GLYCTK (glycerate kinase) - Rat Genome Database

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Gene: GLYCTK (glycerate kinase) Homo sapiens
Analyze
Symbol: GLYCTK
Name: glycerate kinase
RGD ID: 1604750
HGNC Page HGNC:24247
Description: Enables glycerate kinase activity. Involved in protein phosphorylation. Located in Golgi apparatus and cytosol. Implicated in D-glyceric aciduria.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: CG9886-like; HBeAg binding protein 4; HBeAg-binding protein 2; HBeAg-binding protein 4; HBeAgBP4A; HBEBP2; HBEBP4
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38352,287,828 - 52,295,257 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl352,287,089 - 52,295,257 (+)EnsemblGRCh38hg38GRCh38
GRCh37352,321,844 - 52,329,273 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36352,296,912 - 52,302,532 (+)NCBINCBI36Build 36hg18NCBI36
Celera352,301,159 - 52,308,595 (+)NCBICelera
Cytogenetic Map3p21.2NCBI
HuRef352,384,478 - 52,391,914 (+)NCBIHuRef
CHM1_1352,274,371 - 52,281,807 (+)NCBICHM1_1
T2T-CHM13v2.0352,320,727 - 52,349,445 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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Object Symbol
Species
Term
Qualifier
Evidence
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Reference
Notes
Source
Original Reference(s)
GLYCTKHumancongenital disorder of glycosylation In  IAGP (Homo sapiens)8554872ClinVar Annotator: match by term: Congenital disorder of glycosylation type 1NClinVarPMID:28492532
GLYCTKHumanD-glyceric aciduria  IAGP (Homo sapiens)8554872ClinVar Annotator: match by term: D-Glyceric aciduriaClinVarPMID:20949620 more ...
GLYCTKHumanD-glyceric aciduria  IAGP (Homo sapiens) more ...8554872ClinVar more ...ClinVarPMID:28492532
GLYCTKHumanD-glyceric aciduria  IAGP (Homo sapiens) more ...8554872ClinVar more ...ClinVarPMID:25741868 and PMID:28492532
GLYCTKHumanD-glyceric aciduria  IAGP (Homo sapiens)8554872ClinVar Annotator: match by term: D-Glyceric aciduriaClinVarPMID:20949620 and PMID:4434100
GLYCTKHumanD-glyceric aciduria  IAGP (Homo sapiens)8554872ClinVar Annotator: match by term: D-Glyceric aciduriaClinVarPMID:20949620
GLYCTKHumanD-glyceric aciduria  IAGP (Homo sapiens)8554872ClinVar Annotator: match by term: D-Glyceric aciduriaClinVarPMID:25741868 more ...
GLYCTKHumanD-glyceric aciduria  IAGP (Homo sapiens) more ...8554872ClinVar Annotator: match by term: D-Glyceric aciduriaClinVarPMID:25741868
GLYCTKHumanNon Ketotic Hyperglycinemia Syndrome  IAGP (Homo sapiens)8554872ClinVar Annotator: match by term: Non ketotic hyperglycinemia syndromeClinVarPMID:25741868 and PMID:28492532
1 to 9 of 9 rows
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
GLYCTKHumanD-glyceric aciduria  EXP 11554173CTD Direct Evidence: marker/mechanismCTD 
Object Symbol
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Evidence
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Reference
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Original Reference(s)
GLYCTKHumanD-glyceric aciduria  IAGP 7240710 OMIM 

