GALK2

gene
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Also known as GK2

Summary

GALK2 (galactokinase 2, HGNC:4119) is a protein-coding gene on chromosome 15q21.1-q21.2, encoding N-acetylgalactosamine kinase (Q01415). Acts on GalNAc.

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.

Source: NCBI Gene 2585 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 70 total
  • MANE Select transcript: NM_002044

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4119
Approved symbolGALK2
Namegalactokinase 2
Location15q21.1-q21.2
Locus typegene with protein product
StatusApproved
AliasesGK2
Ensembl geneENSG00000156958
Ensembl biotypeprotein_coding
OMIM137028
Entrez2585

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 17 protein_coding, 8 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined

ENST00000327171, ENST00000396509, ENST00000544523, ENST00000558145, ENST00000558399, ENST00000558775, ENST00000558956, ENST00000559040, ENST00000559095, ENST00000559208, ENST00000559423, ENST00000559454, ENST00000559580, ENST00000559883, ENST00000559963, ENST00000560031, ENST00000560119, ENST00000560138, ENST00000560528, ENST00000560654, ENST00000561014, ENST00000561074, ENST00000909176, ENST00000909177, ENST00000909178, ENST00000968617, ENST00000968618, ENST00000968619

RefSeq mRNA: 6 — MANE Select: NM_002044 NM_001001556, NM_001289030, NM_001289031, NM_001352047, NM_001352048, NM_002044

CCDS: CCDS32236, CCDS42034, CCDS73724

Canonical transcript exons

ENST00000560031 — 10 exons

ExonStartEnd
ENSE000014069324932795249331882
ENSE000025582434917024749170375
ENSE000034588504928356649283718
ENSE000035146304931960449319805
ENSE000035287854923922149239367
ENSE000035467144929232749292537
ENSE000035968304920116249201250
ENSE000036282244928198749282085
ENSE000036564624921719049217313
ENSE000036827354923585149235941

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 94.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.7209 / max 157.8898, expressed in 1805 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1465569.59871772
1465585.17621571
1465571.94601056

Top tissues by expression

289 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370194.39gold quality
islet of LangerhansUBERON:000000692.02gold quality
adrenal tissueUBERON:001830391.23gold quality
right adrenal glandUBERON:000123390.50gold quality
left adrenal glandUBERON:000123490.22gold quality
left adrenal gland cortexUBERON:003582589.83gold quality
right adrenal gland cortexUBERON:003582789.82gold quality
colonic epitheliumUBERON:000039789.75gold quality
rectumUBERON:000105289.72gold quality
tendonUBERON:000004389.47gold quality
adrenal glandUBERON:000236988.98gold quality
stromal cell of endometriumCL:000225588.63gold quality
mucosa of transverse colonUBERON:000499188.35gold quality
sural nerveUBERON:001548888.19gold quality
adrenal cortexUBERON:000123588.04gold quality
right lobe of liverUBERON:000111487.60gold quality
middle temporal gyrusUBERON:000277187.59gold quality
ventricular zoneUBERON:000305387.42gold quality
pancreasUBERON:000126486.71gold quality
body of pancreasUBERON:000115086.37gold quality
heart left ventricleUBERON:000208486.32gold quality
monocyteCL:000057686.26gold quality
bronchial epithelial cellCL:000232886.18gold quality
Brodmann (1909) area 23UBERON:001355486.09gold quality
cardiac ventricleUBERON:000208285.88gold quality
gall bladderUBERON:000211085.74gold quality
right uterine tubeUBERON:000130285.73gold quality
mononuclear cellCL:000084285.69gold quality
tibial nerveUBERON:000132385.68gold quality
right atrium auricular regionUBERON:000663185.68gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.57
E-MTAB-7249no128.88

