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PYGL

glycogen phosphorylase L, the group of Glycogen phosphorylases

Basic information

Region (hg38): 14:50857890-50944483

Links

ENSG00000100504 ∙ NCBI:5836 ∙ OMIM:613741 ∙ HGNC:9725 ∙ Uniprot:P06737 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • glycogen storage disease VI (Definitive), mode of inheritance: AR
  • glycogen storage disease VI (Strong), mode of inheritance: AR
  • glycogen storage disease VI (Strong), mode of inheritance: AR
  • glycogen storage disease VI (Strong), mode of inheritance: AR
  • glycogen storage disease VI (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Glycogen storage disease VIARBiochemicalThe condition can include manifestations suc has hypoglycemia, ketosis, and growth retardation, and recommendations for care include laboratory-based monitoring (eg, including liver function tests, glucose, and ketones), radiological monitoring (abdominal imaging), and nutritional recommendations and avoidance of certain medications in order to help improve metabolic to control and prevent the primary complications; Specific care during pregnancy has been recommendedBiochemical13646331; 5904467; 9529348; 9536091; 17705025; 20301788; 21646031; 25266922; 30659246

ClinVar

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

  • Glycogen storage disease, type VI (232 variants)
  • not provided (91 variants)
  • Inborn genetic diseases (40 variants)
  • not specified (33 variants)
  • - (2 variants)
  • PYGL-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PYGL gene is commonly pathogenic or not.

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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
3
clinvar
37
clinvar
5
clinvar
 45
missense
4
clinvar
10
clinvar
95
clinvar
7
clinvar
3
clinvar
 119
nonsense
8
clinvar
4
clinvar
1
clinvar
 13
start loss
0
frameshift
8
clinvar
3
clinvar
1
clinvar
 12
inframe indel
2
clinvar
 2
splice donor/acceptor (+/-2bp)
9
clinvar
4
clinvar
1
clinvar
 14
splice region
?
    Intron variants in splice region, excluding donor/acceptor (+/-2bp)
4
7
2
 13
non coding
?
    UTR, intron and other, non coding variants
1
clinvar
27
clinvar
22
clinvar
37
clinvar
 87
Total 29 22 129 66 46

Highest pathogenic variant AF is 0.0000591

Variants in PYGL

This is a list of pathogenic ClinVar variants found in the PYGL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
14-50858108-A-T Uncertain significance (Sep 01, 2022)1711371
14-50872181-G-A not specified Uncertain significance (Apr 08, 2022)2350010
14-50872209-C-T not specified Likely benign (Jan 26, 2022)2351291
14-50872245-C-A not specified Uncertain significance (Jul 08, 2022)2300369
14-50877959-C-G not specified Uncertain significance (Feb 22, 2023)2460818
14-50877975-T-C not specified Likely benign (May 18, 2023)2507885
14-50877979-C-T Likely benign (Jul 01, 2022)2644234
14-50878002-A-G not specified Uncertain significance (Aug 02, 2021)2375545
14-50878826-C-T not specified Uncertain significance (Oct 05, 2023)3130299
14-50878846-T-C not specified Uncertain significance (Aug 12, 2022)2311854
14-50880523-G-C not specified Uncertain significance (May 06, 2022)3130308
14-50880538-T-C not specified Uncertain significance (Apr 04, 2023)2532636
14-50881610-G-C not specified Uncertain significance (Feb 22, 2023)2487697
14-50881627-G-T Benign (Feb 01, 2024)3024734
14-50885652-C-A not specified Uncertain significance (Aug 14, 2023)2600510
14-50885769-T-C not specified Uncertain significance (Nov 03, 2022)2400979
14-50885781-C-T not specified Uncertain significance (Feb 12, 2024)3130326
14-50885786-A-G not specified Uncertain significance (Sep 06, 2022)2406987
14-50885808-C-T not specified Uncertain significance (Mar 04, 2024)3130333
14-50885816-G-A not specified Uncertain significance (Mar 04, 2024)3130339
14-50901839-A-T not specified Uncertain significance (Oct 29, 2021)2351903
14-50901861-A-G Likely benign (Mar 01, 2023)2498593
14-50903441-A-G not specified Uncertain significance (Jun 29, 2023)2607412
14-50903465-A-G not specified Uncertain significance (Jun 27, 2023)2606600
14-50904105-A-T not specified Uncertain significance (Dec 21, 2022)2338183

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PYGLprotein_codingprotein_codingENST00000216392 2086846
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.71e-170.4924175726796571951257480.424
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2034784661.030.00002545610
Missense in Polyphen246239.071.0292934
Synonymous0.2971771820.9720.00001031601
Loss of Function1.743345.70.7220.00000259525

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American1.311.31
Ashkenazi Jewish0.3380.335
East Asian0.6100.607
Finnish0.3600.361
European (Non-Finnish)0.3430.342
Middle Eastern0.6100.607
South Asian0.4460.442
Other0.4080.407

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 6 (GSD6) [MIM:232700]: A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected. {ECO:0000269|PubMed:9529348}. 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 synthetase deficiency;Glycogenosis, Type III. Cori disease, Debrancher glycogenosis;Mucopolysaccharidosis VI. Sly syndrome;Sucrase-isomaltase deficiency;Glycogenosis, Type IV. Amylopectinosis, Anderson disease;Glycogenosis, Type VI. Hers disease;Starch and Sucrose Metabolism;TNF alpha Signaling Pathway;Glycogen Metabolism;Neutrophil degranulation;Metabolism of carbohydrates;glycogenolysis;Innate Immune System;Immune System;Metabolism;Glycogen breakdown (glycogenolysis);Glycogen metabolism (Consensus)

Recessive Scores

pRec
0.423

Intolerance Scores

loftool
0.0522
rvis_EVS
0.21
rvis_percentile_EVS
67.5

Haploinsufficiency Scores

pHI
0.242
hipred
N
hipred_score
0.492
ghis
0.496

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.992

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pygl
Phenotype

Gene ontology

Biological process
glycogen metabolic process;glycogen catabolic process;5-phosphoribose 1-diphosphate biosynthetic process;response to bacterium;glucose homeostasis;neutrophil degranulation;necroptotic process
Cellular component
extracellular region;cytoplasm;cytosol;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
Molecular function
purine nucleobase binding;protein binding;ATP binding;glucose binding;drug binding;glycogen phosphorylase activity;AMP binding;vitamin binding;pyridoxal phosphate binding;bile acid binding;protein homodimerization activity;linear malto-oligosaccharide phosphorylase activity;SHG alpha-glucan phosphorylase activity