Human Gene PHKA1 (ENST00000339490.7) from GENCODE V44
  Description: Homo sapiens phosphorylase kinase regulatory subunit alpha 1 (PHKA1), transcript variant 2, mRNA. (from RefSeq NM_001122670)
RefSeq Summary (NM_001122670): 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].
Gencode Transcript: ENST00000339490.7
Gencode Gene: ENSG00000067177.15
Transcript (Including UTRs)
   Position: hg38 chrX:72,578,815-72,714,181 Size: 135,367 Total Exon Count: 31 Strand: -
Coding Region
   Position: hg38 chrX:72,581,002-72,713,880 Size: 132,879 Coding Exon Count: 31 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:72,578,815-72,714,181)mRNA (may differ from genome)Protein (1210 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode
GeneCardsHGNCHPRDLynxMalacardsMGI
myGene2neXtProtOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: KPB1_HUMAN
DESCRIPTION: RecName: Full=Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform; Short=Phosphorylase kinase alpha M subunit;
FUNCTION: Phosphorylase b kinase catalyzes the phosphorylation of serine in certain substrates, including troponin I. The alpha chain may bind calmodulin.
ENZYME REGULATION: By phosphorylation of various serine residues. Allosteric regulation by calcium.
PATHWAY: Glycan biosynthesis; glycogen metabolism.
SUBUNIT: Hexadecamer of 4 heterotetramers, each composed of alpha, beta, gamma, and delta subunits. Alpha (PHKA1 or PHKA2) and beta (PHKB) are regulatory subunits, gamma (PHKG1 or PHKG2) is the catalytic subunit, and delta is calmodulin.
SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor; Cytoplasmic side (Potential).
TISSUE SPECIFICITY: Muscle specific. Isoform 1 is predominant in vastus lateralis muscle. Isoform 2 predominates slightly in heart, and it predominates clearly in the other tissues tested.
PTM: Although the final Cys may be farnesylated, the terminal tripeptide is probably not removed, and the C-terminus is not methylated (By similarity).
DISEASE: Defects in PHKA1 are the cause of glycogen storage disease type 9D (GSD9D) [MIM:300559]; also known as X-linked muscle glycogenosis. GSD9D is a metabolic disorder characterized by slowly progressive, predominantly distal muscle weakness and atrophy. Clinical features include exercise intolerance with early fatigability, pain, cramps and occasionally myoglobinuria.
SIMILARITY: Belongs to the phosphorylase b kinase regulatory chain family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PHKA1";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PHKA1
Diseases sorted by gene-association score: muscle glycogenosis* (1589), phka1-related phosphorylase kinase deficiency* (500), glycogen storage disease viii (19), phosphorylase kinase deficiency (8)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.76 RPKM in Muscle - Skeletal
Total median expression: 202.47 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -151.70301-0.504 Picture PostScript Text
3' UTR -536.602187-0.245 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008928 - 6-hairpin_glycosidase-like
IPR012341 - 6hp_glycosidase
IPR011613 - Glyco_hydro_15
IPR008734 - PHK_A/B_su

Pfam Domains:
PF00723 - Glycosyl hydrolases family 15

ModBase Predicted Comparative 3D Structure on P46020
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD Ensembl  
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004689 phosphorylase kinase activity
GO:0005516 calmodulin binding

Biological Process:
GO:0005975 carbohydrate metabolic process
GO:0005977 glycogen metabolic process
GO:0006091 generation of precursor metabolites and energy
GO:0006468 protein phosphorylation

Cellular Component:
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005964 phosphorylase kinase complex
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  X73874 - H.sapiens PHKA 1 mRNA.
BC104944 - Homo sapiens phosphorylase kinase, alpha 1 (muscle), mRNA (cDNA clone MGC:132604 IMAGE:8143947), complete cds.
BC143499 - Homo sapiens phosphorylase kinase, alpha 1 (muscle), mRNA (cDNA clone MGC:177024 IMAGE:9052007), complete cds.
BC143501 - Homo sapiens phosphorylase kinase, alpha 1 (muscle), mRNA (cDNA clone MGC:177026 IMAGE:9052009), complete cds.
BX647542 - Homo sapiens mRNA; cDNA DKFZp779C2145 (from clone DKFZp779C2145).
LF381847 - JP 2014500723-A/189350: Polycomb-Associated Non-Coding RNAs.
MA617424 - JP 2018138019-A/189350: Polycomb-Associated Non-Coding RNAs.
AK123357 - Homo sapiens cDNA FLJ41363 fis, clone BRCAN2003746.
JD157383 - Sequence 138407 from Patent EP1572962.
JD399575 - Sequence 380599 from Patent EP1572962.
JD324706 - Sequence 305730 from Patent EP1572962.
JD130169 - Sequence 111193 from Patent EP1572962.
JD564191 - Sequence 545215 from Patent EP1572962.
JD291000 - Sequence 272024 from Patent EP1572962.
JD218737 - Sequence 199761 from Patent EP1572962.
JD317357 - Sequence 298381 from Patent EP1572962.
X73878 - H.sapiens PHKA 1 unprocessed primary transcript.
JD118971 - Sequence 99995 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04020 - Calcium signaling pathway
hsa04910 - Insulin signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein P46020 (Reactome details) participates in the following event(s):

R-HSA-71541 glycogen phosphorylase (PYGM) dimer b + 2 ATP => glycogen phosphorylase (PYGM) dimer a + 2 ADP
R-HSA-453337 glycogen phosphorylase (PYGB) dimer b + 2 ATP => glycogen phosphorylase (PYGB) dimer a + 2 ADP
R-HSA-70221 Glycogen breakdown (glycogenolysis)
R-HSA-8982491 Glycogen metabolism
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B7ZL05, B7ZL07, ENST00000339490.1, ENST00000339490.2, ENST00000339490.3, ENST00000339490.4, ENST00000339490.5, ENST00000339490.6, KPB1_HUMAN, NM_001122670, P46020, PHKA, Q2M3D7, uc004eay.1, uc004eay.2, uc004eay.3, uc004eay.4, uc004eay.5
UCSC ID: ENST00000339490.7
RefSeq Accession: NM_001122670
Protein: P46020 (aka KPB1_HUMAN)
CCDS: CCDS14421.1, CCDS48137.1, CCDS55453.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PHKA1:
gsd9 (Phosphorylase Kinase Deficiency)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.