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Aliases for GLYCTK Gene

Aliases for GLYCTK Gene

  • Glycerate Kinase 2 3 5
  • EC 2.7.1.31 4 58
  • HBEBP4 3 4
  • HBeAg Binding Protein 4 3
  • HBeAg-Binding Protein 2 3
  • HBeAg-Binding Protein 4 4
  • HBeAgBP4A 3
  • HBEBP2 3

External Ids for GLYCTK Gene

Previous GeneCards Identifiers for GLYCTK Gene

  • GC03P052177
  • GC03P052280
  • GC03P052296

Summaries for GLYCTK Gene

Entrez Gene Summary for GLYCTK Gene

  • This locus encodes a member of the glycerate kinase type-2 family. The encoded enzyme catalyzes the phosphorylation of (R)-glycerate and may be involved in serine degradation and fructose metabolism. Decreased activity of the encoded enzyme may be associated with the disease D-glyceric aciduria. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2009]

GeneCards Summary for GLYCTK Gene

GLYCTK (Glycerate Kinase) is a Protein Coding gene. Diseases associated with GLYCTK include D-Glyceric Aciduria and Glycine Encephalopathy. Among its related pathways are Metabolism and Fructose metabolism. GO annotations related to this gene include glycerate kinase activity.

Additional gene information for GLYCTK Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GLYCTK Gene

Genomics for GLYCTK Gene

Regulatory Elements for GLYCTK Gene

Enhancers for GLYCTK Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03H052236 1.7 FANTOM5 ENCODE dbSUPER 30.1 -48.3 -48301 5 HDGF PKNOX1 FOXA2 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 GLYCTK RAD54L2 PBRM1 RRP9 LOC101929054 WDR82 RFT1 MIR135A1 GLYCTK-AS1 ABHD14B
GH03H052251 1.7 FANTOM5 Ensembl ENCODE dbSUPER 24.8 -33.7 -33685 3 HDGF PKNOX1 SIN3A ZNF121 ATF7 ETV6 RUNX3 CREM IKZF2 EGR2 GLYCTK PBRM1 PPM1M LOC101929054 NT5DC2 WDR82 NISCH PIR61179 GC03M052258 GC03M052257
GH03H052215 1.4 Ensembl ENCODE dbSUPER 22.6 -68.8 -68761 5 TBP HDGF PKNOX1 RB1 ARID4B ZNF2 RAD21 RARA YY1 SCRT2 GLYCTK PPM1M WDR82 MIR135A1 GLYCTK-AS1 DUSP7 TWF2 PARP3 SERBP1P3 ENSG00000280003
GH03H052274 1.7 Ensembl ENCODE dbSUPER 18.5 -4.2 -4235 17 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 YY1 SLC30A9 PBRM1 LOC101929054 PPM1M TWF2 ITIH4 GLYCTK RRP9 RFT1 RAD54L2 DCAF1
GH03H052298 1.5 FANTOM5 Ensembl ENCODE 18.5 +12.6 12564 2 ATF1 ARID4B TCF12 ZNF766 GLIS2 GATA2 ELK1 FOS ATF7 MCM3 PBRM1 GLYCTK PPM1M RFT1 RRP9 TWF2 GLYCTK-AS1 DNAH1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around GLYCTK on UCSC Golden Path with GeneCards custom track

Promoters for GLYCTK Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000152528 811 1401 HDGF PKNOX1 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 FOS SP3

Genomic Location for GLYCTK Gene

Chromosome:
3
Start:
52,287,089 bp from pter
End:
52,295,256 bp from pter
Size:
8,168 bases
Orientation:
Plus strand

Genomic View for GLYCTK Gene

Genes around GLYCTK on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GLYCTK Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GLYCTK Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GLYCTK Gene

Proteins for GLYCTK Gene

  • Protein details for GLYCTK Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IVS8-GLCTK_HUMAN
    Recommended name:
    Glycerate kinase
    Protein Accession:
    Q8IVS8
    Secondary Accessions:
    • Q0P630
    • Q2EZ43
    • Q6Y2K6
    • Q7Z6G5
    • Q86YR8
    • Q8TED2
    • Q8WTY2

    Protein attributes for GLYCTK Gene

    Size:
    523 amino acids
    Molecular mass:
    55253 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH36862.1; Type=Frameshift; Positions=177; Evidence={ECO:0000305};

    Alternative splice isoforms for GLYCTK Gene

neXtProt entry for GLYCTK Gene

Selected DME Specific Peptides for GLYCTK Gene

Q8IVS8:
  • VGFGKAVLGMA
  • QVFEGAEDNLPDRDALRAA
  • LKGGGLAQ
  • EVIASGPTVAS
  • ALPRSVKTVL
  • DLLLVLISGGGSALLPAP
  • CLLAGGEPTV

