seq
MIRT1279466	hsa-miR-4446-5p	CLIP-seq
MIRT1279467	hsa-miR-4667-3p	CLIP-seq
MIRT1279468	hsa-miR-4755-5p	CLIP-seq
MIRT1279469	hsa-miR-4756-3p	CLIP-seq
MIRT1279470	hsa-miR-642a	CLIP-seq

Show/Hide all (35)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0002060	Function	Purine nucleobase binding	IDA	12204691
GO:0003824	Function	Catalytic activity	IEA
GO:0004645	Function	1,4-alpha-oligoglucan phosphorylase activity	IEA
GO:0005515	Function	Protein binding	IPI	25416956, 25910212, 32296183, 33961781
GO:0005524	Function	ATP binding	IDA	10949035
GO:0005536	Function	D-glucose binding	IDA	10980448, 12204691
GO:0005576	Component	Extracellular region	TAS
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005975	Process	Carbohydrate metabolic process	IEA
GO:0005977	Process	Glycogen metabolic process	IEA
GO:0005977	Process	Glycogen metabolic process	IMP	10980448, 17705025
GO:0005980	Process	Glycogen catabolic process	IBA
GO:0005980	Process	Glycogen catabolic process	IEA
GO:0008184	Function	Glycogen phosphorylase activity	IBA
GO:0008184	Function	Glycogen phosphorylase activity	IDA	22225877
GO:0008184	Function	Glycogen phosphorylase activity	IEA
GO:0008184	Function	Glycogen phosphorylase activity	IMP	9529348, 10980448, 17705025
GO:0009617	Process	Response to bacterium	IEA
GO:0016208	Function	AMP binding	IDA	10949035, 10980448
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0019842	Function	Vitamin binding	IDA	12204691
GO:0030170	Function	Pyridoxal phosphate binding	IBA
GO:0030170	Function	Pyridoxal phosphate binding	IEA
GO:0032052	Function	Bile acid binding	IDA	12204691
GO:0034774	Component	Secretory granule lumen	TAS
GO:0042593	Process	Glucose homeostasis	IMP	17705025
GO:0042802	Function	Identical protein binding	IPI	10980448
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0070266	Process	Necroptotic process	IEA
GO:1904813	Component	Ficolin-1-rich granule lumen	TAS

MIM	HGNC	e!Ensembl
613741	9725	ENSG00000100504

P06737

Protein name

Glycogen phosphorylase, liver form (EC 2.4.1.1)

Protein function

Allosteric enzyme that catalyzes the rate-limiting step in glycogen catabolism, the phosphorolytic cleavage of glycogen to produce glucose-1-phosphate, and plays a central role in maintaining cellular and organismal glucose homeostasis. {ECO:000

PDB

1EM6 , 1EXV , 1FA9 , 1FC0 , 1L5Q , 1L5R , 1L5S , 1L7X , 1XOI , 2ATI , 2QLL , 2ZB2 , 3CEH , 3CEJ , 3CEM , 3DD1 , 3DDS , 3DDW , 8EMS

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00343	Phosphorylase	113 → 828	Carbohydrate phosphorylase	Family

Sequence

MAKPLTDQEKRRQISIRGIVGVENVAELKKSFNRHLHFTLVKDRNVATTRDYYFALAHTV
RDHLVGRWIRTQQHYYDKCPKRVYYLSLEFYMGRTLQNTMINLGLQNACDEAIYQLGLDI
EELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEYGIFNQKIRDGWQVEEA
DDWLRYGNPWEKSRPEFMLPVHFYGKVEHTNTGTKWIDTQVVLALPYDTPVPGYMNNTVN
TMRLWSARAPNDFNLRDFNVGDYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFV
VAATLQDIIRRFKASKFGSTRGAGTVFDAFPDQVAIQLNDTHPALAIPELMRIFVDIEKL
PWSKAWELTQKTFAYTNHTVLPEALERWPVDLVEKLLPRHLEIIYEINQKHLDRIVALFP
KDVDRLRRMSLIEEEGSKRINMAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELEPDKF
QNKTNGITPRRWLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFLGDDVFLRELAKVKQ
ENKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKRQLLNCLHVITMYNRIKKDPKKLFV
PRTVIIGGKAAPGYHMAKMIIKLITSVADVVNNDPMVGSKLKVIFLENYRVSLAEKVIPA
TDLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENLFIFGMRIDDVA
ALDKKGYEAKEYYEALPELKLVIDQIDNGFFSPKQPDLFKDIINMLFYHDRFKVFADYEA
YVKCQDKVSQLYMNPKAWNTMVLKNIAASGKFSSDRTIKEYAQNIWNVEPSDLKISLSNE
SNKVNGN

