GeneBe

PYGM

glycogen phosphorylase, muscle associated, the group of Glycogen phosphorylases

Basic information

Region (hg38): 11:64746389-64759974

Links

ENSG00000068976 ∙ NCBI:5837 ∙ OMIM:608455 ∙ HGNC:9726 ∙ Uniprot:P11217 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • glycogen storage disease V (Strong), mode of inheritance: AR
  • glycogen storage disease V (Limited), mode of inheritance: AD
  • glycogen storage disease V (Strong), mode of inheritance: AR
  • glycogen storage disease V (Strong), mode of inheritance: AR
  • glycogen storage disease V (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Glycogen storage disease VARBiochemical; Musculoskeletal; Pharmacogenomic; RenalAvoidance of excessive exercise may be beneficial to avoid rhabdomyolysis and potential renal failure; Sucrose ingestion may be beneficial (eg, prior to exercise); Certain precautions should be taken with general anesthesiaBiochemical; Musculoskeletal; Renal16590445; 14442994; 4502558; 1067063; 101896; 6929403; 3808314; 3466902; 3207360; 2768781; 2391551; 8408630; 8316268; 11168025; 14695410; 16924035; 17705025; 17915571; 18667317; 19251976; 19433441; 20301518; 20957198; 21802952; 21880526; 22608882; 22818872; 22899091

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PYGM gene.

  • Glycogen_storage_disease,_type_V (1410 variants)
  • not_provided (193 variants)
  • not_specified (90 variants)
  • Inborn_genetic_diseases (87 variants)
  • PYGM-related_disorder (30 variants)
  • Tip-toe_gait (19 variants)
  • See_cases (3 variants)
  • Elevated_circulating_creatine_kinase_concentration (2 variants)
  • Glycogen_storage_disease (2 variants)
  • McArdle_disease,_mild (2 variants)
  • High_myopia (1 variants)
  • Hereditary_skeletal_muscle_disorder (1 variants)
  • Malignant_hyperthermia,_susceptibility_to,_1 (1 variants)
  • Rhabdomyolysis (1 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
  • Abnormality_of_metabolism/homeostasis (1 variants)
  • Myopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PYGM gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005609.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
17
clinvar
407
clinvar
3
clinvar
 430
missense
10
clinvar
67
clinvar
408
clinvar
17
clinvar
2
clinvar
 504
nonsense
20
clinvar
20
clinvar
 40
start loss
4
2
 6
frameshift
63
clinvar
57
clinvar
1
clinvar
 121
splice donor/acceptor (+/-2bp)
5
clinvar
54
clinvar
 59
Total 104 201 425 425 5

Highest pathogenic variant AF is 0.0028372484

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PYGMprotein_codingprotein_codingENST00000164139 2013909
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.03e-130.94812525704911257480.00195
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.04695195220.9940.00003875528
Missense in Polyphen247256.20.964092696
Synonymous-0.5182212111.050.00001541637
Loss of Function2.222742.60.6340.00000238479

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.003350.00323
Ashkenazi Jewish0.0001980.000198
East Asian0.0005440.000544
Finnish0.0008320.000832
European (Non-Finnish)0.002930.00293
Middle Eastern0.0005440.000544
South Asian0.0007210.000719
Other0.002610.00261

dbNSFP

Source: dbNSFP

Function
FUNCTION: Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.;
Disease
DISEASE: Glycogen storage disease 5 (GSD5) [MIM:232600]: A metabolic disorder resulting in myopathy characterized by exercise intolerance, cramps, muscle weakness and recurrent myoglobinuria. {ECO:0000269|PubMed:10382911, ECO:0000269|PubMed:10382912, ECO:0000269|PubMed:10417800, ECO:0000269|PubMed:10590419, ECO:0000269|PubMed:10681080, ECO:0000269|PubMed:10714589, ECO:0000269|PubMed:10899452, ECO:0000269|PubMed:11706962, ECO:0000269|PubMed:12031624, ECO:0000269|PubMed:7603523, ECO:0000269|PubMed:8316268, ECO:0000269|PubMed:8535454, ECO:0000269|PubMed:9506549}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Insulin resistance - Homo sapiens (human);Starch and sucrose metabolism - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Necroptosis - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Glycogen Metabolism;Metabolism of carbohydrates;glycogenolysis;Metabolism;Glycogen breakdown (glycogenolysis);Glycogen metabolism (Consensus)

Recessive Scores

pRec
0.128

Intolerance Scores

loftool
0.0422
rvis_EVS
-0.19
rvis_percentile_EVS
39.31

Haploinsufficiency Scores

pHI
0.508
hipred
N
hipred_score
0.414
ghis
0.515

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.994

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pygm
Phenotype
renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
glycogen metabolic process;glycogen catabolic process
Cellular component
cytoplasm;cytosol;extracellular exosome
Molecular function
nucleotide binding;protein binding;glycogen phosphorylase activity;pyridoxal phosphate binding;linear malto-oligosaccharide phosphorylase activity;SHG alpha-glucan phosphorylase activity