PHKG1

protein-coding

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

Gene summary

This gene is a member of the Ser/Thr protein kinase family and encodes a protein with one protein kinase domain and two calmodulin-binding domains. This protein is the catalytic member of a 16 subunit protein kinase complex which contains equimolar ratios of 4 subunit types. The complex is a crucial glycogenolytic regulatory enzyme. This gene has two pseudogenes at chromosome 7q11.21 and one at chromosome 11p11.12. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

Previous symbols:

PHKG

MANE transcript

NM_006213.5

Inheritance

—

ClinVar variants

U:98B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr7:56,080,283-56,092,996

External References & Databases

Ensembl (ENSG00000164776)

Transcript & Mutation Effects

hg38 • Region Span ~12.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PHKG1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 98

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006213.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			97 clinvar	2 clinvar		99
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	98	2	0	100

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006213.5	RefSeq	NP_006204.1	9	MANE Select
ENST00000297373.7	Ensembl	ENSP00000297373.2	9	MANE Select
NM_001258459.2	RefSeq	NP_001245388.1	10	Standard
NM_001258460.2	RefSeq	NP_001245389.1	9	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
phkg1a	Danio rerio	Structure: dorsal longitudinal anastomotic vessel Quality: aplastic abnormal

Gene / Model

Organism

Observed Phenotype

phkg1a

Danio rerio

Structure: dorsal longitudinal anastomotic vessel

Quality: aplastic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glucagon signaling pathway - Homo sapiens (human)
Calcium signaling pathway - Homo sapiens (human)
Insulin signaling pathway - Homo sapiens (human)
Glycogen Metabolism
Metabolism of carbohydrates

Biological Process

carbohydrate metabolic process
glycogen biosynthetic process
protein phosphorylation

Molecular Function

calmodulin-dependent protein kinase activity
phosphorylase kinase activity
calmodulin binding
ATP binding
enzyme binding

Cellular Component

cytosol
phosphorylase kinase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000452681
Coding exons: 10
Length: 12250
Individuals with no LoFs: 125660
Homozygous LoFs: 1
Heterozygous LoFs: 86
Defined: 125747
p: 0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.593	244	272	0.899	0.0000179	2740
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.00021	0.00021	rare
South Asian	0.00098	0.00095	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.187

Intolerance Scores

LoFtool: 0.946
RVIS EVS: -1.42
RVIS percentile EVS: 4.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.893

Gene Damage Prediction

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