GK3

Summary

GK3 (glycerol kinase 3, HGNC:4292) is a protein-coding gene on chromosome 4q32.3, encoding Glycerol kinase 3 (Q14409). May be involved in the regulation of glycerol uptake and metabolism.

Predicted to enable glycerol kinase activity. Predicted to be involved in glycerol metabolic process; glycerol-3-phosphate biosynthetic process; and triglyceride metabolic process. Located in mitochondrion.

Source: NCBI Gene 2713 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001395953

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4292
Approved symbol	GK3
Name	glycerol kinase 3
Location	4q32.3
Locus type	gene with protein product
Status	Approved
Aliases	GKTB
Ensembl gene	ENSG00000229894
Ensembl biotype	protein_coding
OMIM	600149
Entrez	2713

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000505354

RefSeq mRNA: 1 — MANE Select: NM_001395953 NM_001395953

CCDS: CCDS93665

Canonical transcript exons

ENST00000505354 — 1 exons

Exon	Start	End
ENSE00003978315	165277807	165279704

Expression profiles

Bgee: expression breadth broad, 28 present calls, max score 88.84.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.84	gold quality
left testis	UBERON:0004533	78.26	gold quality
testis	UBERON:0000473	78.20	gold quality
right testis	UBERON:0004534	76.51	gold quality
bone marrow cell	CL:0002092	65.35	silver quality
bone marrow	UBERON:0002371	59.81	silver quality
corpus callosum	UBERON:0002336	57.38	gold quality
tonsil	UBERON:0002372	54.60	gold quality
blood	UBERON:0000178	53.58	gold quality
lower esophagus mucosa	UBERON:0035834	47.59	silver quality
colonic epithelium	UBERON:0000397	47.24	gold quality
adrenal tissue	UBERON:0018303	46.66	silver quality
monocyte	CL:0000576	43.24	gold quality
liver	UBERON:0002107	42.66	gold quality
leukocyte	CL:0000738	42.49	gold quality
primary visual cortex	UBERON:0002436	42.30	gold quality
calcaneal tendon	UBERON:0003701	41.74	gold quality
sural nerve	UBERON:0015488	41.19	gold quality
granulocyte	CL:0000094	39.62	gold quality
skeletal muscle tissue	UBERON:0001134	39.34	gold quality
duodenum	UBERON:0002114	38.05	silver quality
ganglionic eminence	UBERON:0004023	37.12	gold quality
uterine cervix	UBERON:0000002	37.10	silver quality
lung	UBERON:0002048	36.82	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.66	gold quality
muscle tissue	UBERON:0002385	35.44	gold quality
urinary bladder	UBERON:0001255	35.05	silver quality
thoracic mammary gland	UBERON:0005200	33.99	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.29

Regulation

Is transcription factor: no

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	GK2	ENSDARG00000053456
mus_musculus	Gk	ENSMUSG00000025059
rattus_norvegicus	Gk	ENSRNOG00000034116
drosophila_melanogaster	CG8298	FBGN0033673
drosophila_melanogaster	Gk2	FBGN0035266
caenorhabditis_elegans		WBGENE00020007

Paralogs (6): XYLB (ENSG00000093217), FGGY (ENSG00000172456), GK5 (ENSG00000175066), GK2 (ENSG00000196475), SHPK (ENSG00000197417), GK (ENSG00000198814)

Protein

Protein identifiers

Glycerol kinase 3 — Q14409 (reviewed: Q14409)

Alternative names: ATP:glycerol 3-phosphotransferase 3, Glycerol kinase 3 pseudogene, Glycerol kinase, testis specific 1

All UniProt accessions (1): Q14409

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in the regulation of glycerol uptake and metabolism.

Subcellular location. Mitochondrion outer membrane. Cytoplasm.

Pathway. Polyol metabolism; glycerol degradation via glycerol kinase pathway; sn-glycerol 3-phosphate from glycerol: step 1/1.

Similarity. Belongs to the FGGY kinase family.