Post-translational modifications for GLYCTK Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for GLYCTK Gene

Gene Families for GLYCTK Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for GLYCTK Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for GLYCTK Gene

Graphical View of Domain Structure for InterPro Entry

Q8IVS8

UniProtKB/Swiss-Prot:

GLCTK_HUMAN :
  • Belongs to the glycerate kinase type-2 family.
Family:
  • Belongs to the glycerate kinase type-2 family.
genes like me logo Genes that share domains with GLYCTK: view

Function for GLYCTK Gene

Molecular function for GLYCTK Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.1 mM for D-glycerate {ECO:0000269 PubMed:20949620};
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + D-glycerate = ADP + 3-phospho-D-glycerate.

Enzyme Numbers (IUBMB) for GLYCTK Gene

Phenotypes From GWAS Catalog for GLYCTK Gene

Gene Ontology (GO) - Molecular Function for GLYCTK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0005524 ATP binding IEA --
GO:0008887 glycerate kinase activity TAS --
GO:0016301 kinase activity IEA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with GLYCTK: view
genes like me logo Genes that share phenotypes with GLYCTK: view

Human Phenotype Ontology for GLYCTK Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for GLYCTK Gene

miRTarBase miRNAs that target GLYCTK

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for GLYCTK
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for GLYCTK Gene

Localization for GLYCTK Gene

Subcellular locations from UniProtKB/Swiss-Prot for GLYCTK Gene

Isoform 1: Cytoplasm.
Isoform 2: Cytoplasm. Mitochondrion.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GLYCTK gene
Compartment Confidence
mitochondrion 5
cytosol 4
golgi apparatus 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Golgi apparatus (2)
  • Rods & Rings (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GLYCTK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 16753811
GO:0005739 mitochondrion IEA --
GO:0005794 Golgi apparatus IDA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with GLYCTK: view

Pathways & Interactions for GLYCTK Gene

genes like me logo Genes that share pathways with GLYCTK: view

Gene Ontology (GO) - Biological Process for GLYCTK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006468 protein phosphorylation IDA 16753811
GO:0016310 phosphorylation IEA --
GO:0061624 fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate TAS --
genes like me logo Genes that share ontologies with GLYCTK: view

No data available for SIGNOR curated interactions for GLYCTK Gene

Drugs & Compounds for GLYCTK Gene

(2) Drugs for GLYCTK Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
3-Phosphoglyceric acid Experimental Pharma 0
ATP Nutra Agonist 0

(2) Additional Compounds for GLYCTK Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
Glyceric acid
  • (R)-glycerate
  • a,b-Hydroxypropionate
  • a,b-Hydroxypropionic acid
  • D-Glycerate
  • D-Glyceric acid
473-81-4
genes like me logo Genes that share compounds with GLYCTK: view

Transcripts for GLYCTK Gene

Unigene Clusters for GLYCTK Gene

Glycerate kinase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for GLYCTK
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for GLYCTK Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b · 6c · 6d ^ 7 ^ 8
SP1: - -
SP2: - - - - - - -
SP3: - -
SP4: - - - - - - - -
SP5: - - - - - - - -
SP6: - - - -
SP7: - -
SP8: - - - -
SP9: - - -
SP10: - -
SP11:

Relevant External Links for GLYCTK Gene

GeneLoc Exon Structure for
GLYCTK
ECgene alternative splicing isoforms for
GLYCTK

Expression for GLYCTK Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GLYCTK Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GLYCTK Gene

This gene is overexpressed in Liver (x22.8).

Protein differential expression in normal tissues from HIPED for GLYCTK Gene

This gene is overexpressed in Gallbladder (46.4) and Liver (20.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for GLYCTK Gene



Protein tissue co-expression partners for GLYCTK Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of GLYCTK Gene:

GLYCTK

SOURCE GeneReport for Unigene cluster for GLYCTK Gene:

Hs.415312

mRNA Expression by UniProt/SwissProt for GLYCTK Gene:

Q8IVS8-GLCTK_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for GLYCTK Gene

  • Liver(4.6)
  • Lung(4.2)
  • Skin(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for GLYCTK Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cerebrospinal fluid
  • head
  • meninges
  • skull
Thorax:
  • chest wall
Abdomen:
  • abdominal wall
  • kidney
  • liver
Pelvis:
  • placenta
  • uterus
Limb:
  • lower limb
  • upper limb
General:
  • blood
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with GLYCTK: view

Primer Products

Orthologs for GLYCTK Gene

This gene was present in the common ancestor of animals.

