GLYCTK (glycerate kinase)

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Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 132158
• Gene name: Glycerate kinase
• Gene symbol: GLYCTK
• Synonyms (NCBI Gene): HBEBP2, HBEBP4, HBeAgBP4A
• Chromosome: 3
• Chromosome location: 3p21.2
• Summary: 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 associa

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121909448	T>G	Likely-pathogenic	Non coding transcript variant, coding sequence variant, genic downstream transcript variant, downstream transcript variant, 3 prime UTR variant, intron variant, missense variant

miRNA Show/Hide all (149)

miRTarBase ID	miRNA	Experiments	Reference
MIRT036629	hsa-miR-940	CLASH	23622248
MIRT1022164	hsa-miR-125a-5p	CLIP-seq
MIRT1022165	hsa-miR-125b	CLIP-seq
MIRT1022166	hsa-miR-1291	CLIP-seq
MIRT1022167	hsa-miR-2110	CLIP-seq
MIRT1022168	hsa-miR-2467-3p	CLIP-seq
MIRT1022169	hsa-miR-3190	CLIP-seq
MIRT1022170	hsa-miR-3202	CLIP-seq
MIRT1022171	hsa-miR-3591-3p	CLIP-seq
MIRT1022172	hsa-miR-3680	CLIP-seq
MIRT1022173	hsa-miR-3909	CLIP-seq
MIRT1022174	hsa-miR-4271	CLIP-seq
MIRT1022175	hsa-miR-4292	CLIP-seq
MIRT1022176	hsa-miR-4308	CLIP-seq
MIRT1022177	hsa-miR-4319	CLIP-seq
MIRT1022178	hsa-miR-4481	CLIP-seq
MIRT1022179	hsa-miR-4533	CLIP-seq
MIRT1022180	hsa-miR-4725-3p	CLIP-seq
MIRT1022181	hsa-miR-4726-3p	CLIP-seq
MIRT1022182	hsa-miR-4742-3p	CLIP-seq
MIRT1022183	hsa-miR-4745-5p	CLIP-seq
MIRT1022184	hsa-miR-4747-5p	CLIP-seq
MIRT1022185	hsa-miR-4758-5p	CLIP-seq
MIRT1022186	hsa-miR-4798-3p	CLIP-seq
MIRT1022187	hsa-miR-491-5p	CLIP-seq
MIRT1022188	hsa-miR-542-3p	CLIP-seq
MIRT1022189	hsa-miR-593	CLIP-seq
MIRT1022190	hsa-miR-615-5p	CLIP-seq
MIRT1922747	hsa-miR-1260	CLIP-seq
MIRT1922748	hsa-miR-1260b	CLIP-seq
MIRT1922749	hsa-miR-188-3p	CLIP-seq
MIRT1922750	hsa-miR-3152-5p	CLIP-seq
MIRT1922751	hsa-miR-3156-3p	CLIP-seq
MIRT1922752	hsa-miR-3938	CLIP-seq
MIRT1922753	hsa-miR-4258	CLIP-seq
MIRT1922754	hsa-miR-4301	CLIP-seq
MIRT1922755	hsa-miR-4326	CLIP-seq
MIRT1922756	hsa-miR-4713-5p	CLIP-seq
MIRT1922757	hsa-miR-942	CLIP-seq
MIRT2002853	hsa-miR-1254	CLIP-seq
MIRT2002854	hsa-miR-1825	CLIP-seq
MIRT1022167	hsa-miR-2110	CLIP-seq
MIRT2002855	hsa-miR-3116	CLIP-seq
MIRT2002856	hsa-miR-3117-5p	CLIP-seq
MIRT2002857	hsa-miR-3130-5p	CLIP-seq
MIRT1922750	hsa-miR-3152-5p	CLIP-seq
MIRT2002858	hsa-miR-3173-3p	CLIP-seq
MIRT1022170	hsa-miR-3202	CLIP-seq
MIRT2002859	hsa-miR-3660	CLIP-seq
MIRT2002860	hsa-miR-371b-5p	CLIP-seq
MIRT2002861	hsa-miR-4256	CLIP-seq
MIRT1022174	hsa-miR-4271	CLIP-seq
MIRT2002862	hsa-miR-4283	CLIP-seq
MIRT2002863	hsa-miR-4437	CLIP-seq
MIRT2002864	hsa-miR-4482	CLIP-seq
MIRT2002865	hsa-miR-4526	CLIP-seq
MIRT1022180	hsa-miR-4725-3p	CLIP-seq
MIRT1022181	hsa-miR-4726-3p	CLIP-seq
MIRT1022184	hsa-miR-4747-5p	CLIP-seq
MIRT2002866	hsa-miR-4774-3p	CLIP-seq
MIRT1022187	hsa-miR-491-5p	CLIP-seq
MIRT2002867	hsa-miR-661	CLIP-seq
MIRT2002868	hsa-miR-890	CLIP-seq
MIRT2235885	hsa-miR-1202	CLIP-seq