1 to 20 of 71 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
GLYCTKHuman(+)-schisandrin B multiple interactionsISOGlyctk (Rattus norvegicus)6480464schizandrin B inhibits the reaction [Carbon Tetrachloride results in decreased expression of GLYCTK mRNA]CTDPMID:31150632
GLYCTKHuman(1->4)-beta-D-glucan multiple interactionsISOGlyctk (Mus musculus)6480464[perfluorooctane sulfonic acid co-treated with Cellulose] results in decreased expression of GLYCTK mRNACTDPMID:36331819
GLYCTKHuman1,1-dichloroethene decreases expressionISOGlyctk (Mus musculus)6480464vinylidene chloride results in decreased expression of GLYCTK mRNACTDPMID:26682919
GLYCTKHuman1,2-dimethylhydrazine decreases expressionISOGlyctk (Mus musculus)64804641 and 2-Dimethylhydrazine results in decreased expression of GLYCTK mRNACTDPMID:22206623
GLYCTKHuman17beta-estradiol decreases expressionISOGlyctk (Mus musculus)6480464Estradiol results in decreased expression of GLYCTK mRNACTDPMID:39298647
GLYCTKHuman2,3,7,8-tetrachlorodibenzodioxine increases expressionEXP 6480464Tetrachlorodibenzodioxin results in increased expression of GLYCTK mRNACTDPMID:20106945 and PMID:21632981
GLYCTKHuman2,3,7,8-tetrachlorodibenzodioxine increases expressionISOGlyctk (Rattus norvegicus)6480464Tetrachlorodibenzodioxin results in increased expression of GLYCTK mRNACTDPMID:33387578
GLYCTKHuman2,3,7,8-tetrachlorodibenzodioxine affects expressionISOGlyctk (Mus musculus)6480464Tetrachlorodibenzodioxin affects the expression of GLYCTK mRNACTDPMID:21570461 and PMID:26377647
GLYCTKHuman4,4'-diaminodiphenylmethane decreases expressionISOGlyctk (Rattus norvegicus)64804644 and 4'-diaminodiphenylmethane results in decreased expression of GLYCTK mRNACTDPMID:30723492
GLYCTKHuman4,4'-sulfonyldiphenol decreases expressionISOGlyctk (Mus musculus)6480464bisphenol S results in decreased expression of GLYCTK mRNACTDPMID:30951980
GLYCTKHuman4,4'-sulfonyldiphenol affects methylationISOGlyctk (Mus musculus)6480464bisphenol S affects the methylation of GLYCTK geneCTDPMID:31683443
GLYCTKHuman4,4'-sulfonyldiphenol affects expressionISOGlyctk (Mus musculus)6480464bisphenol S affects the expression of GLYCTK mRNACTDPMID:39298647
GLYCTKHuman4-hydroxyphenyl retinamide increases expressionISOGlyctk (Mus musculus)6480464Fenretinide results in increased expression of GLYCTK mRNACTDPMID:28973697
GLYCTKHumanacetamide decreases expressionISOGlyctk (Rattus norvegicus)6480464acetamide results in decreased expression of GLYCTK mRNACTDPMID:31881176
GLYCTKHumanaflatoxin B1 affects expressionEXP 6480464Aflatoxin B1 affects the expression of GLYCTK proteinCTDPMID:20106945
GLYCTKHumanaflatoxin B1 decreases methylationEXP 6480464Aflatoxin B1 results in decreased methylation of GLYCTK intronCTDPMID:30157460
GLYCTKHumanaflatoxin B1 decreases expressionEXP 6480464Aflatoxin B1 results in decreased expression of GLYCTK mRNACTDPMID:22100608 and PMID:27153756
GLYCTKHumanbenzo[a]pyrene affects methylationEXP 6480464Benzo(a)pyrene affects the methylation of GLYCTK intronCTDPMID:30157460
GLYCTKHumanbenzo[a]pyrene decreases expressionEXP 6480464Benzo(a)pyrene results in decreased expression of GLYCTK mRNACTDPMID:32234424
GLYCTKHumanbeta-lapachone decreases expressionEXP 6480464beta-lapachone results in decreased expression of GLYCTK mRNACTDPMID:38218311

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Biological Process

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
GLYCTKHumanfructose catabolic process involved_inISOGlyctk (Mus musculus)9068941 PMID:29414685MGIPMID:29414685
GLYCTKHumanfructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate involved_inTAS 150520179 ReactomeReactome:R-HSA-70350
GLYCTKHumanprotein phosphorylation involved_inIDA 150520179 PMID:16753811UniProtPMID:16753811