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting GALK2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-186-5P99.9970.833707
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-548P99.9872.253784
HSA-MIR-477599.9875.006394
HSA-MIR-314899.9775.066478
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-60799.9773.625593
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-365899.9673.874379
HSA-MIR-302E99.9670.742669
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-545-3P99.9570.742783
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-335-3P99.9373.364958
HSA-MIR-205-3P99.9269.923165
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-95-5P99.8972.173973
HSA-MIR-684499.8270.692423
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-570099.6469.882280
HSA-MIR-3942-3P99.5769.032854

Literature-anchored findings (GeneRIF, showing 3)

  • geometry and substrate specificity of the GalNAc kinase active site before and after catalysis (PMID:16006554)
  • GALK2 has an ordered ternary complex mechanism in which ATP is the first substrate to bind (PMID:19874134)
  • Kinetic studies suggest an ordered ternary complex mechanism in which ATP is the first substrate to bind. (PMID:19874134)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriogalk2ENSDARG00000004059
mus_musculusGalk2ENSMUSG00000027207
rattus_norvegicusGalk2ENSRNOG00000009289
drosophila_melanogasterGalkFBGN0263199
caenorhabditis_eleganstag-96WBGENE00006461

Paralogs (2): GALK1 (ENSG00000108479), MVK (ENSG00000110921)

Protein

Protein identifiers

N-acetylgalactosamine kinaseQ01415 (reviewed: Q01415)

Alternative names: GalNAc kinase, Galactokinase 2

All UniProt accessions (14): Q01415, B7ZAX5, H0YK10, H0YK30, H0YLF9, H0YLK3, H0YLL3, H0YLL8, H0YM44, H0YML1, H0YN31, H0YN87, H0YND3, H0YNR7

UniProt curated annotations — full annotation on UniProt →

Function. Acts on GalNAc. Also acts as a galactokinase when galactose is present at high concentrations. May be involved in a salvage pathway for the reutilization of free GalNAc derived from the degradation of complex carbohydrates.

Subunit / interactions. Monomer.

Similarity. Belongs to the GHMP kinase family. GalK subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
Q01415-11yes
Q01415-22

RefSeq proteins (6): NP_001001556, NP_001275959, NP_001275960, NP_001338976, NP_001338977, NP_002035* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000705GalactokinaseFamily
IPR006203GHMP_knse_ATP-bd_CSConserved_site
IPR006204GHMP_kinase_N_domDomain
IPR006206Mevalonate/galactokinaseFamily
IPR013750GHMP_kinase_C_domDomain
IPR014721Ribsml_uS5_D2-typ_fold_subgrHomologous_superfamily
IPR019539GalKase_NDomain
IPR019741Galactokinase_CSConserved_site
IPR020568Ribosomal_Su5_D2-typ_SFHomologous_superfamily
IPR036554GHMP_kinase_C_sfHomologous_superfamily

Pfam: PF00288, PF08544, PF10509

Enzyme classification (BRENDA):

  • EC 2.7.1.157 — N-acetylgalactosamine kinase (BRENDA: 3 organisms, 10 substrates, 4 inhibitors, 56 Km, 27 kcat entries)

Substrate kinetics (BRENDA)

7 substrates with measured Km, best-characterized 7. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
ATP0.006–0.1326
N-ACETYL-ALPHA-D-GALACTOSAMINE0.04–0.959
N-ACETYL-ALPHA-D-GLUCOSAMINE0.051–0.397
N-ACETYL-ALPHA-D-MANNOSAMINE0.25–4.17
N-ACETYL-D-GALACTOSAMINE0.04–0.143
D-GALACTOSE0.51
GALACTOSE0.51

Catalyzed reactions (Rhea), 1 shown:

  • N-acetyl-alpha-D-galactosamine + ATP = N-acetyl-alpha-D-galactosamine 1-phosphate + ADP + H(+) (RHEA:12617)

UniProt features (53 total): helix 20, strand 16, binding site 10, turn 2, chain 1, active site 1, site 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
2A2CX-RAY DIFFRACTION1.65
2A2DX-RAY DIFFRACTION2.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q01415-F195.070.91

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 190 (proton acceptor); 43 (transition state stabilizer)

Ligand- & substrate-binding residues (10): 233; 234; 43; 49; 50; 52; 143; 145; 146; 190

