This is a nuclear gene encoding a mitochondrial enzyme that catalyzes the conversion of 5-phosphonooxy-L-lysine to ammonia, inorganic phosphate, and 2-aminoadipate semialdehyde. Mutations in this gene may cause phosphohydroxylysinuria. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013] See more...

Aliases for PHYKPL Gene

Aliases for PHYKPL Gene

  • 5-Phosphohydroxy-L-Lysine Phospho-Lyase 2 3 4 5
  • Alanine--Glyoxylate Aminotransferase 2-Like 2 3 4
  • 5-Phosphonooxy-L-Lysine Phospho-Lyase 2 3
  • AGXT2L2 3 4
  • Alanine-Glyoxylate Aminotransferase 2-Like 2 2
  • EC 4.2.3.134 4
  • EC 2.6.1.44 51
  • EC 2.6.1.11 51
  • EC 2.6.1.13 51
  • MGC15875 2
  • EC 2.6.1 51
  • PHYKPL 5
  • PHLU 3

External Ids for PHYKPL Gene

Previous HGNC Symbols for PHYKPL Gene

  • AGXT2L2

Previous GeneCards Identifiers for PHYKPL Gene

  • GC05M177636
  • GC05M178208

Summaries for PHYKPL Gene

Entrez Gene Summary for PHYKPL Gene

  • This is a nuclear gene encoding a mitochondrial enzyme that catalyzes the conversion of 5-phosphonooxy-L-lysine to ammonia, inorganic phosphate, and 2-aminoadipate semialdehyde. Mutations in this gene may cause phosphohydroxylysinuria. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

GeneCards Summary for PHYKPL Gene

PHYKPL (5-Phosphohydroxy-L-Lysine Phospho-Lyase) is a Protein Coding gene. Diseases associated with PHYKPL include Phosphohydroxylysinuria. Among its related pathways are Degradation of the extracellular matrix and Lysine degradation. Gene Ontology (GO) annotations related to this gene include pyridoxal phosphate binding and transaminase activity. An important paralog of this gene is ETNPPL.

UniProtKB/Swiss-Prot Summary for PHYKPL Gene

  • Catalyzes the pyridoxal-phosphate-dependent breakdown of 5-phosphohydroxy-L-lysine, converting it to ammonia, inorganic phosphate and 2-aminoadipate semialdehyde.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PHYKPL Gene

Genomics for PHYKPL Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PHYKPL Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PHYKPL on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PHYKPL

Genomic Locations for PHYKPL Gene

Genomic Locations for PHYKPL Gene
chr5:178,207,144-178,232,822
(GRCh38/hg38)
Size:
25,679 bases
Orientation:
Minus strand
chr5:177,635,498-177,659,803
(GRCh37/hg19)
Size:
24,306 bases
Orientation:
Minus strand

Genomic View for PHYKPL Gene

Genes around PHYKPL on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHYKPL Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHYKPL Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHYKPL Gene

Proteins for PHYKPL Gene

  • Protein details for PHYKPL Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IUZ5-AT2L2_HUMAN
    Recommended name:
    5-phosphohydroxy-L-lysine phospho-lyase
    Protein Accession:
    Q8IUZ5
    Secondary Accessions:
    • A8K7P6
    • B3KN36
    • D3DWP9
    • Q8WYS6
    • Q96HW8

    Protein attributes for PHYKPL Gene

    Size:
    450 amino acids
    Molecular mass:
    49711 Da
    Cofactor:
    Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Homotetramer.

    Alternative splice isoforms for PHYKPL Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHYKPL Gene

Selected DME Specific Peptides for PHYKPL Gene

Q8IUZ5:
  • GLAVLNV
  • PDIVTMGK
  • NSGSEANDLALRLA
  • ADEIQVG

Post-translational modifications for PHYKPL Gene

  • Ubiquitination at Lys33
  • Modification sites at PhosphoSitePlus

Domains & Families for PHYKPL Gene

Gene Families for PHYKPL Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for PHYKPL Gene

InterPro:
Blocks:
  • Aminotransferase class-III
ProtoNet:

Suggested Antigen Peptide Sequences for PHYKPL Gene

GenScript: Design optimal peptide antigens:
  • Alanine--glyoxylate aminotransferase 2-like 2 (AT2L2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IUZ5

UniProtKB/Swiss-Prot:

AT2L2_HUMAN :
  • Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.
Family:
  • Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family.
genes like me logo Genes that share domains with PHYKPL: view