Cellular Component
1 to 11 of 11 rows

  
Object Symbol
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Original Reference(s)
GLYCTKHumancytoplasm located_inIDA 150520179 PMID:16753811UniProtPMID:16753811
GLYCTKHumancytoplasm is_active_inIBAPANTHER:PTN000259988 more ...150520179 GO_CentralGO_REF:0000033
GLYCTKHumancytoplasm located_inIEAUniProtKB-SubCell:SL-0086150520179 UniProtGO_REF:0000044
GLYCTKHumancytoplasm located_inIEAUniProtKB-KW:KW-0963150520179 UniProtGO_REF:0000043
GLYCTKHumancytosol located_inIDA 150520179 HPAGO_REF:0000052
GLYCTKHumancytosol located_inTAS 150520179 ReactomeReactome:R-HSA-6799495
GLYCTKHumancytosol is_active_inISOGlyctk (Rattus norvegicus)9068941PMID:6252205MGIPMID:6252205 and REF_RGD_ID:152025517
GLYCTKHumanGolgi apparatus located_inIDA 150520179 HPAGO_REF:0000052
GLYCTKHumanmitochondrion located_inHTP 150520179 PMID:34800366FlyBasePMID:34800366
GLYCTKHumanmitochondrion located_inIEAUniProtKB-SubCell:SL-0173150520179 UniProtGO_REF:0000044
GLYCTKHumanmitochondrion located_inIEAUniProtKB-KW:KW-0496150520179 UniProtGO_REF:0000043
1 to 11 of 11 rows

Molecular Function
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Imported Annotations - SMPDB

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Imported Annotations - KEGG (archival)

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
GLYCTKHumanglycine, serine and threonine metabolic pathway  IEA 6907045 KEGGhsa:00260
GLYCTKHumanglyoxylate and dicarboxylate metabolic pathway  IEA 6907045 KEGGhsa:00630
1 to 20 of 69 rows
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
GLYCTKHumanAbnormal circulating enzyme concentration or activity  IAGP 8699517 HPOORPHA:941
GLYCTKHumanAminoaciduria  IAGP 8699517 HPOMIM:220120
GLYCTKHumanAppendicular spasticity  IAGP 8699517 HPOMIM:220120
GLYCTKHumanAutistic behavior  IAGP 8699517 HPOORPHA:941
GLYCTKHumanAutosomal recessive inheritance  IAGP 8699517 HPOMIM:220120
GLYCTKHumanAxial hypotonia  IAGP 8699517 HPOMIM:220120
GLYCTKHumanBilateral tonic-clonic seizure  IAGP 8699517 HPOMIM:220120
GLYCTKHumanBradycardia  IAGP 8699517 HPOMIM:220120
GLYCTKHumanBrain atrophy  IAGP 8699517 HPOORPHA:941
GLYCTKHumanBrisk reflexes  IAGP 8699517 HPOMIM:220120
GLYCTKHumanCerebral cortical atrophy  IAGP 8699517 HPOMIM:220120
GLYCTKHumanCerebral visual impairment  IAGP 8699517 HPOORPHA:941
GLYCTKHumanChorea  IAGP 8699517 HPOORPHA:941
GLYCTKHumanDeeply set eye  IAGP 8699517 HPOMIM:220120
GLYCTKHumanDelayed CNS myelination  IAGP 8699517 HPOMIM:220120
GLYCTKHumanDelayed speech and language development  IAGP 8699517 HPOORPHA:941
GLYCTKHumanElevated circulating D-glyceric concentration  IAGP 8699517 HPOMIM:220120
GLYCTKHumanElevated CSF D-glyceric acid concentration  IAGP 8699517 HPOMIM:220120
GLYCTKHumanEncephalopathy  IAGP 8699517 HPOMIM:220120
GLYCTKHumanFailure to thrive  IAGP 8699517 HPOMIM:220120
1 to 20 of 69 rows

#
Reference Title
Reference Citation
1. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. RGD HPO Phenotype Annotation Pipeline RGD automated import pipeline for human HPO-to-gene-to-disease annotations
PMID:2537226   PMID:2551543   PMID:8889549   PMID:12477932   PMID:16189514   PMID:16344560   PMID:16753811   PMID:18029348   PMID:19060904   PMID:20800603   PMID:20949620   PMID:21873635  
PMID:21926972   PMID:21988832   PMID:23974872   PMID:25416956   PMID:31837836   PMID:32296183   PMID:32393512   PMID:34800366   PMID:35906200  