Orthologs for GLYCTK Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ptr-mir-135a-1 34
  • 100 (a)
OneToOne
GLYCTK 33
  • 99.68 (n)
dog
(Canis familiaris)
Mammalia GLYCTK 33
  • 86.36 (n)
cfa-mir-135a-1 34
  • 82 (a)
OneToMany
-- 34
  • 80 (a)
OneToMany
cow
(Bos Taurus)
Mammalia GLYCTK 34 33
  • 85.66 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Glyctk 33 16 34
  • 82.66 (n)
rat
(Rattus norvegicus)
Mammalia Glyctk 33
  • 82.6 (n)
oppossum
(Monodelphis domestica)
Mammalia GLYCTK 34
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GLYCTK 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves GLYCTK 34 33
  • 64.9 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GLYCTK 34
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia glyctk 33
  • 58.96 (n)
zebrafish
(Danio rerio)
Actinopterygii glyctk 34 33
  • 57.43 (n)
OneToOne
Dr.13856 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007988 33
  • 54.19 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG9886 33 34
  • 47.32 (n)
worm
(Caenorhabditis elegans)
Secernentea C13B9.2 33 34
  • 45.7 (n)
Species where no ortholog for GLYCTK was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GLYCTK Gene

ENSEMBL:
Gene Tree for GLYCTK (if available)
TreeFam:
Gene Tree for GLYCTK (if available)

Paralogs for GLYCTK Gene

No data available for Paralogs for GLYCTK Gene

Variants for GLYCTK Gene

Sequence variations from dbSNP and Humsavar for GLYCTK Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs121909448 Pathogenic, D-glyceric aciduria (D-GA) [MIM:220120] 52,293,032(+) CTTCT(G/T)CTGCT intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense
rs767047161 Uncertain significance 52,293,014(+) CCACA(A/G)TGACT intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense
rs121909447 untested 52,293,002(+) CACCT(-/T)CCTAG intron-variant, nc-transcript-variant, reference, utr-variant-3-prime, frameshift-variant
rs121909449 untested 52,293,112(+) TGTTC(-/C)TGCGG nc-transcript-variant, downstream-variant-500B, reference, frameshift-variant
rs1000301029 -- 52,295,347(+) CCTGG(C/T)CCAGC downstream-variant-500B, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for GLYCTK Gene

Variant ID Type Subtype PubMed ID
esv3402579 CNV duplication 20981092
nsv470572 CNV loss 18288195
nsv519445 CNV gain+loss 19592680
nsv834694 CNV gain 17160897
nsv834695 CNV loss 17160897
nsv834696 CNV loss 17160897
nsv954859 CNV deletion 24416366

Variation tolerance for GLYCTK Gene

Residual Variation Intolerance Score: 56.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.75; 57.78% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GLYCTK Gene

Human Gene Mutation Database (HGMD)
GLYCTK
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GLYCTK

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GLYCTK Gene

Disorders for GLYCTK Gene

MalaCards: The human disease database

(3) MalaCards diseases for GLYCTK Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
d-glyceric aciduria
  • d-glycerate kinase deficiency
glycine encephalopathy
  • non-ketotic hyperglycinemia
kabuki syndrome 1
  • kabuki syndrome
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

GLCTK_HUMAN
  • D-glyceric aciduria (D-GA) [MIM:220120]: A rare metabolic disease characterized by chronic metabolic acidosis and a highly variable clinical phenotype. Clinical features range from an encephalopathic presentation with seizures, microcephaly, severe mental retardation and early death, to milder manifestations with only speech delay or even normal development. {ECO:0000269 PubMed:20949620}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for GLYCTK

Genetic Association Database (GAD)
GLYCTK
Human Genome Epidemiology (HuGE) Navigator
GLYCTK
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
GLYCTK
genes like me logo Genes that share disorders with GLYCTK: view

No data available for Genatlas for GLYCTK Gene

Publications for GLYCTK Gene

  1. Isolation and characterization of the human D-glyceric acidemia related glycerate kinase gene GLYCTK1 and its alternatively splicing variant GLYCTK2. (PMID: 16753811) Guo JH … Yu L (DNA sequence : the journal of DNA sequencing and mapping 2006) 2 3 4 22 60
  2. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F … Nebel A (Mutation research 2010) 3 45 60
  3. D-glyceric aciduria is caused by genetic deficiency of D-glycerate kinase (GLYCTK). (PMID: 20949620) Sass JO … Walter M (Human mutation 2010) 3 4 60
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 60
  5. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (PMID: 24275569) Bian Y … Zou H (Journal of proteomics 2014) 4 60

Products for GLYCTK Gene

Sources for GLYCTK Gene

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