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	5837
Gene name	Glycogen phosphorylase, muscle associated
Gene symbol	PYGM
Synonyms (NCBI Gene)	GSD5
Chromosome	11
Chromosome location	11q13.1
Summary	This gene encodes a muscle enzyme involved in glycogenolysis. Highly similar enzymes encoded by different genes are found in liver and brain. Mutations in this gene are associated with McArdle disease (myophosphorylase deficiency), a glycogen storage dise

Show/Hide all (90)

SNP ID	Visualize variation	Clinical significance	Consequence
rs61736659	G>C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs114073621	G>A	Pathogenic	Coding sequence variant, stop gained
rs114468011	T>C	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs116135678	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs116180923	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs116315896	C>T	Pathogenic, benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs116987552	G>A	Pathogenic	Coding sequence variant, stop gained
rs119103251	C>T	Pathogenic	Coding sequence variant, missense variant
rs119103252	T>G	Pathogenic	Coding sequence variant, missense variant
rs119103253	C>T	Pathogenic	Coding sequence variant, missense variant
rs119103254	A>G	Pathogenic	Coding sequence variant, missense variant
rs119103255	G>A	Pathogenic, pathogenic-likely-pathogenic	Coding sequence variant, stop gained
rs119103256	G>A,C	Pathogenic	Coding sequence variant, stop gained, missense variant
rs119103257	C>A,T	Pathogenic	Coding sequence variant, stop gained, missense variant
rs119103259	C>T	Likely-pathogenic	Coding sequence variant, synonymous variant
rs119103260	A>C,G	Likely-pathogenic	Coding sequence variant, stop gained, synonymous variant
rs139726186	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant
rs141959242	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant
rs142054672	T>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs143401208	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs144081869	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs200357590	C>A,G,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs201711087	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant
rs267606993	T>A,C,G	Pathogenic, likely-pathogenic	Missense variant, initiator codon variant
rs368602234	->G	Uncertain-significance, benign, conflicting-interpretations-of-pathogenicity	Intron variant
rs370247862	G>A	Pathogenic	Missense variant, coding sequence variant, intron variant
rs377225525	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs397514631	T>C	Pathogenic	Missense variant, coding sequence variant
rs398124208	C>G,T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs398124209	G>C	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs527236146	G>T	Likely-pathogenic	Stop gained, coding sequence variant, intron variant
rs527236147	AAG>-	Pathogenic-likely-pathogenic	Coding sequence variant, inframe deletion
rs558267822	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs568496266	T>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs747513238	A>C	Likely-pathogenic	Splice donor variant
rs749560316	C>G,T	Likely-pathogenic	Splice donor variant
rs750857876	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs752622662	G>A	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant
rs752848974	C>A,T	Likely-pathogenic	Stop gained, coding sequence variant, missense variant
rs752851284	T>C	Likely-pathogenic	Intron variant, splice acceptor variant
rs753181427	C>A,G	Likely-pathogenic	Splice donor variant
rs755117847	CA>-	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant
rs757681143	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs759657964	C>T	Likely-pathogenic	Splice donor variant
rs764313717	T>C	Pathogenic, conflicting-interpretations-of-pathogenicity	Intron variant
rs767739769	G>A	Pathogenic, pathogenic-likely-pathogenic	Coding sequence variant, stop gained
rs768604948	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs769172044	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs769960481	A>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs770037766	->CTTGGTCT	Pathogenic	Coding sequence variant, frameshift variant
rs771427957	C>T	Pathogenic	Splice donor variant
rs772194378	AG>-	Pathogenic	Coding sequence variant, frameshift variant
rs780246932	C>A,G,T	Likely-pathogenic	Missense variant, coding sequence variant, intron variant
rs780656375	G>A,T	Likely-pathogenic	Missense variant, coding sequence variant, synonymous variant
rs786200874	T>-	Pathogenic	Frameshift variant, coding sequence variant
rs786204723	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant, intron variant
rs886041476	->G	Pathogenic	Frameshift variant, coding sequence variant
rs926661627	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1057516259	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057516329	CAGGTAGTAGA>-	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1057516349	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1057516468	A>C	Likely-pathogenic	Splice donor variant
rs1057516598	C>T	Likely-pathogenic	Splice acceptor variant
rs1057516612	CTCC>TCA	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057516629	A>-	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1057517067	->A	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057517145	G>C	Likely-pathogenic	Intron variant, stop gained, coding sequence variant
rs1057517361	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1057517400	TTGC>-	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1057517442	C>G	Likely-pathogenic	Splice donor variant
rs1064797157	T>A	Likely-pathogenic	Splice acceptor variant
rs1085307918	C>A	Likely-pathogenic	Missense variant, intron variant, coding sequence variant
rs1085308021	C>T	Likely-pathogenic	Missense variant, intron variant, coding sequence variant
rs1131691807	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1163710370	C>A	Likely-pathogenic	Splice acceptor variant
rs1212333772	T>C	Likely-pathogenic	Splice acceptor variant
rs1325298827	AGT>-,AGTAGT	Pathogenic, uncertain-significance	Coding sequence variant, inframe insertion, inframe deletion
rs1474863903	C>T	Pathogenic	Intron variant
rs1489442842	->A	Likely-pathogenic	Splice donor variant
rs1555136208	C>T	Likely-pathogenic	Splice donor variant
rs1555136390	->A	Pathogenic	Coding sequence variant, intron variant, stop gained
rs1555136459	C>A	Likely-pathogenic	Coding sequence variant, intron variant, stop gained
rs1555136540	AA>-	Likely-pathogenic	Coding sequence variant, frameshift variant, intron variant
rs1555136752	GC>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1565538121	CGTTGCCCAGCCCC>-	Uncertain-significance, pathogenic	Coding sequence variant, frameshift variant, intron variant
rs1592408302	GG>-	Pathogenic	Frameshift variant, coding sequence variant
rs1592409631	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1592409633	GAG>-	Likely-pathogenic	Inframe deletion, coding sequence variant
rs1592410003	T>A	Pathogenic	Coding sequence variant, stop gained
rs1592412131	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant

Show/Hide all (1)

miRTarBase ID	miRNA	Experiments	Reference
MIRT017225	hsa-miR-335-5p	Microarray	18185580

Show/Hide all (23)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0003824	Function	Catalytic activity	IEA
GO:0004645	Function	1,4-alpha-oligoglucan phosphorylase activity	IEA
GO:0005515	Function	Protein binding	IPI	24722188, 25416956, 31515488, 32296183, 33961781, 36217029
GO:0005737	Component	Cytoplasm	IBA
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	TAS	9633816
GO:0005980	Process	Glycogen catabolic process	IBA
GO:0005980	Process	Glycogen catabolic process	IDA	1150650
GO:0005980	Process	Glycogen catabolic process	IEA
GO:0005980	Process	Glycogen catabolic process	IMP	8316268
GO:0008184	Function	Glycogen phosphorylase activity	IBA
GO:0008184	Function	Glycogen phosphorylase activity	IDA	1150650
GO:0008184	Function	Glycogen phosphorylase activity	IEA
GO:0008184	Function	Glycogen phosphorylase activity	IMP	8316268
GO:0008184	Function	Glycogen phosphorylase activity	TAS	9633816
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0030170	Function	Pyridoxal phosphate binding	IBA
GO:0030170	Function	Pyridoxal phosphate binding	IEA
GO:0070062	Component	Extracellular exosome	HDA	23533145

MIM	HGNC	e!Ensembl
608455	9726	ENSG00000068976

P11217

Protein name

Glycogen phosphorylase, muscle form (EC 2.4.1.1) (Myophosphorylase)

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

1Z8D

Family and domains

Pfam

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

Sequence

MSRPLSDQEKRKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTV
RDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDM
EELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKISGGWQMEEA
DDWLRYGNPWEKARPEFTLPVHFYGHVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVN
TMRLWSAKAPNDFNLKDFNVGGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFV
VAATLQDIIRRFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRILVDLERM
DWDKAWDVTVRTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFP
GDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKF
QNKTNGITPRRWLVLCNPGLAEVIAERIGEDFISDLDQLRKLLSFVDDEAFIRDVAKVKQ
ENKLKFAAYLEREYKVHINPNSLFDIQVKRIHEYKRQLLNCLHVITLYNRIKREPNKFFV
PRTVMIGGKAAPGYHMAKMIIRLVTAIGDVVNHDPAVGDRLRVIFLENYRVSLAEKVIPA
ADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVD
KLDQRGYNAQEYYDRIPELRQVIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYED
YIKCQEKVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPAPDE
AI

