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GALK2 galactokinase 2 [ Homo sapiens (human) ]

Gene ID: 2585, updated on 7-Apr-2024

Summary

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Official Symbol
GALK2provided by HGNC
Official Full Name
galactokinase 2provided by HGNC
Primary source
HGNC:HGNC:4119
See related
Ensembl:ENSG00000156958 MIM:137028; AllianceGenome:HGNC:4119
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
GK2
Summary
This gene encodes a highly efficient N-acetylgalactosamine (GalNAc) kinase, which has galactokinase activity when galactose is present at high concentrations. The encoded protein is a member of the GHMP kinase family. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2017]
Expression
Ubiquitous expression in kidney (RPKM 4.3), duodenum (RPKM 3.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
15q21.1-q21.2
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (49155774..49367740)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (46963986..47175984)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (49447971..49624079)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903489 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:49447830-49448748 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:49461856-49462760 Neighboring gene COP9 signalosome subunit 2 Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 4 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6422 Neighboring gene microRNA 4716 Neighboring gene RPL15 pseudogene 19 Neighboring gene MPRA-validated peak2332 silencer Neighboring gene RNA, 7SL, cytoplasmic 307, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:49524445-49525115 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:49523773-49524444 Neighboring gene Sharpr-MPRA regulatory region 5673 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:49557847-49559046 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:49646702-49647347 Neighboring gene family with sequence similarity 227 member B Neighboring gene signal peptide peptidase like 2A pseudogene Neighboring gene OCT4 hESC enhancer GRCh37_chr15:49664491-49665044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:49671731-49672256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:49672257-49672781 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:49688382-49688895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9387 Neighboring gene fibroblast growth factor 7 Neighboring gene uncharacterized LOC105370811

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. Mechanistic studies on human N-acetylgalactosamine kinase. Agnew A, et al. J Enzyme Inhib Med Chem, 2010 Jun. PMID 19874134
  2. The molecular architecture of human N-acetylgalactosamine kinase. Thoden JB, et al. J Biol Chem, 2005 Sep 23. PMID 16006554
  3. Identification of the GalNAc kinase amino acid sequence. Pastuszak I, et al. J Biol Chem, 1996 Sep 27. PMID 8798585
  4. Kidney N-acetylgalactosamine (GalNAc)-1-phosphate kinase, a new pathway of GalNAc activation. Pastuszak I, et al. J Biol Chem, 1996 Aug 23. PMID 8702831
  5. Cloning of a human galactokinase gene (GK2) on chromosome 15 by complementation in yeast. Lee RT, et al. Proc Natl Acad Sci U S A, 1992 Nov 15. PMID 1438294, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. GALK2 has an ordered ternary complex mechanism in which ATP is the first substrate to bind
    Title: Mechanistic studies on human N-acetylgalactosamine kinase.
  2. Kinetic studies suggest an ordered ternary complex mechanism in which ATP is the first substrate to bind.
    Title: Mechanistic studies on human N-acetylgalactosamine kinase.
  3. geometry and substrate specificity of the GalNAc kinase active site before and after catalysis
    Title: The molecular architecture of human N-acetylgalactosamine kinase.
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

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

  • MGC1745

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables N-acetylgalactosamine kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables galactokinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables galactokinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in carbohydrate metabolic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in carbohydrate phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in galactose metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
N-acetylgalactosamine kinase
Names
galNAc kinase
NP_001001556.1
NP_001275959.1
NP_001275960.1
NP_001338976.1
NP_001338977.1
NP_002035.1
XP_006720524.1
XP_024305660.1
XP_024305662.1
XP_047288303.1
XP_047288304.1
XP_047288305.1
XP_047288306.1
XP_047288307.1
XP_047288308.1
XP_047288309.1
XP_047288310.1
XP_054233652.1
XP_054233653.1
XP_054233654.1
XP_054233655.1
XP_054233656.1
XP_054233657.1
XP_054233658.1
XP_054233659.1
XP_054233660.1
XP_054233661.1
XP_054233662.1

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_001001556.3 → NP_001001556.1  N-acetylgalactosamine kinase isoform 2

    See identical proteins and their annotated locations for NP_001001556.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 5' exon, as compared to variant 1. The encoded isoform (2) has a shorter and alternate N-terminus, as compared to isoform 1.
    Source sequence(s)
    AC022306, AF461816, AL832745, BX096260, BX455251, CA841825, DC390737
    Consensus CDS
    CCDS32236.1
    UniProtKB/TrEMBL
    B4DW43
    Related
    ENSP00000316632.3, ENST00000327171.7
    Conserved Domains (3) summary
    PLN02521
    Location:7 → 444
    PLN02521; galactokinase
    pfam08544
    Location:339 → 419
    GHMP_kinases_C; GHMP kinases C terminal
    pfam10509
    Location:13 → 62
    GalKase_gal_bdg; Galactokinase galactose-binding signature

  2. NM_001289030.2 → NP_001275959.1  N-acetylgalactosamine kinase isoform 3

    See identical proteins and their annotated locations for NP_001275959.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' exon and uses a downstream translation start codon, compared to variant 1. The encoded protein (isoform 3) has a shorter N-terminus, compared to isoform 1. Variants 3 and 4 encode the same protein.
    Source sequence(s)
    AC022306, AK316440, DB457948, EB386877
    Consensus CDS
    CCDS73724.1
    UniProtKB/TrEMBL
    B4DW43, B7ZAX5
    Related
    ENSP00000440312.1, ENST00000544523.5
    Conserved Domains (3) summary
    PLN02521
    Location:2 → 431
    PLN02521; galactokinase
    pfam08544
    Location:326 → 406
    GHMP_kinases_C; GHMP kinases C terminal
    pfam10509
    Location:2 → 49
    GalKase_gal_bdg; Galactokinase galactose-binding signature

