GK3 (glycerol kinase 3) - Rat Genome Database

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Gene: GK3 (glycerol kinase 3) Homo sapiens
Analyze
Symbol: GK3
Name: glycerol kinase 3
RGD ID: 1344552
HGNC Page HGNC:4292
Description: Predicted to enable glycerol kinase activity. Predicted to be involved in glycerol metabolic process; glycerol-3-phosphate biosynthetic process; and triglyceride metabolic process. Predicted to be located in mitochondrial outer membrane. Predicted to be active in mitochondrion.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: GK3P; GKP3; GKTB; glycerol kinase 3 pseudogene; glycerol kinase pseudogene 3
RGD Orthologs
Bonobo
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384165,277,807 - 165,279,704 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4165,277,807 - 165,279,704 (-)EnsemblGRCh38hg38GRCh38
GRCh374166,198,959 - 166,200,856 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364166,418,436 - 166,420,272 (-)NCBINCBI36Build 36hg18NCBI36
Celera4163,534,517 - 163,536,748 (-)NCBICelera
Cytogenetic Map4q32.3NCBI
HuRef4161,950,758 - 161,952,989 (-)NCBIHuRef
CHM1_14166,175,401 - 166,177,632 (-)NCBICHM1_1
T2T-CHM13v2.04168,623,800 - 168,625,697 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7987308   PMID:8125298   PMID:9847074   PMID:12477932   PMID:28514442   PMID:30021884   PMID:31900314   PMID:33961781   PMID:35384245  


Genomics

Comparative Map Data
GK3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384165,277,807 - 165,279,704 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4165,277,807 - 165,279,704 (-)EnsemblGRCh38hg38GRCh38
GRCh374166,198,959 - 166,200,856 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364166,418,436 - 166,420,272 (-)NCBINCBI36Build 36hg18NCBI36
Celera4163,534,517 - 163,536,748 (-)NCBICelera
Cytogenetic Map4q32.3NCBI
HuRef4161,950,758 - 161,952,989 (-)NCBIHuRef
CHM1_14166,175,401 - 166,177,632 (-)NCBICHM1_1
T2T-CHM13v2.04168,623,800 - 168,625,697 (-)NCBIT2T-CHM13v2.0
GK3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23163,019,074 - 163,028,657 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14163,381,706 - 163,386,208 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04157,472,574 - 157,474,784 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14169,556,769 - 169,558,691 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4169,556,969 - 169,558,629 (-)Ensemblpanpan1.1panPan2

