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    PHYKPL 5-phosphohydroxy-L-lysine phospho-lyase [ Homo sapiens (human) ]

    Gene ID: 85007, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PHYKPLprovided by HGNC
    Official Full Name
    5-phosphohydroxy-L-lysine phospho-lyaseprovided by HGNC
    Primary source
    HGNC:HGNC:28249
    See related
    Ensembl:ENSG00000175309 MIM:614683; AllianceGenome:HGNC:28249
    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
    PHLU; AGXT2L2
    Summary
    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]
    Expression
    Ubiquitous expression in small intestine (RPKM 10.2), spleen (RPKM 9.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHYKPL in Genome Data Viewer
    Location:
    5q35.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (178207144..178232822, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (178758757..178783105, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (177635472..177659823, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:177607056-177607598 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177607599-177608139 Neighboring gene NAD(P)HX epimerase pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23742 Neighboring gene germ cell-less 2, spermatogenesis associated Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:177659427-177659965 Neighboring gene heterogeneous nuclear ribonucleoprotein A/B Neighboring gene uncharacterized LOC112267937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23743 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177664463-177665136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177665137-177665810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177673006-177673555 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16720 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:177683188-177683378 Neighboring gene collagen type XXIII alpha 1 chain Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177713093-177713638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177713639-177714182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177714183-177714727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177733440-177733951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177739610-177740112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177758265-177758871 Neighboring gene mitochondrial ribosomal protein L50 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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    Related articles in PubMed

    1. Mutations in the AGXT2L2 gene cause phosphohydroxylysinuria. Veiga-da-Cunha M, et al. J Inherit Metab Dis, 2013 Nov. PMID 23242558
    2. Molecular identification of hydroxylysine kinase and of ammoniophospholyases acting on 5-phosphohydroxy-L-lysine and phosphoethanolamine. Veiga-da-Cunha M, et al. J Biol Chem, 2012 Mar 2. PMID 22241472, Free PMC Article
    3. N(6)-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cheng Y, et al. Cancer Cell, 2021 Jul 12. PMID 34048709, Free PMC Article
    4. Genome-wide YFP fluorescence complementation screen identifies new regulators for telomere signaling in human cells. Lee OH, et al. Mol Cell Proteomics, 2011 Feb. PMID 21044950, Free PMC Article
    5. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. Chen S, et al. Nat Genet, 2018 Jul. PMID 29892012, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Phosphohydroxylysinuria is due to mutations in the AGXT2L2 gene and the resulting lack of activity of phosphohydroxylysine phospholyase in vivo.
      Title: Mutations in the AGXT2L2 gene cause phosphohydroxylysinuria.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    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
    Phosphohydroxylysinuria
    MedGen: C3554344 OMIM: 615011 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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

    • FLJ00272, MGC15875, MGC45484, MGC117348

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables pyridoxal phosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transaminase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    5-phosphohydroxy-L-lysine phospho-lyase
    Names
    5-phosphonooxy-L-lysine phospho-lyase
    alanine--glyoxylate aminotransferase 2-like 2
    NP_001265275.1
    NP_699204.1
    XP_006714988.1
    XP_011532971.1
    XP_011532972.1
    XP_011532973.1
    XP_011532976.1
    XP_016865484.1
    XP_024302008.1
    XP_024302009.1
    XP_024302011.1
    XP_024302013.1
    XP_024302015.1
    XP_024302018.1
    XP_024302019.1
    XP_024302020.1
    XP_047273793.1
    XP_047273794.1
    XP_047273795.1
    XP_047273796.1
    XP_047273797.1
    XP_047273799.1
    XP_054209681.1
    XP_054209682.1
    XP_054209683.1
    XP_054209684.1
    XP_054209685.1
    XP_054209686.1
    XP_054209687.1
    XP_054209688.1
    XP_054209689.1
    XP_054209690.1
    XP_054209691.1
    XP_054209692.1
    XP_054209693.1
    XP_054209694.1
    XP_054209695.1
    XP_054209696.1
    XP_054209697.1
    XP_054209698.1
    XP_054209699.1
    XP_054209700.1