MIRT2235886	hsa-miR-1262	CLIP-seq
MIRT2235887	hsa-miR-1286	CLIP-seq
MIRT2235888	hsa-miR-1289	CLIP-seq
MIRT2235889	hsa-miR-1293	CLIP-seq
MIRT2235890	hsa-miR-1302	CLIP-seq
MIRT2235891	hsa-miR-150	CLIP-seq
MIRT2235892	hsa-miR-1827	CLIP-seq
MIRT2235893	hsa-miR-1976	CLIP-seq
MIRT2235894	hsa-miR-214	CLIP-seq
MIRT2235895	hsa-miR-221	CLIP-seq
MIRT2235896	hsa-miR-222	CLIP-seq
MIRT2235897	hsa-miR-2276	CLIP-seq
MIRT2235898	hsa-miR-29a	CLIP-seq
MIRT2235899	hsa-miR-29b	CLIP-seq
MIRT2235900	hsa-miR-29c	CLIP-seq
MIRT2002856	hsa-miR-3117-5p	CLIP-seq
MIRT2235901	hsa-miR-3135	CLIP-seq
MIRT2235902	hsa-miR-3157-5p	CLIP-seq
MIRT2235903	hsa-miR-3165	CLIP-seq
MIRT2002858	hsa-miR-3173-3p	CLIP-seq
MIRT2235904	hsa-miR-3194-5p	CLIP-seq
MIRT2235905	hsa-miR-3198	CLIP-seq
MIRT2235906	hsa-miR-3612	CLIP-seq
MIRT2235907	hsa-miR-3619-5p	CLIP-seq
MIRT2235908	hsa-miR-3663-3p	CLIP-seq
MIRT2235909	hsa-miR-3668	CLIP-seq
MIRT2002860	hsa-miR-371b-5p	CLIP-seq
MIRT2235910	hsa-miR-3972	CLIP-seq
MIRT2002862	hsa-miR-4283	CLIP-seq
MIRT2235911	hsa-miR-4291	CLIP-seq
MIRT2235912	hsa-miR-4294	CLIP-seq
MIRT2235913	hsa-miR-4298	CLIP-seq
MIRT2235914	hsa-miR-4309	CLIP-seq
MIRT2235915	hsa-miR-4434	CLIP-seq
MIRT2235916	hsa-miR-4436a	CLIP-seq
MIRT2002863	hsa-miR-4437	CLIP-seq
MIRT2235917	hsa-miR-4483	CLIP-seq
MIRT2235918	hsa-miR-4516	CLIP-seq
MIRT2235919	hsa-miR-4648	CLIP-seq
MIRT2235920	hsa-miR-4649-3p	CLIP-seq
MIRT2235921	hsa-miR-4651	CLIP-seq
MIRT2235922	hsa-miR-4666-5p	CLIP-seq
MIRT2235923	hsa-miR-4695-5p	CLIP-seq
MIRT2235924	hsa-miR-4696	CLIP-seq
MIRT2235925	hsa-miR-4701-3p	CLIP-seq
MIRT1022184	hsa-miR-4747-5p	CLIP-seq
MIRT2235926	hsa-miR-4755-3p	CLIP-seq
MIRT2235927	hsa-miR-608	CLIP-seq
MIRT2235928	hsa-miR-637	CLIP-seq
MIRT2235929	hsa-miR-650	CLIP-seq
MIRT2235930	hsa-miR-761	CLIP-seq
MIRT2235931	hsa-miR-873	CLIP-seq
MIRT2235932	hsa-miR-922	CLIP-seq
MIRT2002853	hsa-miR-1254	CLIP-seq
MIRT2235886	hsa-miR-1262	CLIP-seq
MIRT2235888	hsa-miR-1289	CLIP-seq
MIRT2235889	hsa-miR-1293	CLIP-seq
MIRT2002854	hsa-miR-1825	CLIP-seq
MIRT2002855	hsa-miR-3116	CLIP-seq
MIRT2002857	hsa-miR-3130-5p	CLIP-seq
MIRT1922750	hsa-miR-3152-5p	CLIP-seq
MIRT2235903	hsa-miR-3165	CLIP-seq
MIRT2235905	hsa-miR-3198	CLIP-seq
MIRT2235912	hsa-miR-4294	CLIP-seq
MIRT2235914	hsa-miR-4309	CLIP-seq
MIRT2002864	hsa-miR-4482	CLIP-seq
MIRT2235917	hsa-miR-4483	CLIP-seq
MIRT2235925	hsa-miR-4701-3p	CLIP-seq
MIRT2002866	hsa-miR-4774-3p	CLIP-seq
MIRT2002867	hsa-miR-661	CLIP-seq
MIRT2002868	hsa-miR-890	CLIP-seq
MIRT2235885	hsa-miR-1202	CLIP-seq
MIRT2235894	hsa-miR-214	CLIP-seq
MIRT2235904	hsa-miR-3194-5p	CLIP-seq
MIRT2235907	hsa-miR-3619-5p	CLIP-seq
MIRT2235910	hsa-miR-3972	CLIP-seq
MIRT2235930	hsa-miR-761	CLIP-seq
MIRT2235931	hsa-miR-873	CLIP-seq
MIRT2235885	hsa-miR-1202	CLIP-seq
MIRT2235894	hsa-miR-214	CLIP-seq
MIRT2235904	hsa-miR-3194-5p	CLIP-seq
MIRT2235907	hsa-miR-3619-5p	CLIP-seq
MIRT2235910	hsa-miR-3972	CLIP-seq
MIRT2235930	hsa-miR-761	CLIP-seq
MIRT2235931	hsa-miR-873	CLIP-seq