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 103 (showing top): GOBP_POLYOL_METABOLIC_PROCESS, GOBP_POLYOL_CATABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_MALE_GAMETE_GENERATION, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, NKX61_01, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, MORF_ZNF10, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_CILIUM_ORGANIZATION, KEGG_PPAR_SIGNALING_PATHWAY, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOBP_CARBOHYDRATE_METABOLIC_PROCESS

GO Biological Process (3): carbohydrate metabolic process (GO:0005975), galactose metabolic process (GO:0006012), carbohydrate phosphorylation (GO:0046835)

GO Molecular Function (7): galactokinase activity (GO:0004335), ATP binding (GO:0005524), N-acetylgalactosamine kinase activity (GO:0033858), nucleotide binding (GO:0000166), kinase activity (GO:0016301), transferase activity (GO:0016740), phosphotransferase activity, alcohol group as acceptor (GO:0016773)

GO Cellular Component (2): cytosol (GO:0005829), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
phosphotransferase activity, alcohol group as acceptor2
carbohydrate kinase activity2
transferase activity, transferring phosphorus-containing groups2
cellular anatomical structure2
primary metabolic process1
hexose metabolic process1
carbohydrate metabolic process1
phosphorylation1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
nucleoside phosphate binding1
heterocyclic compound binding1
catalytic activity1
cytoplasm1
intracellular anatomical structure1

Protein interactions and networks

STRING

1950 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GALK2UAP1Q16222672
GALK2GALEQ14376666
GALK2AKR1B1P15121586
GALK2TK1P04183580
GALK2GALTP07902554
GALK2MVKQ03426508
GALK2PTGR3Q8N4Q0503
GALK2GALMQ96C23459
GALK2PGM3O95394451
GALK2ARMC6Q6NXE6435
GALK2GNEQ9Y223423
GALK2NAGKQ9UJ70414
GALK2TPI1P00938406
GALK2OTCP00480403
GALK2MAP7D2Q96T17402

IntAct

3 interactions, top by confidence:

ABTypeScore
GALK2POTEFpsi-mi:“MI:0914”(association)0.530

BioGRID (27): GALK2 (Co-fractionation), GALK2 (Co-fractionation), GALK2 (Co-fractionation), GALK2 (Co-fractionation), LTA4H (Co-fractionation), MEMO1 (Co-fractionation), MVD (Co-fractionation), POTEF (Affinity Capture-MS), CCDC18 (Affinity Capture-MS), PABPC3 (Affinity Capture-MS), GNB4 (Affinity Capture-MS), GNB2 (Affinity Capture-MS), PLS1 (Affinity Capture-MS), CD59 (Affinity Capture-MS), AHNAK (Affinity Capture-MS)

ESM2 similar proteins: A1L1F0, A4IFG2, A5A6P1, A5GFY8, C3K0A7, D9IVE5, O43175, P10688, P10895, P18407, P25335, Q01415, Q02JZ8, Q09913, Q0V9A9, Q1ED21, Q2KIG4, Q32NH8, Q3B8C3, Q3KFK9, Q3TV70, Q48KS4, Q4K8H3, Q4R964, Q4ZVG8, Q58DU8, Q5EAD2, Q5PQR3, Q5R6J8, Q5R7M2, Q61753, Q640T1, Q68FH4, Q6AYP0, Q6DGA6, Q6LPX9, Q86WQ0, Q87YX4, Q8BIP0, Q8C726

Diamond homologs: A0KQH8, A1A900, A1KG98, A4W899, A5U003, A5UDQ5, A5UHX0, A7MIX5, A7MV01, A7ZJD2, A7ZY13, A8GBA5, A9MJI2, B1IXX9, B1LM48, B1YIH8, B2GEP6, B2TUY8, B2VBV2, B5ETC9, B5YRF5, B6I7R1, B7IDE2, B7LAF8, B7LK02, B7M6C0, B7MGL4, B7MPP1, B7N9Z9, B7NNH9, B7ULN0, C1AKV1, C4ZXS8, O42821, P04385, P09608, P0A6T3, P0A6T4, P13045, P31767