    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_033253.2 RefSeqGene

      Range
      5021..29352
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001278346.1 → NP_001265275.1  5-phosphohydroxy-L-lysine phospho-lyase isoform 3

      See identical proteins and their annotated locations for NP_001265275.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site at the 5' exon and initiates translation at a downstream in-frame start codon, compared to variant 2. The encoded isoform (3) has a shorter N-terminus, compared to isoform 2.
      Source sequence(s)
      AK292061, BC028002, BC037238, BC037567, BX417194, HY267487
      UniProtKB/Swiss-Prot
      Q8IUZ5
      Related
      ENST00000489262.5
      Conserved Domains (2) summary
      cd00610
      Location:1 → 392
      OAT_like; Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, ...
      TIGR00707
      Location:1 → 392
      argD; transaminase, acetylornithine/succinylornithine family

    2. NM_153373.4 → NP_699204.1  5-phosphohydroxy-L-lysine phospho-lyase isoform 2

      See identical proteins and their annotated locations for NP_699204.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes the longer isoform (2).
      Source sequence(s)
      AC136632, AK292061, BC037567, BX417194, HY267487
      Consensus CDS
      CCDS4434.1
      UniProtKB/Swiss-Prot
      A8K7P6, B3KN36, D3DWP9, Q8IUZ5, Q8WYS6, Q96HW8
      Related
      ENSP00000310978.5, ENST00000308158.10
      Conserved Domains (1) summary
      cl28400
      Location:1 → 433
      HemL; Glutamate-1-semialdehyde aminotransferase [Coenzyme transport and metabolism]

    RNA

    1. NR_103508.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) contains multiple differences compared to variant 2, including the lack of multiple internal exons. This variant is represented as non-coding because the use of the translational start codon used in variant 2 renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK292061, BC008009, BX417194, HY267487
      Related
      ENST00000474052.5

    2. NR_103509.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site at the 5' exon and lacks multiple internal exons, compared to variant 2. This variant is represented as non-coding because the use of the translational start codon used in variant 2 renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC028002, BC037238, BX417194, HY267487
      Related
      ENST00000494126.6

    3. NR_103510.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains two alternate internal exons, compared to variant 2. This variant is represented as non-coding because the use of the translational start codon used in variant 2 renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC039012, BX417194, HY267487
      Related
      ENST00000493197.5

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      178207144..178232822 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417838.1 → XP_047273794.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X8

    2. XM_047417837.1 → XP_047273793.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X5

    3. XM_011534670.4 → XP_011532972.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X2

      Conserved Domains (1) summary
      cd00610
      Location:59 → 442
      OAT_like; Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, ...

    4. XM_011534674.3 → XP_011532976.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X9

      Conserved Domains (2) summary
      COG0160
      Location:7 → 330
      GabT; 4-aminobutyrate aminotransferase or related aminotransferase [Amino acid transport and metabolism]
      cl18945
      Location:30 → 328
      AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

    5. XM_024446240.2 → XP_024302008.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X7

      Conserved Domains (1) summary
      cl28400
      Location:1 → 352
      HemL; Glutamate-1-semialdehyde aminotransferase [Coenzyme transport and metabolism]

    6. XM_011534671.3 → XP_011532973.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X3

      Conserved Domains (2) summary
      cd00610
      Location:30 → 439
      OAT_like; Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, ...
      COG0160
      Location:7 → 441
      GabT; 4-aminobutyrate aminotransferase or related aminotransferase [Amino acid transport and metabolism]

    7. XM_011534669.3 → XP_011532971.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X1

      Conserved Domains (2) summary
      cd00610
      Location:30 → 443
      OAT_like; Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, ...
      COG0160
      Location:7 → 445
      GabT; 4-aminobutyrate aminotransferase or related aminotransferase [Amino acid transport and metabolism]

    8. XM_006714925.3 → XP_006714988.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X6

      Conserved Domains (2) summary
      cd00610
      Location:30 → 391
      OAT_like; Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, ...
      COG0160
      Location:7 → 393
      GabT; 4-aminobutyrate aminotransferase or related aminotransferase [Amino acid transport and metabolism]