Function for PHYKPL Gene

Molecular function for PHYKPL Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the pyridoxal-phosphate-dependent breakdown of 5-phosphohydroxy-L-lysine, converting it to ammonia, inorganic phosphate and 2-aminoadipate semialdehyde.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(5R)-5-phosphooxy-L-lysine + H2O = (S)-2-amino-6-oxohexanoate + NH4(+) + phosphate; Xref=Rhea:RHEA:34091, ChEBI:CHEBI:15377, ChEBI:CHEBI:28938, ChEBI:CHEBI:43474, ChEBI:CHEBI:57882, ChEBI:CHEBI:58321; EC=4.2.3.134;.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=16 uM for 5-phosphohydroxy-L-lysine (at 30 degrees Celsius) {ECO:0000269|PubMed:22241472}; Vmax=256 nmol/min/mg enzyme {ECO:0000269|PubMed:22241472};

Enzyme Numbers (IUBMB) for PHYKPL Gene

Phenotypes From GWAS Catalog for PHYKPL Gene

Gene Ontology (GO) - Molecular Function for PHYKPL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0005515 protein binding IPI 21044950
GO:0008483 transaminase activity IEA --
GO:0016829 lyase activity IEA --
GO:0030170 pyridoxal phosphate binding IEA --
genes like me logo Genes that share ontologies with PHYKPL: view
genes like me logo Genes that share phenotypes with PHYKPL: view

Animal Models for PHYKPL Gene

MGI Knock Outs for PHYKPL:
  • Phykpl Phykpl<tm1a(EUCOMM)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for PHYKPL

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHYKPL

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PHYKPL Gene

Localization for PHYKPL Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHYKPL Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHYKPL gene
Compartment Confidence
mitochondrion 4
nucleus 3
cytosol 3
peroxisome 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PHYKPL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with PHYKPL: view

Pathways & Interactions for PHYKPL Gene

genes like me logo Genes that share pathways with PHYKPL: view

Gene Ontology (GO) - Biological Process for PHYKPL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006554 lysine catabolic process TAS --
GO:0030574 collagen catabolic process TAS --
genes like me logo Genes that share ontologies with PHYKPL: view

No data available for SIGNOR curated interactions for PHYKPL Gene

Drugs & Compounds for PHYKPL Gene

(5) Drugs for PHYKPL Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 16
Ammonia Approved Pharma 0
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
L-Alanine Nutra Agonist, Full agonist, Target Glycine receptor agonist 198

(2) Additional Compounds for PHYKPL Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
(S)-2-amino-6-oxohexanoate
  • 2-amino-6-oxo-HEXANOIC ACID
  • 6-oxo-L-Norleucine
  • Allysine
  • L-2-Aminoadipate 6-semialdehyde
  • L-6-Oxonorleucine
5-phosphonooxy-L-lysine
  • 5-Phosphonooxy-L-lysine
  • O-Phosphohydroxy-L-lysine
genes like me logo Genes that share compounds with PHYKPL: view

Transcripts for PHYKPL Gene

mRNA/cDNA for PHYKPL Gene

2 REFSEQ mRNAs :
19 NCBI additional mRNA sequence :
18 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PHYKPL

Alternative Splicing Database (ASD) splice patterns (SP) for PHYKPL Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c · 4d ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b · 7c · 7d ^ 8a · 8b · 8c ^ 9 ^ 10a · 10b ^ 11a · 11b ·
SP1: - - - - - - - - - -
SP2: -
SP3: - - - - - - - -
SP4: - - - -
SP5: - - - - -
SP6: -
SP7: - - - - - - - - - - - -
SP8: - - - - - - - - -
SP9: - - - - - - - - - - - -
SP10: - - - - - - - - - - - - - - -
SP11: - - -
SP12: - - - - - -
SP13: -
SP14: - - - - - - - - - - - - - - - -
SP15: - - -
SP16:
SP17: -
SP18: -

ExUns: 11c · 11d ^ 12a · 12b · 12c ^ 13 ^ 14a · 14b ^ 15 ^ 16
SP1:
SP2: - - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14: - - - - - - -
SP15:
SP16:
SP17:
SP18:

Relevant External Links for PHYKPL Gene

GeneLoc Exon Structure for
PHYKPL

Expression for PHYKPL Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PHYKPL Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PHYKPL Gene

This gene is overexpressed in Peripheral blood mononuclear cells (10.6), Lymph node (7.1), and Oral epithelium (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PHYKPL Gene



Protein tissue co-expression partners for PHYKPL Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PHYKPL

Evidence on tissue expression from TISSUES for PHYKPL Gene

  • Nervous system(4.3)
  • Liver(4.3)
  • Stomach(4.3)
  • Muscle(4.2)
  • Pancreas(4.2)
genes like me logo Genes that share expression patterns with PHYKPL: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PHYKPL Gene

