HYKK hydroxylysine kinase [Homo sapiens (human)] - Gene

Summary

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, Apr 2022]
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

Location:: 15q25.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (78507577..78537373)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (76370249..76400048)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (78799919..78829715)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Fine mapping of chromosome 15q25.1 lung cancer susceptibility in African-Americans.
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.
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.

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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

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

EC 2.7.1.81

NP_001077081.1

EC 2.7.1.81

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)

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
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