Variants

.
Variants in GK3
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q31.23-35.2(chr4:148356485-189548183)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051789]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051789]|See cases [RCV000051789] Chr4:148356485..189548183 [GRCh38]
Chr4:149277637..190469337 [GRCh37]
Chr4:149497087..190706331 [NCBI36]
Chr4:4q31.23-35.2		 pathogenic
GRCh38/hg38 4q22.2-32.3(chr4:92913386-165299707)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|See cases [RCV000051775] Chr4:92913386..165299707 [GRCh38]
Chr4:93834537..166220859 [GRCh37]
Chr4:94053560..166440309 [NCBI36]
Chr4:4q22.2-32.3		 pathogenic
GRCh38/hg38 4q32.1-35.2(chr4:158568335-189975660)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053325]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053325]|See cases [RCV000053325] Chr4:158568335..189975660 [GRCh38]
Chr4:159489487..190828225 [GRCh37]
Chr4:159708937..191133809 [NCBI36]
Chr4:4q32.1-35.2		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:163651681-189975519)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053327]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053327]|See cases [RCV000053327] Chr4:163651681..189975519 [GRCh38]
Chr4:164572833..190828225 [GRCh37]
Chr4:164792283..191133668 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
NM_001161521.1(KLHL2):c.557-14761C>T single nucleotide variant Malignant melanoma [RCV000066326] Chr4:165279598 [GRCh38]
Chr4:166200750 [GRCh37]
Chr4:166420200 [NCBI36]
Chr4:4q32.3		 not provided
GRCh38/hg38 4q32.2-34.1(chr4:162723818-172501433)x1 copy number loss See cases [RCV000053326] Chr4:162723818..172501433 [GRCh38]
Chr4:163644970..173422584 [GRCh37]
Chr4:163864420..173659159 [NCBI36]
Chr4:4q32.2-34.1		 pathogenic
GRCh38/hg38 4q32.1-32.3(chr4:158387928-166845726)x3 copy number gain See cases [RCV000136603] Chr4:158387928..166845726 [GRCh38]
Chr4:159309080..167766877 [GRCh37]
Chr4:159528530..168003452 [NCBI36]
Chr4:4q32.1-32.3		 pathogenic|uncertain significance
GRCh38/hg38 4q31.1-35.2(chr4:138510532-189963195)x3 copy number gain See cases [RCV000136810] Chr4:138510532..189963195 [GRCh38]
Chr4:139431686..190828225 [GRCh37]
Chr4:139651136..191121344 [NCBI36]
Chr4:4q31.1-35.2		 pathogenic
GRCh38/hg38 4q32.3(chr4:164837643-167576305)x1 copy number loss See cases [RCV000142339] Chr4:164837643..167576305 [GRCh38]
Chr4:165758795..168497456 [GRCh37]
Chr4:165978245..168734031 [NCBI36]
Chr4:4q32.3		 uncertain significance
GRCh38/hg38 4q31.21-35.2(chr4:145042668-189975519)x3 copy number gain See cases [RCV000135845] Chr4:145042668..189975519 [GRCh38]
Chr4:145963820..190828225 [GRCh37]
Chr4:146183270..191133668 [NCBI36]
Chr4:4q31.21-35.2		 pathogenic
GRCh38/hg38 4q32.1-35.2(chr4:160757699-190091407)x3 copy number gain See cases [RCV000140982] Chr4:160757699..190091407 [GRCh38]
Chr4:161678851..191012562 [GRCh37]
Chr4:161898301..191246543 [NCBI36]
Chr4:4q32.1-35.2		 pathogenic
GRCh38/hg38 4q32.2-35.2(chr4:162013220-189975519)x3 copy number gain See cases [RCV000050649] Chr4:162013220..189975519 [GRCh38]
Chr4:162934372..190828225 [GRCh37]
Chr4:163153822..191133668 [NCBI36]
Chr4:4q32.2-35.2		 pathogenic
GRCh38/hg38 4q28.1-35.1(chr4:125432943-185761887)x3 copy number gain See cases [RCV000138578] Chr4:125432943..185761887 [GRCh38]
Chr4:126354098..186683041 [GRCh37]
Chr4:126573548..186920035 [NCBI36]
Chr4:4q28.1-35.1		 pathogenic|likely benign
GRCh38/hg38 4q28.3-35.2(chr4:131985253-190095391)x3 copy number gain See cases [RCV000137721] Chr4:131985253..190095391 [GRCh38]
Chr4:132906408..190828225 [GRCh37]
Chr4:133125858..191250527 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic|likely benign
GRCh38/hg38 4q32.2-32.3(chr4:161590861-165734658)x3 copy number gain See cases [RCV000143095] Chr4:161590861..165734658 [GRCh38]
Chr4:162512013..166655810 [GRCh37]
Chr4:162731463..166875260 [NCBI36]
Chr4:4q32.2-32.3		 uncertain significance
GRCh38/hg38 4q28.3-35.2(chr4:134935616-190036318)x3 copy number gain See cases [RCV000143559] Chr4:134935616..190036318 [GRCh38]
Chr4:135856771..190957473 [GRCh37]
Chr4:136076221..191194467 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic
GRCh38/hg38 4q26-35.2(chr4:118065569-190042639)x3 copy number gain See cases [RCV000051785] Chr4:118065569..190042639 [GRCh38]