GLYCTK
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38352,287,828 - 52,295,257 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl352,287,089 - 52,295,257 (+)EnsemblGRCh38hg38GRCh38
GRCh37352,321,844 - 52,329,273 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36352,296,912 - 52,302,532 (+)NCBINCBI36Build 36hg18NCBI36
Celera352,301,159 - 52,308,595 (+)NCBICelera
Cytogenetic Map3p21.2NCBI
HuRef352,384,478 - 52,391,914 (+)NCBIHuRef
CHM1_1352,274,371 - 52,281,807 (+)NCBICHM1_1
T2T-CHM13v2.0352,320,727 - 52,349,445 (+)NCBIT2T-CHM13v2.0
Glyctk
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399106,030,058 - 106,037,353 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9106,030,056 - 106,035,337 (-)EnsemblGRCm39 Ensembl
GRCm389106,152,859 - 106,160,158 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9106,152,857 - 106,158,138 (-)EnsemblGRCm38mm10GRCm38
MGSCv379106,055,191 - 106,060,469 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369106,010,961 - 106,016,239 (-)NCBIMGSCv36mm8
Celera9105,776,846 - 105,782,154 (-)NCBICelera
Cytogenetic Map9F1NCBI
cM Map957.46NCBI
Glyctk
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88115,676,071 - 115,681,403 (-)NCBIGRCr8
mRatBN7.28106,795,461 - 106,802,675 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8106,797,343 - 106,802,397 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8112,421,933 - 112,426,948 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08110,621,106 - 110,626,120 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08108,463,912 - 108,468,926 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08114,846,210 - 114,853,374 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8114,848,084 - 114,853,103 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08114,211,573 - 114,218,732 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8106,120,103 - 106,125,121 (-)NCBICelera
Cytogenetic Map8q32NCBI
Glyctk
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555323,936,160 - 3,942,868 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555323,933,964 - 3,939,858 (+)NCBIChiLan1.0ChiLan1.0
GLYCTK
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2252,282,866 - 52,290,724 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1352,287,680 - 52,295,495 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0352,230,128 - 52,237,561 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1353,459,271 - 53,466,702 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl353,458,563 - 53,466,702 (+)Ensemblpanpan1.1panPan2
GLYCTK
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12037,462,651 - 37,495,581 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2037,462,659 - 37,465,807 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2037,442,602 - 37,477,128 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02037,811,192 - 37,845,947 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2037,788,578 - 37,845,938 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12037,175,116 - 37,209,637 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02037,583,786 - 37,618,386 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02037,868,469 - 37,902,996 (-)NCBIUU_Cfam_GSD_1.0
Glyctk
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560266,866,696 - 66,872,727 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365293,628,822 - 3,635,236 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365293,627,194 - 3,635,568 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GLYCTK
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1334,433,399 - 34,440,264 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11334,433,403 - 34,440,037 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21337,565,182 - 37,572,167 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GLYCTK
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12213,648,499 - 13,653,813 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2213,651,024 - 13,653,801 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041153,247,974 - 153,253,449 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Glyctk
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247306,089,167 - 6,099,660 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247306,088,702 - 6,095,621 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

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Variants in GLYCTK
188 total Variants