Gene ontology (GO) Show/Hide all (19)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0005515	Function	Protein binding	IPI	16189514, 19060904, 25416956, 32296183
GO:0005524	Function	ATP binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	16753811
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IEA
GO:0005794	Component	Golgi apparatus	IDA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0006468	Process	Protein phosphorylation	IDA	16753811
GO:0008887	Function	Glycerate kinase activity	EXP	2537226
GO:0008887	Function	Glycerate kinase activity	IBA
GO:0008887	Function	Glycerate kinase activity	IDA	16753811, 31837836
GO:0008887	Function	Glycerate kinase activity	IEA
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0061624	Process	Fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate	TAS

Other IDs

• MIM: 610516
• HGNC: 24247
• e!Ensembl: ENSG00000168237

Protein

• UniProt ID: Q8IVS8
• Protein name: Glycerate kinase (EC 2.7.1.31) (HBeAg-binding protein 4)
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05161	MOFRL	402 → 514	MOFRL family	Family
  PF13660	DUF4147	37 → 289	Domain of unknown function (DUF4147)	Domain

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:16753811}.
• Sequence:

  MAAALQVLPRLARAPLHPLLWRGSVARLASSMALAEQARQLFESAVGAVLPGPMLHRALS
  LDPGGRQLKVRDRNFQLRQNLYLVGFGKAVLGMAAAAEELLGQHLVQGVISVPKGIRAAM
  ERAGKQEMLLKPHSRVQVFEGAEDNLPDRDALRAALAIQQLAEGLTADDLLLVLISGGGS
  ALLPAPIPPVTLEEKQTLTRLLAARGATIQELNTIRKALSQLKGGGLAQAAYPAQVVSLI
  LSDVVGDPVEVIASGPTVASSHNVQDCLHILNRYGLRAALPRSVKTVLSRADSDPHGPHT
  CGHVLNVIIGSNVLALAEAQRQAEALGYQAVVLSAAMQGDVKSMAQFYGLLAHVARTRLT
  PSMAGASVEEDAQLHELAAELQIPDLQLEEALETMAWGRGPVCLLAGGEPTVQLQGSGRG
  GRNQELALRVGAELRRWPLGPIDVLFLSGGTDGQDGPTEAAGAWVTPELASQAAAEGLDI
  ATFLAHNDSHTFFCCLQGGAHLLHTGMTGTNVMDTHLLFLRPR

