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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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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
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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)

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

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