  3. NM_001289031.1 → NP_001275960.1  N-acetylgalactosamine kinase isoform 3

    See identical proteins and their annotated locations for NP_001275960.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 5' coding region, and uses a downstream translation start codon, compared to variant 1. The encoded protein (isoform 3) has a shorter N-terminus, compared to isoform 1. Variants 3 and 4 encode the same protein.
    Source sequence(s)
    AC022306, AK301361, BQ921903, DB457948, DC298656
    Consensus CDS
    CCDS73724.1
    UniProtKB/TrEMBL
    B4DW43, B7ZAX5
    Related
    ENSP00000379766.2, ENST00000396509.6
    Conserved Domains (3) summary
    PLN02521
    Location:2 → 431
    PLN02521; galactokinase
    pfam08544
    Location:326 → 406
    GHMP_kinases_C; GHMP kinases C terminal
    pfam10509
    Location:2 → 49
    GalKase_gal_bdg; Galactokinase galactose-binding signature

  4. NM_001352047.1 → NP_001338976.1  N-acetylgalactosamine kinase isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC013452, AC022306
    Conserved Domains (1) summary
    cl26519
    Location:1 → 319
    GalKase_gal_bdg; Galactokinase galactose-binding signature

  5. NM_001352048.2 → NP_001338977.1  N-acetylgalactosamine kinase isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC013452, AC022306
    Conserved Domains (1) summary
    cl26519
    Location:1 → 319
    GalKase_gal_bdg; Galactokinase galactose-binding signature

  6. NM_002044.4 → NP_002035.1  N-acetylgalactosamine kinase isoform 1

    See identical proteins and their annotated locations for NP_002035.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC022306, AL832745, BC005141, BX096260, BX455251, CA841825, DB457948
    Consensus CDS
    CCDS42034.1
    UniProtKB/Swiss-Prot
    Q01415, Q7Z4Q4
    UniProtKB/TrEMBL
    B4DW43
    Related
    ENSP00000453129.1, ENST00000560031.6
    Conserved Domains (1) summary
    cl26519
    Location:18 → 455
    GalKase_gal_bdg; Galactokinase galactose-binding signature

RNA

  1. NR_147895.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC013452, AC022306

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    49155774..49367740
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047432349.1 → XP_047288305.1  N-acetylgalactosamine kinase isoform X3

  2. XM_047432347.1 → XP_047288303.1  N-acetylgalactosamine kinase isoform X1

  3. XM_024449892.2 → XP_024305660.1  N-acetylgalactosamine kinase isoform X4

    UniProtKB/TrEMBL
    B4DW43
    Conserved Domains (1) summary
    cl26519
    Location:2 → 427
    GalKase_gal_bdg; Galactokinase galactose-binding signature

  4. XM_024449894.2 → XP_024305662.1  N-acetylgalactosamine kinase isoform X6

    UniProtKB/TrEMBL
    B4DW43
    Conserved Domains (1) summary
    cl26519
    Location:2 → 394
    GalKase_gal_bdg; Galactokinase galactose-binding signature

  5. XM_047432353.1 → XP_047288309.1  N-acetylgalactosamine kinase isoform X8

  6. XM_047432350.1 → XP_047288306.1  N-acetylgalactosamine kinase isoform X5

  7. XM_047432354.1 → XP_047288310.1  N-acetylgalactosamine kinase isoform X9

  8. XM_006720461.5 → XP_006720524.1  N-acetylgalactosamine kinase isoform X2

    UniProtKB/TrEMBL
    B4DW43
    Conserved Domains (3) summary
    PLN02521
    Location:18 → 448
    PLN02521; galactokinase
    pfam08544
    Location:350 → 430
    GHMP_kinases_C; GHMP kinases C terminal
    pfam10509
    Location:24 → 73
    GalKase_gal_bdg; Galactokinase galactose-binding signature

  9. XM_047432348.1 → XP_047288304.1  N-acetylgalactosamine kinase isoform X1

  10. XM_047432351.1 → XP_047288307.1  N-acetylgalactosamine kinase isoform X7

  11. XM_047432352.1 → XP_047288308.1  N-acetylgalactosamine kinase isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    46963986..47175984
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377680.1 → XP_054233655.1  N-acetylgalactosamine kinase isoform X3

  2. XM_054377677.1 → XP_054233652.1  N-acetylgalactosamine kinase isoform X1

  3. XM_054377681.1 → XP_054233656.1  N-acetylgalactosamine kinase isoform X4

  4. XM_054377683.1 → XP_054233658.1  N-acetylgalactosamine kinase isoform X6

  5. XM_054377686.1 → XP_054233661.1  N-acetylgalactosamine kinase isoform X8

  6. XM_054377682.1 → XP_054233657.1  N-acetylgalactosamine kinase isoform X5

  7. XM_054377687.1 → XP_054233662.1  N-acetylgalactosamine kinase isoform X9

  8. XM_054377679.1 → XP_054233654.1  N-acetylgalactosamine kinase isoform X2

  9. XM_054377678.1 → XP_054233653.1  N-acetylgalactosamine kinase isoform X1

  10. XM_054377684.1 → XP_054233659.1  N-acetylgalactosamine kinase isoform X7

  11. XM_054377685.1 → XP_054233660.1  N-acetylgalactosamine kinase isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q01415.1 GenPept UniProtKB/Swiss-Prot:Q01415

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