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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 58
  • EC 2.6.1.11 58
  • EC 2.6.1.13 58
  • EC 2.6.1 58
  • 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 Degradation of the extracellular matrix and Metabolism. 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

Regulatory Elements for PHYKPL Gene

Enhancers for PHYKPL Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05H178229 1.3 ENCODE dbSUPER 16 +1.0 956 3.8 FOXA2 ATF1 SIN3A DMAP1 GLI4 YY1 ZNF121 ZNF766 GLIS2 ELK1 PHYKPL GMCL1P1 LOC105377753 OR1X5P LOC105377752 LOC100129457 PIR36838
GH05H178236 1.4 Ensembl ENCODE dbSUPER 14.4 -6.7 -6725 5.7 FOXA2 PKNOX1 NFIB ZBTB40 YY1 ZNF766 EGR1 ZNF143 EGR2 USF2 PHYKPL GC05P178327
GH05H178234 1.1 Ensembl ENCODE 9.6 -2.4 -2379 0.8 PKNOX1 NFXL1 ZBTB7B RAD21 GLIS2 ZNF143 RUNX3 CREM SMARCA5 ZNF654 PHYKPL GC05P178327
GH05H178220 1.3 FANTOM5 ENCODE dbSUPER 5.7 +8.3 8275 8.6 CTCF KLF1 SALL2 ZIC2 ZNF121 GLIS2 POLR2A SCRT2 PRDM10 ZNF548 HNRNPAB ZNF354B RPL21P60 ZNF354C FAM193B ENSG00000254035 RMND5B ZFP2 COL23A1 PHYKPL
GH05H178248 0.7 Ensembl ENCODE 6.5 -16.7 -16697 1.4 ZSCAN4 HNF4A COL23A1 PHYKPL GC05P178327
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PHYKPL on UCSC Golden Path with GeneCards custom track

Promoters for PHYKPL Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000191421 422 1201 ATF1 SIN3A DMAP1 GLI4 ZNF121 ZNF766 GLIS2 ELK1 ZNF143 KLF7

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

  • Ubiquitination at posLast=3333
  • 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

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

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:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Phenotypes From GWAS Catalog , 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 0
Ammonia Approved Pharma 0
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Pyridoxal Phosphate Nutra Target, cofactor 16

(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

Clone 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

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 Sequence Context AA Info Type
rs142181517 Pathogenic, Phosphohydroxylysinuria (PHLU) [MIM:615011] 178,211,964(+) TCTCT(A/T)CCATG nc-transcript-variant, reference, synonymous-codon, missense
rs201105857 Pathogenic, Phosphohydroxylysinuria (PHLU) [MIM:615011] 178,222,564(+) CCCTC(C/T)GGCCT intron-variant, nc-transcript-variant, reference, missense
rs1000002225 -- 178,214,545(+) AGCCT(G/T)TGTCT intron-variant
rs1000008202 -- 178,221,701(+) TCCTC(C/T)TCTCC intron-variant
rs1000290605 -- 178,230,282(+) CAGGA(A/G)TTCCT intron-variant, utr-variant-5-prime

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

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

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)

Relevant External Links 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, ClinVar, 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.

Relevant External Links for PHYKPL

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 60
  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 60
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  5. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 60

Products for PHYKPL Gene

Sources for PHYKPL Gene

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