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PHKA2 phosphorylase kinase regulatory subunit alpha 2 [ Homo sapiens (human) ]

Gene ID: 5256, updated on 5-Mar-2024

Summary

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Official Symbol
PHKA2provided by HGNC
Official Full Name
phosphorylase kinase regulatory subunit alpha 2provided by HGNC
Primary source
HGNC:HGNC:8926
See related
Ensembl:ENSG00000044446 MIM:300798; AllianceGenome:HGNC:8926
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PHK; PYK; XLG; PYKL; XLG2; GSD9A
Summary
Phosphorylase kinase is a polymer of 16 subunits, four each of alpha, beta, gamma and delta. The alpha subunit includes the skeletal muscle and hepatic isoforms, and the hepatic isoform is encoded by this gene. The beta subunit is the same in both the muscle and hepatic isoforms, and encoded by one gene. The gamma subunit also includes the skeletal muscle and hepatic isoforms, which are encoded by two different genes. The delta subunit is a calmodulin and can be encoded by three different genes. The gamma subunits contain the active site of the enzyme, whereas the alpha and beta subunits have regulatory functions controlled by phosphorylation. The delta subunit mediates the dependence of the enzyme on calcium concentration. Mutations in this gene cause glycogen storage disease type 9A, also known as X-linked liver glycogenosis. Alternatively spliced transcript variants have been reported, but the full-length nature of these variants has not been determined.[provided by RefSeq, Feb 2010]
Expression
Ubiquitous expression in fat (RPKM 8.9), ovary (RPKM 8.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
Xp22.13
Exon count:
33
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (18892298..18984114, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (18475012..18566828, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (18910416..19002232, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29459 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:18880662-18881162 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:18881163-18881663 Neighboring gene BLOC1S6 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18889999-18890500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18890501-18891000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29460 Neighboring gene HAUS augmin like complex subunit 1 pseudogene 2 Neighboring gene PHKA2 antisense RNA 1 Neighboring gene RNA, 7SL, cytoplasmic 48, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:19002034-19002534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29461 Neighboring gene uncharacterized LOC101928415 Neighboring gene adhesion G protein-coupled receptor G2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:19125111-19125740 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:19182810-19182961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29462 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:19278446-19278946 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:19309116-19309616 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:19309617-19310117 Neighboring gene mitogen-activated protein kinase kinase kinase 15 Neighboring gene pyruvate dehydrogenase E1 subunit alpha 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. PHKA2 variants expand the phenotype of phosphorylase B kinase deficiency to include patients with ketotic hypoglycemia only. Benner A, et al. Am J Med Genet A, 2021 Oct. PMID 34117828, Free PMC Article
  2. Benign or not benign? Deep phenotyping of liver Glycogen Storage Disease IX. Fernandes SA, et al. Mol Genet Metab, 2020 Nov. PMID 33317799, Free PMC Article
  3. A novel frameshift PHKA2 mutation in a family with glycogen storage disease type IXa: A first report in Vietnam and review of literature. Nguyen NL, et al. Clin Chim Acta, 2020 Sep. PMID 32387637
  4. A novel PHKA2 mutation in a Chinese child with glycogen storage disease type IXa: a case report and literature review. Fu J, et al. BMC Med Genet, 2019 Mar 29. PMID 30925902, Free PMC Article
  5. PHKA2 mutation spectrum in Korean patients with glycogen storage disease type IX: prevalence of deletion mutations. Choi R, et al. BMC Med Genet, 2016 Apr 21. PMID 27103379, Free PMC Article

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PHKA2 variants expand the phenotype of phosphorylase B kinase deficiency to include patients with ketotic hypoglycemia only.
    Title: PHKA2 variants expand the phenotype of phosphorylase B kinase deficiency to include patients with ketotic hypoglycemia only.
  2. A novel frameshift PHKA2 mutation in a family with glycogen storage disease type IXa: A first report in Vietnam and review of literature.
    Title: A novel frameshift PHKA2 mutation in a family with glycogen storage disease type IXa: A first report in Vietnam and review of literature.
  3. Benign or not benign? Deep phenotyping of liver Glycogen Storage Disease IX.
    Title: Benign or not benign? Deep phenotyping of liver Glycogen Storage Disease IX.
  4. Study identified a novel mutation in PHKA2 (c.2972C > G, p.G991A) in patients with relatively rare phenotype of GSD IXa, including hypoglycaemia and delayed motor development.
    Title: A novel PHKA2 mutation in a Chinese child with glycogen storage disease type IXa: a case report and literature review.
  5. Clinical data and analyzed the PHKA2 gene of 17 Chinese male patients suspected of having Glycogen storage disease (GSD) type IXa; study detected 14 mutations in 17 patients, including 8 novel mutations; exons 2 and 4 were hot spots.
    Title: Clinical and genetic characteristics of 17 Chinese patients with glycogen storage disease type IXa.
  6. In this study we summarized the PHKA2 mutation spectrum in Korean glycogen storage disease type IX patients and found that the most common mutation type was gross deletion.
    Title: PHKA2 mutation spectrum in Korean patients with glycogen storage disease type IX: prevalence of deletion mutations.
  7. The present case also represents the first known reported case of liver PhK deficiency with an PHKA2 mutation and liver cirrhosis.
    Title: Glycogen storage disease type IX: novel PHKA2 missense mutation and cirrhosis.
  8. We found that the missense mutation p.Pro1205Leu in the PHKA2 gene is a common cause of hepatic phosphorylase-kinase deficiency in Dutch patients, suggesting a founder-effect
    Title: Common mutation in the PHKA2 gene with variable phenotype in patients with liver phosphorylase b kinase deficiency.
  9. two novel mutations found in two GSD type IX patients with different residual enzyme activities
    Title: Novel mutations in PHKA2 gene in glycogen storage disease type IX patients from Hong Kong, China.
  10. Results show that phosphorylase kinase (PhK) alpha subunit missense mutations or small in-frame deletions/insertions may have a direct impact on the PhK alpha functions.
    Title: 3D mapping of glycogenosis-causing mutations in the large regulatory alpha subunit of phosphorylase kinase.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Glycogen storage disease IXa1
MedGen: C3694531 OMIM: 306000 GeneReviews: Phosphorylase Kinase Deficiency
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
retropepsin gag-pol The alpha subunit of phosphorylase kinase is preferentially cleaved at arg748-val749 by HIV-1 protease PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC133071