Chr4:118986724..190828225 [GRCh37]
Chr4:119206172..191200788 [NCBI36]
Chr4:4q26-35.2		 pathogenic
GRCh38/hg38 4q32.1-33(chr4:155162982-170959553)x1 copy number loss See cases [RCV000141861] Chr4:155162982..170959553 [GRCh38]
Chr4:156084134..171880704 [GRCh37]
Chr4:156303584..172117279 [NCBI36]
Chr4:4q32.1-33		 pathogenic
GRCh38/hg38 4q27-35.2(chr4:121518223-190062270)x3 copy number gain See cases [RCV000051786] Chr4:121518223..190062270 [GRCh38]
Chr4:122439378..190828225 [GRCh37]
Chr4:122658828..191220419 [NCBI36]
Chr4:4q27-35.2		 pathogenic
GRCh38/hg38 4q31.22-34.1(chr4:147317283-173675559)x3 copy number gain See cases [RCV000051788] Chr4:147317283..173675559 [GRCh38]
Chr4:148238435..174596710 [GRCh37]
Chr4:148457885..174833285 [NCBI36]
Chr4:4q31.22-34.1		 pathogenic
GRCh38/hg38 4q32.2-32.3(chr4:161592038-165721577)x3 copy number gain See cases [RCV000051791] Chr4:161592038..165721577 [GRCh38]
Chr4:162513190..166642729 [GRCh37]
Chr4:162732640..166862179 [NCBI36]
Chr4:4q32.2-32.3		 pathogenic
GRCh38/hg38 4q32.3-35.2(chr4:164039530-189982708)x1 copy number loss See cases [RCV000053347] Chr4:164039530..189982708 [GRCh38]
Chr4:164960682..190828225 [GRCh37]
Chr4:165180132..191140857 [NCBI36]
Chr4:4q32.3-35.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:280
Count of miRNA genes:256
Interacting mature miRNAs:268
Transcripts:ENST00000413616, ENST00000505354
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1 312
Low 38 145 36 29 253 28 91 11 16 46 85 93 2 19 22
Below cutoff 1336 1763 1214 426 1179 290 2796 1013 2171 242 703 1237 145 866 1617 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000505354   ⟹   ENSP00000489687
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4165,277,807 - 165,279,704 (-)Ensembl
RefSeq Acc Id: NM_001395953   ⟹   NP_001382882
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384165,277,807 - 165,279,704 (-)NCBI
T2T-CHM13v2.04168,623,800 - 168,625,697 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001382882 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAF84971 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000489687
  ENSP00000489687.1
Reference Protein Sequences
RefSeq Acc Id: ENSP00000489687   ⟸   ENST00000505354
RefSeq Acc Id: NP_001382882   ⟸   NM_001395953
- UniProtKB: Q14409 (UniProtKB/Swiss-Prot),   Q6NXP9 (UniProtKB/Swiss-Prot),   A8K8B7 (UniProtKB/TrEMBL)
Protein Domains
Carbohydrate kinase FGGY C-terminal   Carbohydrate kinase FGGY N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q14409-F1-model_v2 AlphaFold Q14409 1-553 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:4292 AgrOrtholog
COSMIC GK3 COSMIC
Ensembl Genes ENSG00000229894 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000505354 ENTREZGENE
  ENST00000505354.3 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.420.40 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000229894 GTEx
HGNC ID HGNC:4292 ENTREZGENE
Human Proteome Map GK3 Human Proteome Map
InterPro ATPase_NBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Carb_kinase_FGGY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Carb_kinase_FGGY_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Carb_kinase_FGGY_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Carb_kinase_FGGY_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GK1-3_metazoa UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glycerol_kin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 2713 ENTREZGENE
PANTHER GLYCEROL KINASE 3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SUGAR KINASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam FGGY_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FGGY_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA28703 PharmGKB
PIRSF GlpK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE FGGY_KINASES_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FGGY_KINASES_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Actin-like ATPase domain UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A8K8B7 ENTREZGENE, UniProtKB/TrEMBL
  GLPK3_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q6NXP9 ENTREZGENE
UniProt Secondary Q6NXP9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-09-26 GK3  glycerol kinase 3  GK3P  glycerol kinase 3 pseudogene  Symbol and/or name change 19259463 PROVISIONAL