RefSeq proteins (1): NP_001382882* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000577	Carb_kinase_FGGY	Family
IPR005999	Glycerol_kin	Family
IPR018483	Carb_kinase_FGGY_CS	Conserved_site
IPR018484	FGGY_N	Domain
IPR018485	FGGY_C	Domain
IPR042018	GK1-3_metazoan-type	Family
IPR043129	ATPase_NBD	Homologous_superfamily

Pfam: PF00370, PF02782

Catalyzed reactions (Rhea), 1 shown:

• glycerol + ATP = sn-glycerol 3-phosphate + ADP + H(+) (RHEA:21644)

UniProt features (11 total): binding site 8, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q14409-F1	92.56	0.82

Functional residue map

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

Ligand- & substrate-binding residues (8): 20; 24; 94; 148; 259; 281; 326; 427–431

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-75109	Triglyceride biosynthesis

MSigDB gene sets: 56 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, chr4q32, STOSSI_RESPONSE_TO_ESTRADIOL, EGFR_UP.V1_UP, REACTOME_METABOLISM_OF_LIPIDS, MTOR_UP.N4.V1_UP, PTEN_DN.V2_UP, REACTOME_TRIGLYCERIDE_METABOLISM, HOXA9_DN.V1_DN, STK33_SKM_UP, KRAS.DF.V1_UP, PAX3_TARGET_GENES, GSE10325_MYELOID_VS_LUPUS_MYELOID_DN, GSE11864_UNTREATED_VS_CSF1_IN_MAC_DN

GO Biological Process (6): glycerol metabolic process (GO:0006071), triglyceride metabolic process (GO:0006641), glycerol catabolic process (GO:0019563), glycerol-3-phosphate biosynthetic process (GO:0046167), carbohydrate metabolic process (GO:0005975), glycerol-3-phosphate metabolic process (GO:0006072)

GO Molecular Function (6): glycerol kinase activity (GO:0004370), ATP binding (GO:0005524), nucleotide binding (GO:0000166), kinase activity (GO:0016301), transferase activity (GO:0016740), phosphotransferase activity, alcohol group as acceptor (GO:0016773)

GO Cellular Component (4): mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), cytoplasm (GO:0005737), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Triglyceride metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transferase activity, transferring phosphorus-containing groups	2
cellular anatomical structure	2
carbohydrate metabolic process	1
polyol metabolic process	1
acylglycerol metabolic process	1
glycerol metabolic process	1
alditol catabolic process	1
glycerol-3-phosphate metabolic process	1
organophosphate biosynthetic process	1
carbohydrate derivative biosynthetic process	1
primary metabolic process	1
alditol phosphate metabolic process	1
kinase activity	1
phosphotransferase activity, alcohol group as acceptor	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
catalytic activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrial membrane	1
organelle outer membrane	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1097 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GK3	TKFC	Q3LXA3	352
GK3	VDAC3	Q9Y277	348
GK3	H6PD	O95479	302
GK3	GUK1	Q16774	298
GK3	GPD2	P43304	296
GK3	HSPG2	P98160	282
GK3	MCEE	Q96PE7	271
GK3	TPI1	P00938	255
GK3	MTLN	Q8NCU8	254
GK3	SORD	Q00796	248
GK3	PC	P11498	245
GK3	FAR2	Q96K12	244
GK3	LPCAT2	Q7L5N7	241
GK3	GPD1	P21695	235
GK3	DOLK	Q9UPQ8	232

IntAct

9 interactions, top by confidence:

A	B	Type	Score
GK3	DNAJC1	psi-mi:“MI:0915”(physical association)	0.400
GK3	HNRNPU	psi-mi:“MI:0915”(physical association)	0.400
GK	SCGB1D2	psi-mi:“MI:0914”(association)	0.350
NDUFA4	COX7A2L	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
GK3	APOD	psi-mi:“MI:0914”(association)	0.350
FECH	GTPBP10	psi-mi:“MI:0914”(association)	0.350
FLT3	KIF2A	psi-mi:“MI:2364”(proximity)	0.270

ESM2 similar proteins: A2AKQ0, A2VE55, A5GFZ5, C9WPN6, F1QGW6, F6RQL9, O60762, O70152, O77676, P00516, P0C605, P20461, P32189, P35250, P37273, P41091, P53033, P81795, Q05B83, Q0IID9, Q13126, Q13976, Q14409, Q15B89, Q1JQ93, Q2KHU8, Q2KJ61, Q2TBV5, Q2VIR3, Q3MHF7, Q5HZM6, Q5MB13, Q5R797, Q5RDC9, Q5RIC0, Q5ZHS1, Q5ZMS3, Q63060, Q641W4, Q64516

Diamond homologs: A0KAA1, A0KIT3, A1R6X6, A1TGD7, A3QIN4, A4FNR2, A4JHM8, A4SPA7, A4T5Y1, A5CS23, A5G146, A5U920, A5UU55, A5VE44, A5VZG7, A6M1Y8, A6WIC0, A6WXV2, A8F679, A8FQ89, A8H995, A8I8V7, A9AFH2, A9KY18, A9W8T7, A9WJ21, A9WS93, B0K643, B0KUG0, B0RMN0, B0TQM6, B1JY43, B1KKY8, B1LWN6, B1MFT1, B1YWB2, B1ZGW7, B2IE09, B2SYH7, B7KN92