1 to 10 of 212 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
GLYCTK, 1-BP DEL, 1448T deletion D-Glyceric aciduria [RCV000023820] Chr3:3p21 pathogenic|likely benign
GLYCTK, 1-BP DEL, 1558C deletion D-Glyceric aciduria [RCV000023822] Chr3:3p21 pathogenic
NM_145262.4(GLYCTK):c.1478T>G (p.Phe493Cys) single nucleotide variant D-Glyceric aciduria [RCV000023821]|not provided [RCV001852029] Chr3:52293032 [GRCh38]
Chr3:52327048 [GRCh37]
Chr3:3p21.2		 pathogenic|likely pathogenic|conflicting interpretations of pathogenicity|uncertain significance
GRCh38/hg38 3p21.31-14.3(chr3:49461000-55314500)x1 copy number loss See cases [RCV000051511] Chr3:49461000..55314500 [GRCh38]
Chr3:49498433..55348528 [GRCh37]
Chr3:49473437..55323568 [NCBI36]
Chr3:3p21.31-14.3		 pathogenic
NM_145262.4(GLYCTK):c.1448del (p.Phe483fs) deletion D-Glyceric aciduria [RCV000077847] Chr3:52293001 [GRCh38]
Chr3:52327017 [GRCh37]
Chr3:3p21.2		 pathogenic|not provided
NM_145262.4(GLYCTK):c.1558del (p.Leu520fs) deletion D-Glyceric aciduria [RCV000077848] Chr3:52293111 [GRCh38]
Chr3:52327127 [GRCh37]
Chr3:3p21.2		 pathogenic|not provided
NM_145262.4(GLYCTK):c.1181C>T (p.Thr394Ile) single nucleotide variant not provided [RCV000514109] Chr3:52292735 [GRCh38]
Chr3:52326751 [GRCh37]
Chr3:3p21.2		 benign|likely benign
GRCh38/hg38 3p21.2-14.3(chr3:51394434-55064449)x1 copy number loss See cases [RCV000143631] Chr3:51394434..55064449 [GRCh38]
Chr3:51431865..55098476 [GRCh37]
Chr3:51406905..55073516 [NCBI36]
Chr3:3p21.2-14.3		 likely pathogenic
NM_145262.4(GLYCTK):c.1460A>G (p.Asn487Ser) single nucleotide variant D-Glyceric aciduria [RCV001250085]|not provided [RCV001529483]|not specified [RCV000238629] Chr3:52293014 [GRCh38]
Chr3:52327030 [GRCh37]
Chr3:3p21.2		 uncertain significance
GRCh37/hg19 3p21.2-14.2(chr3:52086599-59689209)x1 copy number loss See cases [RCV000239886] Chr3:52086599..59689209 [GRCh37]
Chr3:3p21.2-14.2		 pathogenic
1 to 10 of 212 rows

Predicted Target Of
Summary Value
Count of predictions:6005
Count of miRNA genes:1042
Interacting mature miRNAs:1300
Transcripts:ENST00000305690, ENST00000354773, ENST00000436784, ENST00000461183, ENST00000471180, ENST00000473032, ENST00000473583, ENST00000477382, ENST00000486393, ENST00000489173
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.


The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
597385643GWAS1481717_Hplatelet count QTL GWAS1481717 (human)2e-10platelet quantity (VT:0003179)platelet count (CMO:0000029)35229174352291744Human
1298487BFD1_HBody fluid distribution QTL 1 (human)3.94Body fluid distributionimpedance ratio33638071262380712Human
597431465GWAS1527539_Htestosterone measurement QTL GWAS1527539 (human)5e-10testosterone measurementserum testosterone level (CMO:0000568)35228840152288402Human
597393581GWAS1489655_Hhemoglobin measurement QTL GWAS1489655 (human)1e-09hemoglobin measurementhemoglobin measurement (CMO:0000508)35229174352291744Human
1298489RA4_HRheumatoid arthritis QTL 4 (human)0.0283Joint/bone inflammationrheumatoid arthritis33638071262380712Human
1643509BW293_HBody Weight QTL 293 (human)1.42Body weightBMI33638071262380712Human
2289308BW392_HBody weight QTL 392 (human)1.42Body weightBMI33638071262380712Human
1331643COPD16_HChronic obstructive pulmonary disease QTL 16 (human)1.07Chronic airflow obstructionpost-BD FEV1 minus pre-BD FEV1/pre-BD FEV1 x 10034938065175380651Human

WI-17518  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37352,327,342 - 52,327,468UniSTSGRCh37
Build 36352,302,382 - 52,302,508RGDNCBI36
Celera352,306,665 - 52,306,791RGD
Cytogenetic Map3p21.1UniSTS
HuRef352,389,984 - 52,390,110UniSTS
GeneMap99-GB4 RH Map3161.8UniSTS
Whitehead-RH Map3212.9UniSTS
NCBI RH Map3491.2UniSTS
RH78133  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37352,327,219 - 52,327,338UniSTSGRCh37
Build 36352,302,259 - 52,302,378RGDNCBI36
Celera352,306,542 - 52,306,661RGD
Cytogenetic Map3p21.1UniSTS
HuRef352,389,861 - 52,389,980UniSTS
GeneMap99-GB4 RH Map3162.3UniSTS
NCBI RH Map3492.0UniSTS




adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
1204 2439 2788 2253 4973 1726 2351 6 624 1951 465 2269 7306 6472 53 3734 1 852 1744 1617 175 1


