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    PHKA1 phosphorylase kinase regulatory subunit alpha 1 [ Homo sapiens (human) ]

    Gene ID: 5255, updated on 3-Nov-2024

    Summary

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    Official Symbol
    PHKA1provided by HGNC
    Official Full Name
    phosphorylase kinase regulatory subunit alpha 1provided by HGNC
    Primary source
    HGNC:HGNC:8925
    See related
    Ensembl:ENSG00000067177 MIM:311870; AllianceGenome:HGNC:8925
    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
    PHKA
    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 skeletal muscle 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 9D, also known as X-linked muscle glycogenosis. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene. A pseudogene has been found on chromosome 1.[provided by RefSeq, Feb 2010]
    Expression
    Ubiquitous expression in adrenal (RPKM 5.8), thyroid (RPKM 4.1) and 24 other tissues See more
    Orthologs
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    Genomic context

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    See PHKA1 in Genome Data Viewer
    Location:
    Xq13.1
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (72578814..72714306, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (71011736..71147907, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (71798664..71934154, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373250 Neighboring gene Sharpr-MPRA regulatory region 2135 Neighboring gene NANOG hESC enhancer GRCh37_chrX:71528736-71529237 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:71532082-71532582 Neighboring gene Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29761 Neighboring gene histone deacetylase 8 Neighboring gene RNA, U2 small nuclear 68, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:71773892-71775091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29762 Neighboring gene MATR3 pseudogene 1 Neighboring gene PHKA1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:71933452-71934442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:71934443-71935431 Neighboring gene small nucleolar RNA U3 Neighboring gene CAPZA1 pseudogene 3

    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 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. Muscle phosphorylase kinase deficiency: a neutral metabolic variant or a disease? Preisler N, et al. Neurology, 2012 Jan 24. PMID 22238410
    2. Is muscle glycogenolysis impaired in X-linked phosphorylase b kinase deficiency? Ørngreen MC, et al. Neurology, 2008 May 13. PMID 18401027
    3. Myopathy and phosphorylase kinase deficiency caused by a mutation in the PHKA1 gene. Wuyts W, et al. Am J Med Genet A, 2005 Feb 15. PMID 15637709
    4. Muscle phosphorylase b kinase deficiency revisited. Echaniz-Laguna A, et al. Neuromuscul Disord, 2010 Feb. PMID 20080404
    5. A novel PHKA1 mutation associating myopathy and cognitive impairment: Expanding the spectrum of phosphorylase kinase b (PhK) deficiency. Bisciglia M, et al. J Neurol Sci, 2021 May 15. PMID 33799212

    See all (51) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel PHKA1 mutation associating myopathy and cognitive impairment: Expanding the spectrum of phosphorylase kinase b (PhK) deficiency.
      Title: A novel PHKA1 mutation associating myopathy and cognitive impairment: Expanding the spectrum of phosphorylase kinase b (PhK) deficiency.
    2. muscle PHKA deficiency may present as an almost asymptomatic condition, despite a mild impairment of muscle
      Title: Muscle phosphorylase kinase deficiency: a neutral metabolic variant or a disease?
    3. X-linked PHK deficiency causes a mild metabolic myopathy with blunted muscle glycogen breakdown and impaired lactate production during dynamic exercise, which impairs oxidative capacity only marginally
      Title: Is muscle glycogenolysis impaired in X-linked phosphorylase b kinase deficiency?
    4. alpha- and beta-subunits possess amino-terminal glucoamylase-like domains and suggests that they might possess a previously overlooked amylase activity
      Title: Glucoamylase-like domains in the alpha- and beta-subunits of phosphorylase kinase.
    Submit: New GeneRIF Correction

    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 IXd
    MedGen: C1845151 OMIM: 300559 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

    • MGC132604

    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 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 positive regulation of glycogen catabolic process IMP
    Inferred from Mutant Phenotype
    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, skeletal muscle isoform
    Names
    phosphorylase kinase alpha M subunit
    phosphorylase kinase, alpha 1 (muscle), muscle glycogenosis
    NP_001116142.1
    NP_001165907.1
    NP_001417997.1
    NP_002628.2
    XP_006724724.1
    XP_047298116.1
    XP_047298117.1
    XP_047298118.1
    XP_054183171.1
    XP_054183172.1
    XP_054183173.1
    XP_054183174.1

    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_016599.2 RefSeqGene

      Range
      4876..140368
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001122670.2 → NP_001116142.1  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform isoform 2

      See identical proteins and their annotated locations for NP_001116142.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC240504, AW450116, BC104944, BJ998054, BX647542, DR002787, X73874
      Consensus CDS
      CCDS48137.1
      UniProtKB/TrEMBL
      A6NIT2
      Related
      ENSP00000342469.3, ENST00000339490.7
      Conserved Domains (1) summary
      pfam00723
      Location:8 → 439
      Glyco_hydro_15; Glycosyl hydrolases family 15

    2. NM_001172436.2 → NP_001165907.1  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform isoform 3

      See identical proteins and their annotated locations for NP_001165907.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons in the middle and 3' coding regions, respectively, compared to variant 1, resulting in a shorter protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      AC240504, AW450116, BC143501, BX647542, DA171597, DA998603, DR002787
      Consensus CDS
      CCDS55453.1
      UniProtKB/TrEMBL
      A6NIT2
      Related
      ENSP00000441251.1, ENST00000541944.5
      Conserved Domains (1) summary
      pfam00723
      Location:8 → 439
      Glyco_hydro_15; Glycosyl hydrolases family 15

    3. NM_001431068.1 → NP_001417997.1  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform

      Status: REVIEWED

      Source sequence(s)
      AC240504, BX295541, BX295542
      UniProtKB/TrEMBL
      A6NMN0
      Related
      ENSP00000362640.3, ENST00000373539.3

    4. NM_002637.4 → NP_002628.2  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform isoform 1

      See identical proteins and their annotated locations for NP_002628.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC240504, AW450116, BC104944, BJ998054, BX647542, DR002787, X73874
      Consensus CDS
      CCDS14421.1
      UniProtKB/Swiss-Prot
      B7ZL05, B7ZL07, P46020, Q2M3D7
      UniProtKB/TrEMBL
      A6NIT2
      Related
      ENSP00000362643.4, ENST00000373542.9
      Conserved Domains (1) summary
      pfam00723
      Location:8 → 439
      Glyco_hydro_15; Glycosyl hydrolases family 15

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      72578814..72714306 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442162.1 → XP_047298118.1  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform isoform X4

    2. XM_047442161.1 → XP_047298117.1  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform isoform X2

    3. XM_047442160.1 → XP_047298116.1  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform isoform X1

      UniProtKB/Swiss-Prot
      B7ZL05, B7ZL07, P46020, Q2M3D7

    4. XM_006724661.3 → XP_006724724.1  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform isoform X3

      UniProtKB/TrEMBL
      A6NIT2
      Related
      ENSP00000362646.3, ENST00000373545.7
      Conserved Domains (1) summary
      pfam00723
      Location:8 → 439
      Glyco_hydro_15; Glycosyl hydrolases family 15

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      71011736..71147907 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327199.1 → XP_054183174.1  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform isoform X4

    2. XM_054327197.1 → XP_054183172.1  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform isoform X2

    3. XM_054327196.1 → XP_054183171.1  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform isoform X1

      UniProtKB/Swiss-Prot
      B7ZL05, B7ZL07, P46020, Q2M3D7

    4. XM_054327198.1 → XP_054183173.1  phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P46020.2 GenPept UniProtKB/Swiss-Prot:P46020

    Gene LinkOut

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