    9. XM_024446243.2 → XP_024302011.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X12

      Conserved Domains (1) summary
      cl28400
      Location:2 → 257
      HemL; Glutamate-1-semialdehyde aminotransferase [Coenzyme transport and metabolism]

    10. XM_024446250.2 → XP_024302018.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X15

      Conserved Domains (1) summary
      cl28400
      Location:9 → 235
      HemL; Glutamate-1-semialdehyde aminotransferase [Coenzyme transport and metabolism]

    11. XM_024446245.2 → XP_024302013.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X13

      Conserved Domains (1) summary
      cl28400
      Location:9 → 245
      HemL; Glutamate-1-semialdehyde aminotransferase [Coenzyme transport and metabolism]

    12. XM_024446247.2 → XP_024302015.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X14

      Conserved Domains (1) summary
      cl28400
      Location:58 → 244
      HemL; Glutamate-1-semialdehyde aminotransferase [Coenzyme transport and metabolism]

    13. XM_047417840.1 → XP_047273796.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X10

    14. XM_047417839.1 → XP_047273795.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X10

    15. XM_017009995.2 → XP_016865484.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X4

    16. XM_024446241.2 → XP_024302009.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X10

      Conserved Domains (1) summary
      cl28400
      Location:1 → 319
      HemL; Glutamate-1-semialdehyde aminotransferase [Coenzyme transport and metabolism]

    17. XM_047417841.1 → XP_047273797.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X11

    18. XM_047417843.1 → XP_047273799.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X18

    19. XM_024446252.2 → XP_024302020.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X17

      Conserved Domains (1) summary
      cl28400
      Location:1 → 232
      HemL; Glutamate-1-semialdehyde aminotransferase [Coenzyme transport and metabolism]

    20. XM_024446251.2 → XP_024302019.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X16

      Conserved Domains (1) summary
      cl28400
      Location:1 → 206
      HemL; Glutamate-1-semialdehyde aminotransferase [Coenzyme transport and metabolism]

    RNA

    1. XR_007058651.1 RNA Sequence

    2. XR_007058650.1 RNA Sequence

    3. XR_002956187.2 RNA Sequence

    4. XR_007058649.1 RNA Sequence

    5. XR_007058648.1 RNA Sequence

    6. XR_007058654.1 RNA Sequence

    7. XR_007058652.1 RNA Sequence

    8. XR_007058653.1 RNA Sequence

    9. XR_002956188.2 RNA Sequence

    10. XR_002956189.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      178758757..178783105 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353713.1 → XP_054209688.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X8

    2. XM_054353710.1 → XP_054209685.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X5

    3. XM_054353707.1 → XP_054209682.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X2

    4. XM_054353714.1 → XP_054209689.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X9

    5. XM_054353712.1 → XP_054209687.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X7

    6. XM_054353708.1 → XP_054209683.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X3

    7. XM_054353706.1 → XP_054209681.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X1

    8. XM_054353711.1 → XP_054209686.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X6

    9. XM_054353719.1 → XP_054209694.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X12

    10. XM_054353722.1 → XP_054209697.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X15

    11. XM_054353720.1 → XP_054209695.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X13

    12. XM_054353721.1 → XP_054209696.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X14

    13. XM_054353717.1 → XP_054209692.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X10

    14. XM_054353715.1 → XP_054209690.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X10

    15. XM_054353709.1 → XP_054209684.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X4

    16. XM_054353716.1 → XP_054209691.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X10

    17. XM_054353718.1 → XP_054209693.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X11

    18. XM_054353725.1 → XP_054209700.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X18

    19. XM_054353724.1 → XP_054209699.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X17

    20. XM_054353723.1 → XP_054209698.1  5-phosphohydroxy-L-lysine phospho-lyase isoform X16

    RNA

    1. XR_008487186.1 RNA Sequence

    2. XR_008487188.1 RNA Sequence

    3. XR_008487185.1 RNA Sequence

    4. XR_008487184.1 RNA Sequence

    5. XR_008487187.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IUZ5.1 GenPept UniProtKB/Swiss-Prot:Q8IUZ5

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