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Aliases for PHYKPL Gene

Aliases for PHYKPL Gene

  • 5-Phosphohydroxy-L-Lysine Phospho-Lyase 2 3 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 56
  • EC 2.6.1.11 56
  • EC 2.6.1.13 56
  • EC 2.6.1 56
  • PHLU 3

External Ids for PHYKPL Gene

Previous HGNC Symbols for PHYKPL Gene

  • AGXT2L2

Previous GeneCards Identifiers for PHYKPL Gene

  • GC05M177636

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 Viral mRNA Translation and Degradation of the extracellular matrix. 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 for PHYKPL Gene

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

Additional gene information for PHYKPL Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHYKPL Gene

Genomics for PHYKPL Gene

GeneHancer (GH) Regulatory Elements for PHYKPL Gene

Promoters and enhancers for PHYKPL Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I178229 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 566 +1.0 955 3.8 FOXA2 ATF1 SIN3A DMAP1 GLI4 ZNF48 YY1 ZNF121 ZNF766 GLIS2 PHYKPL PIR36838
GH05I178203 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 12.2 +23.1 23078 12.3 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B NEUROD1 SIN3A DMAP1 ZNF2 HNRNPAB ENSG00000247679 FAM193B ZNF879 LOC202181 ZNF354C ZFP2 ENSG00000254035 ZNF454 CLK4
GH05I177308 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 11.9 +921.8 921828 4.9 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B E2F8 MXD3 FAM193B RGS14 UIMC1 NSD1 PHYKPL HNRNPAB ENSG00000251414 ZNF346 ENSG00000250909
GH05I178236 Enhancer 1.2 Ensembl ENCODE dbSUPER 14.5 -6.7 -6725 5.7 FOXA2 PKNOX1 NFIB ZBTB40 YY1 ZNF335 ZNF766 EGR1 ZNF143 EGR2 PHYKPL GC05P178327 COL23A1
GH05I177377 Enhancer 1.3 Ensembl ENCODE 11.8 +853.8 853755 2.2 HDGF FOXA2 MLX ARNT ARID4B DMAP1 IRF4 YY1 SLC30A9 POLR2B SLC34A1 RGS14 FAM193B NSD1 FAF2 ENSG00000247679 MXD3 ZNF346-IT1 UIMC1 LOC202181
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PHYKPL on UCSC Golden Path with GeneCards custom track

Genomic Locations for PHYKPL Gene

Genomic Locations for PHYKPL Gene
chr5:178,208,474-178,232,822
(GRCh38/hg38)
Size:
24,349 bases
Orientation:
Minus strand
chr5:177,635,498-177,659,803
(GRCh37/hg19)

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

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

Suggested Antigen Peptide Sequences for PHYKPL Gene

GenScript: Design optimal peptide antigens:

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 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};
UniProtKB/Swiss-Prot CatalyticActivity:
(5R)-5-phosphonooxy-L-lysine + H(2)O = (S)-2-amino-6-oxohexanoate + NH(3) + phosphate.
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.

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:0005515 protein binding IPI 21044950
GO:0008453 alanine-glyoxylate transaminase activity IBA --
GO:0008483 transaminase activity IEA --
GO:0016740 transferase activity IEA --
GO:0016829 lyase activity TAS --
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:

Inhibitory RNA Products

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
peroxisome 3
nucleus 3
cytosol 3

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 IBA --
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
L-Alanine Approved Nutra Full agonist, Agonist, Target Glycine receptor agonist 0
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 17
Ammonia Approved Pharma 0
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
(S)-2-amino-6-oxohexanoate
5-phosphonooxy-L-lysine
genes like me logo Genes that share compounds with PHYKPL: view

Transcripts for PHYKPL Gene

CRISPR Products

Inhibitory RNA Products

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
ECgene alternative splicing isoforms for
PHYKPL

Expression for PHYKPL Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for PHYKPL Gene



Protein tissue co-expression partners for PHYKPL Gene

NURSA nuclear receptor signaling pathways regulating expression of PHYKPL Gene:

PHYKPL

Evidence on tissue expression from TISSUES for PHYKPL Gene

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

Primer Products

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 33
  • 98.22 (n)
cow
(Bos Taurus)
Mammalia PHYKPL 34
  • 92 (a)
OneToOne
AGXT2L2 33
  • 90.27 (n)
dog
(Canis familiaris)
Mammalia PHYKPL 33 34
  • 87.04 (n)
rat
(Rattus norvegicus)
Mammalia LOC100910122 33
  • 86.12 (n)
mouse
(Mus musculus)
Mammalia Phykpl 33 16 34
  • 86.04 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PHYKPL 34
  • 81 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PHYKPL 34
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHYKPL 34
  • 74 (a)
OneToOne
AGXT2L2 33
  • 70.24 (n)
lizard
(Anolis carolinensis)
Reptilia PHYKPL 34
  • 69 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii PHYKPL 34
  • 66 (a)
OneToOne
zgc:123007 33
  • 65.91 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG8745 34
  • 45 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea T01B11.2 34
  • 43 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ARG8 34
  • 22 (a)
OneToMany
soybean
(Glycine max)
eudicotyledons Gma.7120 33
rice
(Oryza sativa)
Liliopsida Os.15830 33
Species where no ortholog for PHYKPL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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)

Paralogs for PHYKPL Gene

Paralogs for PHYKPL Gene

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

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

Variants for PHYKPL Gene

Sequence variations from dbSNP and Humsavar for PHYKPL Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs142181517 pathogenic, Phosphohydroxylysinuria, Phosphohydroxylysinuria (PHLU) [MIM:615011] 178,211,964(-) T/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant, synonymous_variant
rs201105857 pathogenic, Phosphohydroxylysinuria, Phosphohydroxylysinuria (PHLU) [MIM:615011] 178,222,564(-) C/T coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs1000002225 -- 178,214,545(-) G/T intron_variant
rs1000008202 -- 178,221,701(-) C/T intron_variant
rs1000290605 -- 178,230,282(-) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant

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: HGMD, OMIM, ClinVar, GTR, Swiss-Prot, 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.

Additional Disease Information for PHYKPL

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 58
  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 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 58

Products for PHYKPL Gene

Sources for PHYKPL Gene

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