1 to 30 of 36 rows
RefSeq Transcripts NG_023246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001144951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_145262 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_026699 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_026700 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_026701 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_026702 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017005730 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024453351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024453352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047447465 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047447466 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047447467 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054345280 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054345281 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054345282 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001740022 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001740023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_245095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA100208 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC092045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF448855 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF529373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI380271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK074215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY134474 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY172690 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY295075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC021896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC036862 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
1 to 30 of 36 rows

Ensembl Acc Id: ENST00000305690   ⟹   ENSP00000301965
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl352,287,820 - 52,293,005 (+)Ensembl
Ensembl Acc Id: ENST00000436784   ⟹   ENSP00000389175
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl352,287,828 - 52,295,257 (+)Ensembl
Ensembl Acc Id: ENST00000461183   ⟹   ENSP00000417264
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl352,287,089 - 52,293,166 (+)Ensembl
Ensembl Acc Id: ENST00000471180   ⟹   ENSP00000417526
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl352,287,835 - 52,293,471 (+)Ensembl
Ensembl Acc Id: ENST00000473032   ⟹   ENSP00000418951
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl352,287,820 - 52,293,469 (+)Ensembl
Ensembl Acc Id: ENST00000473583
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl352,290,074 - 52,292,482 (+)Ensembl
Ensembl Acc Id: ENST00000477382   ⟹   ENSP00000419008
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl352,290,314 - 52,293,005 (+)Ensembl
Ensembl Acc Id: ENST00000486393   ⟹   ENSP00000419868
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl352,287,820 - 52,293,475 (+)Ensembl
Ensembl Acc Id: ENST00000489173
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl352,290,684 - 52,293,475 (+)Ensembl
RefSeq Acc Id: NM_001144951   ⟹   NP_001138423
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,295,257 (+)NCBI
GRCh37352,321,836 - 52,329,272 (+)RGD
Celera352,301,159 - 52,308,595 (+)RGD
HuRef352,384,478 - 52,391,914 (+)ENTREZGENE
CHM1_1352,274,371 - 52,279,556 (+)NCBI
T2T-CHM13v2.0352,320,727 - 52,328,156 (+)NCBI
Sequence:
RefSeq Acc Id: NM_145262   ⟹   NP_660305
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,295,257 (+)NCBI
GRCh37352,321,836 - 52,329,272 (+)RGD
Build 36352,296,912 - 52,302,532 (+)NCBI Archive
Celera352,301,159 - 52,308,595 (+)RGD
HuRef352,384,478 - 52,391,914 (+)ENTREZGENE
CHM1_1352,274,371 - 52,281,807 (+)NCBI
T2T-CHM13v2.0352,320,727 - 52,328,156 (+)NCBI
Sequence:
RefSeq Acc Id: NR_026699
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,295,257 (+)NCBI
GRCh37352,321,836 - 52,329,272 (+)RGD