• Sequence length: 523

Pathways

KEGG Pathway	Reactome Pathway
Pentose phosphate pathway	Fructose catabolism
Glycine, serine and threonine metabolism
Glycerolipid metabolism
Glyoxylate and dicarboxylate metabolism
Metabolic pathways
Carbon metabolism

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
D-Glyceric aciduria	Pathogenic	rs121909447, rs121909449	RCV000077847 RCV000077848	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
GLYCTK-related disorder	Likely benign; Uncertain significance; Conflicting classifications of pathogenicity; Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Uncertain significance	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (16)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Bipolar Disorder	Bipolar disorder	Pubtator	29947131	Associate	★☆☆☆☆ Found in Text Mining only
Cerebral cortical atrophy	Cerebral cortical atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
D-glycericacidemia	Deficiency of glycerate kinase	BEFREE	20949620		★☆☆☆☆ Found in Text Mining only
D-glycericacidemia	Deficiency of glycerate kinase	ORPHANET_DG	20949620		★☆☆☆☆ Found in Text Mining only
D-glycericacidemia	Deficiency of glycerate kinase	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
D-glycericacidemia	Deficiency of glycerate kinase	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neonatal Hypotonia	Hypotonia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nonketotic Hyperglycinemia	Nonketotic Hyperglycinemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Primary hyperoxaluria type 2	Hyperoxaluria	BEFREE	28462797		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	29947131		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	Pubtator	29947131	Associate	★☆☆☆☆ Found in Text Mining only
Spastic Quadriplegia	Spastic Quadriplegia	HPO_DG			★☆☆☆☆ Found in Text Mining only

Related Genes

Sort by: Blended Diseases Pathways Evidence source

PGLS 2 shared pathwaysPentose phosphate pathway, Carbon metabolism Related via 2 shared pathways including Pentose phosphate pathway, Carbon metabolism. IDNK 2 shared pathwaysPentose phosphate pathway, Carbon metabolism Related via 2 shared pathways including Pentose phosphate pathway, Carbon metabolism. H6PD 2 shared pathwaysPentose phosphate pathway, Carbon metabolism Related via 2 shared pathways including Pentose phosphate pathway, Carbon metabolism. GLDC 3 shared pathwaysGlycine, serine and threonine metabolism, Glyoxylate and dicarboxylate metabolism, Carbon metabolism Related via 3 shared pathways including Glycine, serine and threonine metabolism, Glyoxylate and dicarboxylate metabolism. AMT 3 shared pathwaysGlycine, serine and threonine metabolism, Glyoxylate and dicarboxylate metabolism, Carbon metabolism Related via 3 shared pathways including Glycine, serine and threonine metabolism, Glyoxylate and dicarboxylate metabolism.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
PGLS	0	[]	2	["Pentose phosphate pathway","Carbon metabolism"]	0	[]
IDNK	0	[]	2	["Pentose phosphate pathway","Carbon metabolism"]	0	[]
H6PD	0	[]	2	["Pentose phosphate pathway","Carbon metabolism"]	0	[]
GLDC	0	[]	3	["Glycine, serine and threonine metabolism","Glyoxylate and dicarboxylate metabolism","Carbon metabolism"]	0	[]
AMT	0	[]	3	["Glycine, serine and threonine metabolism","Glyoxylate and dicarboxylate metabolism","Carbon metabolism"]	0	[]

Diseases Linked via Similar Genes

Asthma Linked via 2 of 5 related genesH6PD, GLDC Glycine encephalopathy Linked via 2 of 5 related genesGLDC, AMT Hyperglycemia Linked via 2 of 5 related genesGLDC, AMT Osteoporosis Linked via 1 of 5 related genesPGLS Eczema Linked via 1 of 5 related genesH6PD

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Asthma	2	["H6PD","GLDC"]
Glycine encephalopathy	2	["GLDC","AMT"]
Hyperglycemia	2	["GLDC","AMT"]
Osteoporosis	1	["PGLS"]
Eczema	1	["H6PD"]