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calmodulin binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphorylase kinase activity TAS
Traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in carbohydrate metabolic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in generation of precursor metabolites and energy TAS
Traceable Author Statement
more info
 PubMed 
involved_in glycogen metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in protein modification process TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of phosphorylase kinase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
phosphorylase b kinase regulatory subunit alpha, liver isoform
Names
phosphorylase kinase alpha L subunit
phosphorylase kinase alpha-subunit
NP_000283.1
XP_005274605.1
XP_005274607.1
XP_006724559.1
XP_011543839.1
XP_011543840.1
XP_016885069.1
XP_047298119.1
XP_047298120.1
XP_047298121.1
XP_047298122.1
XP_054183175.1
XP_054183176.1
XP_054183177.1
XP_054183178.1
XP_054183179.1
XP_054183180.1
XP_054183181.1
XP_054183182.1
XP_054183183.1
XP_054183184.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_016622.1 RefSeqGene

    Range
    5249..97065
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000292.3 → NP_000283.1  phosphorylase b kinase regulatory subunit alpha, liver isoform

    See identical proteins and their annotated locations for NP_000283.1

    Status: REVIEWED

    Source sequence(s)
    BC014036, CD722555, W63591, X80497
    Consensus CDS
    CCDS14190.1
    UniProtKB/Swiss-Prot
    A8K1T1, P46019, Q6LAJ5, Q7Z6W0, Q96CR3, Q9UDA1
    Related
    ENSP00000369274.4, ENST00000379942.5
    Conserved Domains (1) summary
    pfam00723
    Location:8 → 439
    Glyco_hydro_15; Glycosyl hydrolases family 15

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    18892298..18984114 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442165.1 → XP_047298121.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X7

  2. XM_047442164.1 → XP_047298120.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X6

  3. XM_047442163.1 → XP_047298119.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X5

  4. XM_011545537.4 → XP_011543839.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X3

    Conserved Domains (1) summary
    pfam00723
    Location:8 → 406
    Glyco_hydro_15; Glycosyl hydrolases family 15

  5. XM_005274550.6 → XP_005274607.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X4

    Conserved Domains (1) summary
    pfam00723
    Location:8 → 439
    Glyco_hydro_15; Glycosyl hydrolases family 15

  6. XM_005274548.6 → XP_005274605.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X2

    Conserved Domains (1) summary
    pfam00723
    Location:8 → 439
    Glyco_hydro_15; Glycosyl hydrolases family 15

  7. XM_006724496.5 → XP_006724559.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X1

    Conserved Domains (1) summary
    pfam00723
    Location:8 → 439
    Glyco_hydro_15; Glycosyl hydrolases family 15

  8. XM_047442166.1 → XP_047298122.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X8

  9. XM_017029580.3 → XP_016885069.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X9

  10. XM_011545538.4 → XP_011543840.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X10

    Conserved Domains (1) summary
    pfam00723
    Location:463 → 580
    Glyco_hydro_15; Glycosyl hydrolases family 15

RNA

  1. XR_950461.4 RNA Sequence

  2. XR_001755697.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    18475012..18566828 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327206.1 → XP_054183181.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X7

  2. XM_054327205.1 → XP_054183180.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X6

  3. XM_054327204.1 → XP_054183179.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X5

  4. XM_054327202.1 → XP_054183177.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X3

  5. XM_054327203.1 → XP_054183178.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X4

  6. XM_054327201.1 → XP_054183176.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X2

  7. XM_054327200.1 → XP_054183175.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X1

  8. XM_054327207.1 → XP_054183182.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X8

  9. XM_054327208.1 → XP_054183183.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X9

  10. XM_054327209.1 → XP_054183184.1  phosphorylase b kinase regulatory subunit alpha, liver isoform isoform X10

RNA

  1. XR_008485480.1 RNA Sequence

  2. XR_008485481.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P46019.1 GenPept UniProtKB/Swiss-Prot:P46019

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