PYGB

glycogen phosphorylase B, the group of Glycogen phosphorylases

Basic information

Region (hg38): 20:25248084-25298012

Links

ENSG00000100994 ∙ NCBI:5834 ∙ OMIM:138550 ∙ HGNC:9723 ∙ Uniprot:P11216 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (40 variants)
• not provided (14 variants)
• not specified (1 variants)
• Short stature (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PYGB 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				1	2	3
missense			40	1		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1	8	10
Total	0	0	41	3	10

Variants in PYGB

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

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

Position	Type	Phenotype	Significance	ClinVar
20-25248188-C-T		not specified	Uncertain significance (Aug 02, 2022)
20-25248194-A-C		not specified	Uncertain significance (Aug 08, 2023)
20-25248200-A-T		not specified	Uncertain significance (Aug 16, 2022)
20-25248266-A-C		not specified	Uncertain significance (Apr 28, 2022)
20-25248276-A-G		not specified	Uncertain significance (Dec 21, 2023)
20-25248292-C-A		not specified	Uncertain significance (Sep 20, 2023)
20-25248309-G-A		not specified	Uncertain significance (Jun 02, 2023)
20-25248348-C-G			Likely benign (Mar 29, 2018)
20-25248352-C-G		not specified	Uncertain significance (May 16, 2023)
20-25259238-G-A		not specified	Uncertain significance (Dec 13, 2023)
20-25259273-C-T		not specified	Uncertain significance (Oct 03, 2023)
20-25259274-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-25271392-T-C		not specified	Uncertain significance (Jun 23, 2023)
20-25271400-A-G		not specified	Uncertain significance (Nov 09, 2021)
20-25271412-G-T		not specified	Uncertain significance (May 03, 2023)
20-25271431-A-G		not specified	Uncertain significance (Jan 08, 2024)
20-25274603-C-T			Benign (Jun 29, 2018)
20-25274653-A-G		not specified	Uncertain significance (Nov 17, 2022)
20-25274682-G-A		not specified	Uncertain significance (Dec 27, 2022)
20-25274682-G-T		not specified	Uncertain significance (Dec 06, 2022)
20-25276686-A-G		not specified	Uncertain significance (Sep 26, 2023)
20-25276693-C-G		not specified	Uncertain significance (Jun 28, 2022)
20-25276731-C-T		not specified	Uncertain significance (Mar 11, 2022)
20-25277264-G-A		not specified	Uncertain significance (Dec 27, 2023)
20-25277279-C-T		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PYGB	protein_coding	protein_coding	ENST00000216962	20	49946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.41e-14	0.912	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0473	555	552	1.01	0.0000360	5537
Missense in Polyphen		229	253.1	0.90478		2532
Synonymous	-1.51	272	242	1.12	0.0000174	1619
Loss of Function	2.14	29	44.4	0.653	0.00000226	494

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000941	0.000916
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000218	0.000217
Finnish	0.000371	0.000370
European (Non-Finnish)	0.000257	0.000255
Middle Eastern	0.000218	0.000217
South Asian	0.000360	0.000359
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycogen phosphorylase that regulates glycogen mobilization (PubMed:27402852). Phosphorylase is an important allosteric enzyme in carbohydrate metabolism (PubMed:3346228). Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates (PubMed:3346228). However, all known phosphorylases share catalytic and structural properties (PubMed:3346228). {ECO:0000269|PubMed:27402852, ECO:0000303|PubMed:3346228}.
• 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;Neutrophil degranulation;Metabolism of carbohydrates;glycogenolysis;Innate Immune System;Immune System;Metabolism;EGFR1;Glycogen breakdown (glycogenolysis);Glycogen metabolism (Consensus)

Recessive Scores

• pRec: 0.449

Intolerance Scores

• loftool: 0.0325
• rvis_EVS: -1.46
• rvis_percentile_EVS: 3.89

Haploinsufficiency Scores

• pHI: 0.0814
• hipred: N
• hipred_score: 0.492
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pygb

Gene ontology

• Biological process: glycogen catabolic process;neutrophil degranulation
• Cellular component: extracellular region;cytoplasm;membrane;azurophil granule lumen;extracellular exosome
• Molecular function: protein binding;glycogen phosphorylase activity;pyridoxal phosphate binding;linear malto-oligosaccharide phosphorylase activity;SHG alpha-glucan phosphorylase activity