Orthologs for PHYKPL Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PHYKPL Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia AGXT2L2 30
  • 98.22 (n)
Cow
(Bos Taurus)
Mammalia PHYKPL 31
  • 92 (a)
OneToOne
AGXT2L2 30
  • 90.27 (n)
Dog
(Canis familiaris)
Mammalia PHYKPL 30 31
  • 87.04 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia LOC100910122 30
  • 86.12 (n)
Mouse
(Mus musculus)
Mammalia Phykpl 30 17 31
  • 86.04 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PHYKPL 31
  • 81 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PHYKPL 31
  • 55 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PHYKPL 31
  • 74 (a)
OneToOne
AGXT2L2 30
  • 70.24 (n)
Lizard
(Anolis carolinensis)
Reptilia PHYKPL 31
  • 69 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii PHYKPL 31
  • 66 (a)
OneToOne
zgc:123007 30
  • 65.91 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG8745 31
  • 45 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea T01B11.2 31
  • 43 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ARG8 31
  • 22 (a)
OneToMany
Soybean
(Glycine max)
eudicotyledons Gma.7120 30
Rice
(Oryza sativa)
Liliopsida Os.15830 30
Species where no ortholog for PHYKPL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for PHYKPL Gene

ENSEMBL:
Gene Tree for PHYKPL (if available)
TreeFam:
Gene Tree for PHYKPL (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PHYKPL: view image

Paralogs for PHYKPL Gene

Paralogs for PHYKPL Gene

(3) SIMAP similar genes for PHYKPL Gene using alignment to 8 proteins:

  • AT2L2_HUMAN
  • D6RAR0_HUMAN
  • D6RCB8_HUMAN
  • D6RD89_HUMAN
  • H0Y9N3_HUMAN
  • H0YAK5_HUMAN
  • H7BXR0_HUMAN
  • H7BYK2_HUMAN
genes like me logo Genes that share paralogs with PHYKPL: view

Variants for PHYKPL Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PHYKPL Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs142181517 Pathogenic: Phosphohydroxylysinuria. Phosphohydroxylysinuria (PHLU) [MIM:615011] 178,211,964(-) T/Ap.Glu437Val MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs201105857 Pathogenic: Phosphohydroxylysinuria. Phosphohydroxylysinuria (PHLU) [MIM:615011] 178,222,564(-) C/Tp.Gly240Arg MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs7707147 - p.His126Arg

Additional dbSNP identifiers (rs#s) for PHYKPL Gene

Structural Variations from Database of Genomic Variants (DGV) for PHYKPL Gene

Variant ID Type Subtype PubMed ID
dgv1060e199 CNV deletion 23128226
esv3607710 CNV loss 21293372
nsv1019404 CNV gain 25217958
nsv1120062 OTHER inversion 24896259
nsv473044 CNV novel sequence insertion 20440878
nsv527792 CNV loss 19592680

Variation tolerance for PHYKPL Gene

Residual Variation Intolerance Score: 17% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.17; 61.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHYKPL Gene

Human Gene Mutation Database (HGMD)
PHYKPL
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHYKPL

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHYKPL Gene

Disorders for PHYKPL Gene

MalaCards: The human disease database

(1) MalaCards diseases for PHYKPL Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, and GeneCards

Disorder Aliases PubMed IDs
phosphohydroxylysinuria
  • phlu
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

AT2L2_HUMAN
  • Phosphohydroxylysinuria (PHLU) [MIM:615011]: A condition characterized by elevated phosphohydroxylysine in the urine. There is no clinical phenotype associated with this finding other than the urinary metabolites. {ECO:0000269 PubMed:23242558}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with PHYKPL: view

No data available for Genatlas for PHYKPL Gene

Publications for PHYKPL Gene

  1. Molecular identification of hydroxylysine kinase and of ammoniophospholyases acting on 5-phosphohydroxy-L-lysine and phosphoethanolamine. (PMID: 22241472) Veiga-da-Cunha M … Van Schaftingen E (The Journal of biological chemistry 2012) 2 3 4
  2. Mutations in the AGXT2L2 gene cause phosphohydroxylysinuria. (PMID: 23242558) Veiga-da-Cunha M … Van Schaftingen E (Journal of inherited metabolic disease 2013) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. (PMID: 31515488) Fragoza R … Yu H (Nature communications 2019) 3

Products for PHYKPL Gene

  • Signalway Proteins for PHYKPL

Sources for PHYKPL Gene