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

70 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance63
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3534 predictions. Top by Δscore:

VariantEffectΔscore
15:49170250:G:GTdonor_gain1.0000
15:49189978:G:GTdonor_gain1.0000
15:49201155:T:Gacceptor_gain1.0000
15:49201159:CAGGT:Cacceptor_loss1.0000
15:49201160:A:AGacceptor_gain1.0000
15:49201160:A:Tacceptor_loss1.0000
15:49201160:AG:Aacceptor_gain1.0000
15:49201161:G:Aacceptor_loss1.0000
15:49201161:G:GAacceptor_gain1.0000
15:49201161:GG:Gacceptor_gain1.0000
15:49201161:GGT:Gacceptor_gain1.0000
15:49201161:GGTT:Gacceptor_gain1.0000
15:49201161:GGTTA:Gacceptor_gain1.0000
15:49201233:G:GTdonor_gain1.0000
15:49201247:A:AGdonor_gain1.0000
15:49201247:A:Gdonor_gain1.0000
15:49201247:ATAGG:Adonor_loss1.0000
15:49201252:T:Gdonor_loss1.0000
15:49217184:TTCTA:Tacceptor_loss1.0000
15:49217186:CTA:Cacceptor_loss1.0000
15:49217187:TA:Tacceptor_loss1.0000
15:49217188:A:AGacceptor_gain1.0000
15:49217189:G:GGacceptor_gain1.0000
15:49217189:GGA:Gacceptor_gain1.0000
15:49217189:GGAGA:Gacceptor_gain1.0000
15:49217309:TATCC:Tdonor_gain1.0000
15:49217311:TCC:Tdonor_gain1.0000
15:49217312:CC:Cdonor_gain1.0000
15:49217313:CG:Cdonor_loss1.0000
15:49217314:G:GGdonor_gain1.0000

AlphaMissense

3001 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:49239305:A:CS148R0.999
15:49239307:T:AS148R0.999
15:49239307:T:GS148R0.999
15:49282051:A:CD190A0.999
15:49282051:A:TD190V0.999
15:49282052:C:AD190E0.999
15:49282052:C:GD190E0.999
15:49283581:T:CF207L0.999
15:49283583:T:AF207L0.999
15:49283583:T:GF207L0.999
15:49201236:G:CR43T0.998
15:49201237:A:CR43S0.998
15:49201237:A:TR43S0.998
15:49201243:C:AN45K0.998
15:49201243:C:GN45K0.998
15:49217190:G:AG48E0.998
15:49217190:G:TG48V0.998
15:49217202:A:TD52V0.998
15:49235903:T:AW107R0.998
15:49235903:T:CW107R0.998
15:49282050:G:CD190H0.998
15:49282060:T:AI193K0.998
15:49217193:A:TE49V0.997
15:49217201:G:CD52H0.997
15:49217202:A:CD52A0.997
15:49217203:T:AD52E0.997
15:49217203:T:GD52E0.997
15:49239299:A:CS146R0.997
15:49239301:C:AS146R0.997
15:49239301:C:GS146R0.997

dbSNP variants (sampled 300 via entrez): RS1000003640 (15:49235809 G>A), RS1000008209 (15:49358636 C>G,T), RS1000017721 (15:49306012 A>G), RS1000032296 (15:49217620 A>C,G,T), RS1000036230 (15:49328215 T>A), RS1000041699 (15:49280126 C>A), RS1000063705 (15:49357433 A>G), RS1000087799 (15:49266666 A>C), RS1000127130 (15:49183633 C>T), RS1000150421 (15:49265621 C>G,T), RS1000183190 (15:49363821 T>C), RS1000190135 (15:49210503 G>A,T), RS1000211049 (15:49200895 A>G), RS1000221810 (15:49243560 T>A,G), RS1000221955 (15:49167003 T>C)

