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

Gene ID: 85007, updated on 5-Mar-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
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Genomic context

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Location:
5q35.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (178207144..178232822, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (178758757..178783105, complement)
105.20220307 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
  • 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_2023_10

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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