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

80 predictions. Top by Δscore:

Variant	Effect	Δscore
4:165279202:G:GG	donor_gain	0.6200
4:165278168:GC:G	acceptor_gain	0.5600
4:165279199:GAA:G	donor_gain	0.5500
4:165279209:C:G	donor_gain	0.5300
4:165278167:A:AG	acceptor_gain	0.5200
4:165278168:G:GG	acceptor_gain	0.5200
4:165279036:T:TA	acceptor_gain	0.5000
4:165279037:A:AA	acceptor_gain	0.5000
4:165279201:A:G	donor_gain	0.5000
4:165278168:GCATT:G	acceptor_gain	0.4900
4:165278158:A:T	acceptor_gain	0.4500
4:165278166:CAGCA:C	acceptor_gain	0.4400
4:165279056:G:GT	acceptor_gain	0.4300
4:165279057:T:TT	acceptor_gain	0.4300
4:165278177:TG:T	acceptor_gain	0.3900
4:165278178:G:GC	acceptor_gain	0.3600
4:165279053:T:G	acceptor_gain	0.3600
4:165279060:A:AG	acceptor_gain	0.3600
4:165279061:G:GG	acceptor_gain	0.3600
4:165278168:GCA:G	acceptor_gain	0.3500
4:165278279:GC:G	donor_gain	0.3400
4:165278175:TCTG:T	acceptor_gain	0.3300
4:165279055:TG:T	acceptor_gain	0.3300
4:165278176:CTG:C	acceptor_gain	0.3200
4:165278219:G:GC	acceptor_gain	0.3200
4:165278221:TTC:T	donor_gain	0.3200
4:165279053:TCTG:T	acceptor_gain	0.3100
4:165278167:A:T	acceptor_gain	0.2900
4:165278186:A:AG	acceptor_gain	0.2800
4:165278217:C:CG	acceptor_gain	0.2800

AlphaMissense

3628 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:165278549:C:T	G366E	0.999
4:165278564:A:T	V361D	0.999
4:165278794:G:C	F284L	0.999
4:165278794:G:T	F284L	0.999
4:165278796:A:G	F284L	0.999
4:165279306:A:G	W114R	0.999
4:165279306:A:T	W114R	0.999
4:165278139:A:G	W503R	0.998
4:165278139:A:T	W503R	0.998
4:165278331:C:G	A439P	0.998
4:165278451:C:G	A399P	0.998
4:165278501:C:T	G382E	0.998
4:165278514:C:A	G378W	0.998
4:165278550:C:A	G366W	0.998
4:165278558:G:T	A363E	0.998
4:165278655:A:G	W331R	0.998
4:165278655:A:T	W331R	0.998
4:165279035:C:A	R204M	0.998
4:165279035:C:G	R204T	0.998
4:165279196:A:C	S150R	0.998
4:165279196:A:T	S150R	0.998
4:165279198:T:G	S150R	0.998
4:165279348:A:G	W100R	0.998
4:165279348:A:T	W100R	0.998
4:165278137:C:A	W503C	0.997
4:165278137:C:G	W503C	0.997
4:165278443:A:C	C401W	0.997
4:165278513:C:T	G378E	0.997
4:165278514:C:G	G378R	0.997
4:165278514:C:T	G378R	0.997

dbSNP variants (sampled 300 via entrez): RS1000427358 (4:165278873 C>T), RS10009579 (4:165281385 G>A), RS1001458716 (4:165281331 A>T), RS10016586 (4:165278238 C>T), RS10020255 (4:165279670 G>A,C), RS10023176 (4:165280399 G>A,T), RS1003331068 (4:165280729 CTT>C), RS1004439085 (4:165278932 C>G,T), RS1005041370 (4:165277601 G>A), RS1007174547 (4:165281536 C>T), RS1008597701 (4:165279950 T>C), RS1010626401 (4:165281642 C>A,G), RS1011627290 (4:165280084 C>G,T), RS1014122829 (4:165277552 T>G), RS1016390874 (4:165278028 T>C)

Disease associations

OMIM: gene MIM:600149 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
ciglitazone	affects binding, increases expression	1
Acetaminophen	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	decreases expression	1
Nanotubes, Carbon	increases expression	1

Clinical trials (associated diseases)

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