Disease associations

OMIM: gene MIM:137028 | disease phenotypes: MIM:210900

GenCC curated gene-disease

Mondo (2): Bloom syndrome (MONDO:0008876), familial colorectal cancer (MONDO:0023113)

Orphanet (1): Bloom syndrome (Orphanet:125)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

StudyTraitp-value
GCST004744_32Lung adenocarcinoma3.000000e-12
GCST004744_33Lung adenocarcinoma5.000000e-10
GCST004748_34Lung cancer1.000000e-06
GCST004749_39Lung cancer in ever smokers9.000000e-06
GCST90002395_220Mean platelet volume1.000000e-12

MeSH disease descriptors (1)

DescriptorNameTree numbers
D001816Bloom SyndromeC16.131.077.137; C16.320.798.313; C18.452.284.100; C20.673.795.313

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Vehicle Emissionsincreases abundance, increases expression, decreases expression, decreases reaction2
Benzo(a)pyreneaffects methylation, increases expression2
Valproic Aciddecreases methylation, increases expression2
Particulate Matterdecreases expression, decreases reaction, increases abundance, increases expression2
dicrotophosdecreases expression1
tungsten carbidedecreases expression, affects binding1
testosterone enanthateaffects expression1
triphenyl phosphateaffects expression1
quercitrinincreases expression1
arseniteaffects binding, increases reaction1
cobaltous chloridedecreases expression1
4-aminophenylarsenoxideaffects binding, decreases reaction1
tamibarotenedecreases expression1
perfluorooctane sulfonic acidincreases expression1
abrineincreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amidedecreases expression, decreases reaction1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Arsenic Trioxideaffects binding, decreases reaction1
Acetaminophendecreases expression1
Arsenicaffects methylation1
Atrazinedecreases expression1
Cobaltaffects binding, decreases expression1
Methyl Methanesulfonateincreases expression1
Plant Extractsaffects cotreatment, increases expression1
Progesteroneincreases expression1
Tobacco Smoke Pollutionincreases methylation1
Tretinoindecreases expression1
Tunicamycinincreases expression1
Cyclosporineincreases expression1

Cellosaurus cell lines

5 cell lines: 3 cancer cell line, 2 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_DX01HAP1 GALK2 (-) 1Cancer cell lineMale
CVCL_DX02HAP1 GALK2 (-) 2Cancer cell lineMale
CVCL_DX36HAP1 GALK2 (-) NAGK (-)Cancer cell lineMale
CVCL_VR13HEK293T GALK2 KO clone 7Transformed cell lineFemale
CVCL_VR15HEK293T GALE+GALK2 KO clone 7Transformed cell lineFemale

Clinical trials (associated diseases)

10 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00021437Not specifiedCOMPLETEDBiological Significance of the Bloom’s Syndrome Protein
NCT04251325Not specifiedUNKNOWNSocio-demographic Characteristics of Basic Life Support Course Participants
NCT04353089Not specifiedUNKNOWNGeographical Association Between Basic Life Support Courses, Bystander Cardiopulmonary Resuscitation and Survival
NCT00349817Not specifiedUNKNOWNGenetics Education: Preparing Physicians for the Future
NCT02645084Not specifiedCOMPLETEDIdentifying Patients With Hereditary and Familial Colorectal Cancer by Using an Online Risk Tool
NCT03365986Not specifiedUNKNOWNSystemic Screening for Hereditary Colorectal Cancer in China
NCT04197856Not specifiedACTIVE_NOT_RECRUITINGDirect Information to At-risk Relatives
NCT04280666Not specifiedUNKNOWNNext-generation Sequencing of Colorectal Cancer Somatic Cells to Guide Genetic Susceptibility Gene Mutations Screening.
NCT05495776Not specifiedRECRUITINGProspective Multicenter Registry Study to Assess the Frequency of Lynch Syndrome Among Patients With Colorectal Cancer
NCT07307664Not specifiedRECRUITINGIncreasing Germline Genetic Testing for Patients With Cancer
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Bloom syndrome, familial colorectal cancer