Sequence length

847

Interactions

View interactions

	KEGG		Reactome
	Starch and sucrose metabolism Metabolic pathways Necroptosis Insulin signaling pathway Glucagon signaling pathway Insulin resistance		Neutrophil degranulation Glycogen breakdown (glycogenolysis)

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 (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Acute myeloid leukemia	Likely pathogenic; Pathogenic	rs113993981	RCV005887471	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Familial cancer of breast	Pathogenic	rs765425704	RCV005870888	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glycogen storage disease, type VI	Pathogenic; Likely pathogenic	rs1243388778, rs774646420, rs750567664, rs754629447, rs2502448999, rs2503486792, rs2503479112, rs2503523725, rs2503489724, rs786204785, rs150547274, rs1042609342, rs2503512754, rs2050602182, rs1469198620 View all (34 more)	RCV001330995 RCV001390321 RCV002250285 RCV002444366 RCV002444367 View all (46 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PYGL-related disorder	Pathogenic	rs2503489724	RCV003404048	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Thyroid cancer, nonmedullary, 1	Likely pathogenic; Pathogenic	rs113993981	RCV005887472	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Uterine corpus endometrial carcinoma	Pathogenic	rs113993982	RCV005887470	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Uveal melanoma	Pathogenic	rs113993982	RCV005887469	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (21)

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.
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARCINOMA, HEPATOCELLULAR	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHILDHOOD ACUTE LYMPHOBLASTIC LEUKEMIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHILDHOOD ONSET ASTHMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROESOPHAGEAL REFLUX DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen storage disease	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
GLYCOGEN STORAGE DISEASE DUE TO LIVER GLYCOGEN PHOSPHORYLASE DEFICIENCY	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLYCOGEN STORAGE DISEASE TYPE VI	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLYCOGEN STORAGE DISEASE VI	—	ClinGen, GWAS catalog, HPO ClinGen, GWAS catalog, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RECTUM CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (41)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Alzheimer Disease	Alzheimer disease	Pubtator	40183343	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	37063425	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral Infarction	Ischemic stroke	Pubtator	25135788	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	30820706, 33058866	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophageal neoplasm	Pubtator	34516362	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gerstmann-Straussler-Scheinker Disease	Gerstmann-Straussler-Scheinker syndrome	BEFREE	17705025		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	35764612	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	34512630	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease	Glycogen Storage Disease	GENOMICS_ENGLAND_DG	27604308		★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Glycogen storage disease due to liver glycogen phosphorylase deficiency	Glycogen Storage Disease	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease Type I	Glycogen Storage Disease	BEFREE	17994282		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease Type III	Glycogen Storage Disease	BEFREE	17994282		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease Type V	Glycogen Storage Disease	BEFREE	17705025		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease Type VI	Glycogen Storage Disease	CLINVAR_DG	21646031, 22899091, 25266922, 9529348, 9536091		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease Type VI	Glycogen Storage Disease	GENOMICS_ENGLAND_DG	27604308, 9536091		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease Type VI	Glycogen Storage Disease	BEFREE	28984260, 9536091		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease Type VI	Glycogen storage disease	Pubtator	30659246, 32268899, 32961316, 37264426, 9529348	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease Type VI	Glycogen Storage Disease	UNIPROT_DG	9529348		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease Type VI	Glycogen Storage Disease	CTD_human_DG	9529348, 9536091		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease Type VI	Glycogen Storage Disease	ORPHANET_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen storage disease, type IX	Glycogen Storage Disease	BEFREE	17994282		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hepatomegaly	Hepatomegaly	Pubtator	32268899, 32961316	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypercholesterolemia	Hypercholesterolemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperlipidemia	Hyperlipidemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypertriglyceridemia	Hypertriglyceridemia	Pubtator	32268899	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	Pubtator	32961316	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoglycemia	Hypoglycemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	35611851	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	37063425	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Ischemic Stroke	Ischemic stroke	Pubtator	25135788	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Failure Chronic	Kidney failure	Pubtator	30212930	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	CTD_human_DG	2885971		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mucocutaneous Lymph Node Syndrome	Kawasaki disease	Pubtator	38427757	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	37063425	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Precursor Cell Lymphoblastic Leukemia Lymphoma	Lymphoblastic Leukemia	GWASCAT_DG	23007406		★★★★★ ★☆☆☆☆ Found in Text Mining only
Precursor Cell Lymphoblastic Leukemia Lymphoma	Lymphoblastic Leukemia	GWASDB_DG	23007406		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pulmonary Arterial Hypertension	Pulmonary arterial hypertension	Pubtator	35611851	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	33628816, 37371537	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stroke	Stroke	Pubtator	25135788	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uveal melanoma	Uveal melanoma	Pubtator	37955612	Associate	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

PYGL (glycogen phosphorylase L)