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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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    See PHKA2 in Genome Data Viewer
    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
    		Compare labs

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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