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    HYKK hydroxylysine kinase [ Homo sapiens (human) ]

    Gene ID: 123688, updated on 2-Nov-2024

    Summary

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    Official Symbol
    HYKKprovided by HGNC
    Official Full Name
    hydroxylysine kinaseprovided by HGNC
    Primary source
    HGNC:HGNC:34403
    See related
    Ensembl:ENSG00000188266 MIM:614681; AllianceGenome:HGNC:34403
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    AGPHD1
    Summary
    Enables hydroxylysine kinase activity. Predicted to be involved in lysine catabolic process. Predicted to be located in mitochondrial matrix. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 1.5), duodenum (RPKM 1.5) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HYKK in Genome Data Viewer
    Location:
    15q25.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (78507577..78537373)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (76370249..76400048)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (78799919..78829715)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6711 Neighboring gene iron responsive element binding protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:78759180-78759680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:78759681-78760181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9919 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:78833042-78833934 Neighboring gene proteasome 20S subunit alpha 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6713 Neighboring gene cholinergic receptor nicotinic alpha 5 subunit Neighboring gene cholinergic receptor nicotinic alpha 3 subunit

    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. Meta-analysis of the association between the rs8034191 polymorphism in AGPHD1 and lung cancer risk. Zhang L, et al. Asian Pac J Cancer Prev, 2015. PMID 25854352
    2. Genetic association between AGPHD1 variant and lung cancer risk. Wang H, et al. Cell Biochem Biophys, 2014 Dec. PMID 25074529
    3. Strong association between two polymorphisms on 15q25.1 and lung cancer risk: a meta-analysis. Gu M, et al. PLoS One, 2012. PMID 22701590, Free PMC Article
    4. Blood-based CHRNA3 single nucleotide polymorphism and outcome in advanced non-small-cell lung cancer patients. Carcereny E, et al. Lung Cancer, 2010 Jun. PMID 19733931
    5. Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium. Truong T, et al. J Natl Cancer Inst, 2010 Jul 7. PMID 20548021, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CHRNA3 rs1051730 (G > A) and AGPHD1 rs8034191 (A > G) were more susceptible to lung cancers than noncarriers.
      Title: Different effects of the three polymorphisms on 15q25.1 onlung cancer risk: Evidence from published literatures.
    2. The association between AGPHD1 single nucleotide polymorphism rs8034191 and lung cancer risk was significant using multiple genetic models, suggesting that AGPHD1 single nucleotide polymorphism rs8034191 is a risk factor for lung cancer.
      Title: Meta-analysis of the association between the rs8034191 polymorphism in AGPHD1 and lung cancer risk.
    3. The variant rs8034191 in the AGPHD1 gene may not modify the genetic risk of lung cancer in Asian populations.
      Title: Genetic association between AGPHD1 variant and lung cancer risk.
    4. Women with the variant AA genotype of CHRNA5 rs16969968 or variant CC genotype of LOC123688 rs8034191 were at significantly increased risk of heavy smoking.
      Title: Single nucleotide polymorphisms in CHRNA5 rs16969968, CHRNA3 rs578776, and LOC123688 rs8034191 are associated with heaviness of smoking in women in Northeastern Ontario, Canada.
    5. AGPHD1 gene rs8034191-T allele might be a risk-conferring factor for the development of lung cancer in Caucasians, but not in East-Asians.
      Title: Strong association between two polymorphisms on 15q25.1 and lung cancer risk: a meta-analysis.
    6. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Genetic variations on chromosomes 5p15 and 15q25 and bladder cancer risk: findings from the Los Angeles-Shanghai bladder case-control study.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Fine mapping of chromosome 15q25.1 lung cancer susceptibility in African-Americans.
    8. Meta-analysis of gene-disease association. (HuGE Navigator)
      Title: Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium.
    9. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Blood-based CHRNA3 single nucleotide polymorphism and outcome in advanced non-small-cell lung cancer patients.
    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

    EBI GWAS Catalog

    Description
    A genome-wide association study in chronic obstructive pulmonary disease (COPD): identification of two major susceptibility loci.
    EBI GWAS Catalog
    A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25.
    EBI GWAS Catalog
    Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study.
    EBI GWAS Catalog
    Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer.
    EBI GWAS Catalog
    Genome-Wide Association Identifies Regulatory Loci Associated with Distinct Local Histogram Emphysema Patterns.
    EBI GWAS Catalog
    Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1.
    EBI GWAS Catalog
    Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction.
    EBI GWAS Catalog
    Genome-wide association study of smoking behaviours in patients with COPD.
    EBI GWAS Catalog

    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

    Potential readthrough

    Included gene: PSMA4

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables amino acid kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables hydroxylysine kinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables hydroxylysine kinase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in lysine catabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in phosphorylation 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
    hydroxylysine kinase
    Names
    5-hydroxy-L-lysine kinase
    5-hydroxylysine kinase
    aminoglycoside phosphotransferase domain-containing protein 1
    NP_001013641.2
    NP_001077081.1

    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.

    mRNA and Protein(s)

    1. NM_001013619.4 → NP_001013641.2  hydroxylysine kinase isoform 1

      See identical proteins and their annotated locations for NP_001013641.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC027228, AW327432, BM045979, DN831396
      Consensus CDS
      CCDS42063.1
      UniProtKB/Swiss-Prot
      A2RU49, B7ZMA5, F8W6X5, Q6ZTN0
      Related
      ENSP00000373640.4, ENST00000388988.9
      Conserved Domains (2) summary
      COG2334
      Location:8 → 343
      SrkA; Ser/Thr protein kinase RdoA involved in Cpx stress response, MazF antagonist [Signal transduction mechanisms]
      cl21453
      Location:19 → 308
      PKc_like; Protein Kinases, catalytic domain

    2. NM_001083612.2 → NP_001077081.1  hydroxylysine kinase isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains a distinct 3' coding exon and 3' UTR, comapred to variant 1. The resulting protein (isoform 2) has a shorter C-terminus compared to isoform 1.
      Source sequence(s)
      BC132753, BM045979, BM826406
      Consensus CDS
      CCDS45318.1
      UniProtKB/TrEMBL
      A0A0C4DGM4
      Related
      ENSP00000386197.2, ENST00000408962.6
      Conserved Domains (1) summary
      cl21453
      Location:19 → 217
      PKc_like; Protein Kinases, catalytic domain

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      78507577..78537373
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      76370249..76400048
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2RU49.2 GenPept UniProtKB/Swiss-Prot:A2RU49

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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