Sequence length

842

Interactions

View interactions

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

1410

Show/Hide Causal Diseases (10)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of metabolism/homeostasis	Likely pathogenic	rs779392056	RCV001814419
Acute rhabdomyolysis	Likely pathogenic; Pathogenic	rs767739769, rs2496637644	RCV005865264 RCV005865644
Glycogen storage disease	Pathogenic	rs768604948	RCV004017747
Glycogen storage disease, type V	Likely pathogenic; Pathogenic	rs398124208, rs398124209, rs398124210, rs750080547, rs749560316, rs2135836123, rs2135836264, rs2135840980, rs1565531128, rs2135831473, rs1272600960, rs1191939323, rs779562449, rs2058376454, rs2058377004 View all (209 more)	RCV000169330 RCV001047041 RCV000175318 RCV001377990 RCV001379674 RCV001376828 RCV001378761 RCV001379809 RCV001388132 RCV001382486 RCV001383627 RCV001382415 RCV001381560 RCV001381789 RCV001381049 RCV001386380 RCV001390883 RCV001381787 RCV001382416 RCV001542478 RCV002568994 RCV001729978 RCV001784892 RCV001784893 RCV001783653 RCV001783654 RCV001806322 RCV001867107 RCV002046146 RCV001999785 RCV001941724 RCV001963967 RCV002019558 RCV001953787 RCV002049213 RCV002007330 RCV001993352 RCV001994670 RCV000128551 RCV000128553 RCV001942146 RCV002002518 RCV001950413 RCV001968726 RCV001875127 RCV001889940 RCV001937863 RCV001920289 RCV000144425 RCV003089156 RCV002225179 RCV000002388 RCV000002389 RCV000002390 RCV000002392 RCV000002394 RCV000002396 RCV000002397 RCV000002398 RCV000002399 RCV000002400 RCV000002402 RCV000002403 RCV000002404 RCV001851580 RCV000454242 RCV002470069 RCV000169141 RCV000169167 RCV000169547 RCV000169106 RCV003058322 RCV000763265 RCV002705561 RCV002720543 RCV002751300 RCV002861541 RCV002857232 RCV002903557 RCV002952971 RCV002988528 RCV003010313 RCV003003236 RCV003012205 RCV003014369 RCV003045214 RCV003034713 RCV003034797 RCV003049784 RCV003047010 RCV003061859 RCV001387933 RCV003471757 RCV003471758 RCV003463409 RCV003463410 RCV003463411 RCV003463412 RCV003463413 RCV003471759 RCV003471760 RCV003463414 RCV003463415 RCV003471761 RCV003463416 RCV003463417 RCV003463418 RCV003463419 RCV003463420 RCV003463422 RCV003471762 RCV003463423 RCV003463424 RCV003463425 RCV003463426 RCV003463427 RCV003463428 RCV003471764 RCV003471765 RCV003471766 RCV003498035 RCV003498270 RCV003498201 RCV003499518 RCV003499893 RCV003499895 RCV003499971 RCV003499973 RCV003499974 RCV003497578 RCV003497777 RCV003498317 RCV003498403 RCV003499363 RCV003499348 RCV003604166 RCV003604313 RCV003604307 RCV003604359 RCV003604446 RCV003604849 RCV003604867 RCV003604927 RCV003605004 RCV003602547 RCV003602569 RCV003602843 RCV003603033 RCV003836283 RCV003851037 RCV003861695 RCV004574655 RCV004574656 RCV004574657 RCV004574658 RCV004574659 RCV004574660 RCV004574662 RCV004574664 RCV004574665 RCV000409749 RCV000409053 RCV000411646 RCV000410560 RCV000410171 RCV000411206 RCV000409723 RCV000411312 RCV000410338 RCV000409547 RCV000409188 RCV000411263 RCV000410907 RCV000411763 RCV000410172 RCV000412395 RCV000409457 RCV000412392 RCV000409722 RCV000411559 RCV000409435 RCV001782972 RCV000669086 RCV001036939 RCV000498994 RCV001783020 RCV000557171 RCV000033140 RCV000033141 RCV003465329 RCV000631182 RCV000668975 RCV000668989 RCV000673149 RCV000669604 RCV000668678 RCV000670071 RCV000667359 RCV000671611 RCV000664848 RCV000665175 RCV000671988 RCV000671584 RCV000668184 RCV000666659 RCV000690159 RCV000706083 RCV000821091 RCV003768171 RCV000761339 RCV000778335 RCV000791057 RCV000815465 RCV000805625 RCV000815772 RCV000988569 RCV000988571 RCV000991439 RCV001063572 RCV001063010 RCV001062130 RCV001068074 RCV001047414 RCV001051694 RCV001051949 RCV001041989 RCV001068083 RCV005049766 RCV001222438 RCV001220462 RCV001214599 RCV001216334 RCV001211508 RCV001204475 RCV001202839 RCV001233784 RCV001246104 RCV001239494 RCV001242446 RCV001244443 RCV001244574 RCV001267843
Hereditary skeletal muscle disorder	Pathogenic	rs116987552	RCV005624665
Lung cancer	Likely pathogenic	rs1394587447	RCV005927720
McArdle disease, mild	Likely pathogenic; Pathogenic	rs1474863903, rs764313717	RCV000002405 RCV000002406
PYGM-related disorder	Likely pathogenic; Pathogenic	rs144081869, rs757681143, rs1212333772	RCV003407258 RCV003409682 RCV004753050
See cases	Pathogenic	rs116987552, rs119103259, rs114073621	RCV002251857 RCV002251858 RCV003324712
Tip-toe gait	Pathogenic; Likely pathogenic	rs779562449, rs116987552, rs144081869, rs1057517442, rs1005687078, rs780193588	RCV003318688 RCV003319158 RCV003319973 RCV003319195 RCV003319218 RCV003319223

