PHKG1

phosphorylase kinase catalytic subunit gamma 1, the group of Phosphorylase kinase subunits

Basic information

Region (hg38): 7:56080282-56092996

Previous symbols: [ "PHKG" ]

Links

ENSG00000164776 ∙ NCBI:5260 ∙ OMIM:172470 ∙ HGNC:8930 ∙ Uniprot:Q16816 ∙ 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 PHKG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHKG1 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						0
missense			40	1		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	1	0

Variants in PHKG1

This is a list of pathogenic ClinVar variants found in the PHKG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-56081068-C-T		not specified	Uncertain significance (Aug 13, 2021)
7-56081104-C-T		not specified	Uncertain significance (Jul 21, 2021)
7-56081119-G-A		not specified	Uncertain significance (Jan 30, 2024)
7-56081155-A-G		not specified	Uncertain significance (Jun 03, 2022)
7-56081176-C-T		not specified	Uncertain significance (Dec 20, 2022)
7-56081185-G-A		not specified	Uncertain significance (Dec 18, 2023)
7-56081187-C-T		not specified	Uncertain significance (Apr 01, 2024)
7-56081197-G-A		not specified	Uncertain significance (Jun 17, 2024)
7-56081214-C-T		not specified	Uncertain significance (Mar 19, 2024)
7-56081221-C-T		not specified	Uncertain significance (Feb 14, 2023)
7-56081222-G-C		not specified	Uncertain significance (May 23, 2023)
7-56081223-A-G		not specified	Uncertain significance (Oct 26, 2021)
7-56081229-C-T		not specified	Uncertain significance (Jun 22, 2024)
7-56081248-G-A		not specified	Uncertain significance (Nov 09, 2021)
7-56081250-C-T		not specified	Uncertain significance (Mar 29, 2023)
7-56081251-G-A		not specified	Uncertain significance (Jan 03, 2022)
7-56081269-G-A		not specified	Uncertain significance (Oct 27, 2021)
7-56081284-C-T		not specified	Uncertain significance (Oct 12, 2021)
7-56081643-C-T		not specified	Uncertain significance (Jun 22, 2023)
7-56081644-G-A		not specified	Uncertain significance (Mar 15, 2024)
7-56081659-G-A		not specified	Uncertain significance (Nov 03, 2022)
7-56081695-G-A		not specified	Uncertain significance (Apr 23, 2024)
7-56081703-G-C		not specified	Uncertain significance (Feb 07, 2023)
7-56081712-G-A		not specified	Uncertain significance (Dec 20, 2022)
7-56081751-G-A		not specified	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHKG1	protein_coding	protein_coding	ENST00000452681	10	12250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.57e-15	0.0406	125660	1	86	125747	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.593	244	272	0.899	0.0000179	2740
Missense in Polyphen		99	110.39	0.89679		1124
Synonymous	-0.109	115	114	1.01	0.00000786	794
Loss of Function	0.534	24	27.0	0.889	0.00000172	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00149	0.00149
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000939	0.0000924
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.0000544	0.0000544
South Asian	0.000980	0.000948
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of the phosphorylase b kinase (PHK), which mediates the neural and hormonal regulation of glycogen breakdown (glycogenolysis) by phosphorylating and thereby activating glycogen phosphorylase. In vitro, phosphorylates PYGM, TNNI3, MAPT/TAU, GAP43 and NRGN/RC3 (By similarity). {ECO:0000250}.
• Pathway: Glucagon signaling pathway - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Glycogen Metabolism;Metabolism of carbohydrates;Metabolism;Glycogen breakdown (glycogenolysis);Glycogen metabolism (Consensus)

Recessive Scores

• pRec: 0.187

Intolerance Scores

• loftool: 0.946
• rvis_EVS: -1.42
• rvis_percentile_EVS: 4.11

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.473
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.893

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phkg1

Zebrafish Information Network

• Gene name: phkg1a
• Affected structure: dorsal longitudinal anastomotic vessel
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: carbohydrate metabolic process;glycogen biosynthetic process;protein phosphorylation
• Cellular component: cytosol;phosphorylase kinase complex
• Molecular function: calmodulin-dependent protein kinase activity;phosphorylase kinase activity;calmodulin binding;ATP binding;enzyme binding;tau-protein kinase activity