Show/Hide Unknown Diseases (11)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign; Likely benign	rs75633423	RCV005886500
Cervical cancer	Benign; Likely benign	rs75633423	RCV005886501
EBV-positive nodal T- and NK-cell lymphoma	Conflicting classifications of pathogenicity	rs141265458	RCV004559144
Elevated circulating creatine kinase concentration	Uncertain significance	rs2058348746, rs759130375	RCV001328499 RCV001281578
Familial cancer of breast	Conflicting classifications of pathogenicity	rs142234258	RCV005891987
Hepatocellular carcinoma	Conflicting classifications of pathogenicity	rs150622626	RCV005895900
High myopia	Uncertain significance	rs148839812	RCV000785674
Malignant tumor of esophagus	Conflicting classifications of pathogenicity	rs142234258	RCV005891988
Myopathy	Benign	rs768761419	RCV000850323
Rhabdomyolysis	Conflicting classifications of pathogenicity	rs370144967	RCV003409926
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs75633423	RCV005886502

Show/Hide Text Mining Associations (13)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acute Kidney Injury	Associate	30900170
Camptocormia	Associate	39375813
Down Syndrome	Associate	15716609
Dysferlinopathy	Associate	39350328
Glycogen Storage Disease Type V	Associate	10063833, 10362816, 10382911, 10450796, 20957198, 22234204, 25045239, 25741863, 26913921, 27899787, 28925366, 28967462, 29143597, 29371640, 29391358 View all (16 more)
Multiple Endocrine Neoplasia Type 1	Associate	11549605
Muscle Weakness	Associate	29143597, 39375813
Muscular Diseases	Associate	39375813
Myopathy with Lactic Acidosis Hereditary	Associate	29143597
Pituitary Neoplasms	Associate	10389976
Rhabdomyolysis	Associate	30900170, 32978841
Squamous Cell Carcinoma of Head and Neck	Inhibit	31324732
Vitelliform Macular Dystrophy	Associate	7977378

PYGM (glycogen phosphorylase, muscle associated)