Celera352,301,159 - 52,308,595 (+)RGD
HuRef352,384,478 - 52,391,914 (+)ENTREZGENE
CHM1_1352,274,371 - 52,281,807 (+)NCBI
T2T-CHM13v2.0352,320,727 - 52,328,156 (+)NCBI
Sequence:
RefSeq Acc Id: NR_026700
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,295,257 (+)NCBI
GRCh37352,321,836 - 52,329,272 (+)RGD
Celera352,301,159 - 52,308,595 (+)RGD
HuRef352,384,478 - 52,391,914 (+)ENTREZGENE
CHM1_1352,274,371 - 52,281,807 (+)NCBI
T2T-CHM13v2.0352,320,727 - 52,328,156 (+)NCBI
Sequence:
RefSeq Acc Id: NR_026701
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,295,257 (+)NCBI
GRCh37352,321,836 - 52,329,272 (+)RGD
Celera352,301,159 - 52,308,595 (+)RGD
HuRef352,384,478 - 52,391,914 (+)ENTREZGENE
CHM1_1352,274,371 - 52,281,807 (+)NCBI
T2T-CHM13v2.0352,320,727 - 52,328,156 (+)NCBI
Sequence:
RefSeq Acc Id: NR_026702
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,295,257 (+)NCBI
GRCh37352,321,836 - 52,329,272 (+)RGD
Celera352,301,159 - 52,308,595 (+)RGD
HuRef352,384,478 - 52,391,914 (+)ENTREZGENE
CHM1_1352,274,371 - 52,281,807 (+)NCBI
T2T-CHM13v2.0352,320,727 - 52,328,156 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017005730   ⟹   XP_016861219
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,295,257 (+)NCBI
Sequence:
RefSeq Acc Id: XM_024453351   ⟹   XP_024309119
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,295,257 (+)NCBI
Sequence:
RefSeq Acc Id: XM_024453352   ⟹   XP_024309120
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,295,257 (+)NCBI
Sequence:
RefSeq Acc Id: XM_047447465   ⟹   XP_047303421
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,293,471 (+)NCBI
RefSeq Acc Id: XM_047447466   ⟹   XP_047303422
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,293,471 (+)NCBI
RefSeq Acc Id: XM_047447467   ⟹   XP_047303423
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,293,471 (+)NCBI
RefSeq Acc Id: XM_054345280   ⟹   XP_054201255
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0352,320,727 - 52,349,445 (+)NCBI
RefSeq Acc Id: XM_054345281   ⟹   XP_054201256
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0352,320,727 - 52,326,376 (+)NCBI
RefSeq Acc Id: XM_054345282   ⟹   XP_054201257
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0352,320,727 - 52,326,376 (+)NCBI
1 to 30 of 38 rows
Protein RefSeqs NP_001138423 (Get FASTA)   NCBI Sequence Viewer  
  NP_660305 (Get FASTA)   NCBI Sequence Viewer  
  XP_016861219 (Get FASTA)   NCBI Sequence Viewer  
  XP_024309119 (Get FASTA)   NCBI Sequence Viewer  
  XP_024309120 (Get FASTA)   NCBI Sequence Viewer  
  XP_047303421 (Get FASTA)   NCBI Sequence Viewer  
  XP_047303422 (Get FASTA)   NCBI Sequence Viewer  
  XP_047303423 (Get FASTA)   NCBI Sequence Viewer  
  XP_054201255 (Get FASTA)   NCBI Sequence Viewer  
  XP_054201256 (Get FASTA)   NCBI Sequence Viewer  
  XP_054201257 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH21896 (Get FASTA)   NCBI Sequence Viewer  
  AAH36862 (Get FASTA)   NCBI Sequence Viewer  
  AAH42151 (Get FASTA)   NCBI Sequence Viewer  
  AAM95456 (Get FASTA)   NCBI Sequence Viewer  
  AAO17719 (Get FASTA)   NCBI Sequence Viewer  
  AAP41923 (Get FASTA)   NCBI Sequence Viewer  
  AAP51132 (Get FASTA)   NCBI Sequence Viewer  
  AAQ09607 (Get FASTA)   NCBI Sequence Viewer  
  ABD22985 (Get FASTA)   NCBI Sequence Viewer  
  BAB85018 (Get FASTA)   NCBI Sequence Viewer  
  EAW65205 (Get FASTA)   NCBI Sequence Viewer  
  EAW65206 (Get FASTA)   NCBI Sequence Viewer  
  EAW65207 (Get FASTA)   NCBI Sequence Viewer  
  EAW65208 (Get FASTA)   NCBI Sequence Viewer  
  EAW65209 (Get FASTA)   NCBI Sequence Viewer  
  EAW65210 (Get FASTA)   NCBI Sequence Viewer  
  EAW65211 (Get FASTA)   NCBI Sequence Viewer  
  EAW65212 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000301965
1 to 30 of 38 rows
1 to 5 of 18 rows
1 to 5 of 18 rows
RefSeq Acc Id: NP_660305   ⟸   NM_145262
- Peptide Label: isoform 1
- UniProtKB: Q8TED2 (UniProtKB/Swiss-Prot),   Q86YR8 (UniProtKB/Swiss-Prot),   Q7Z6G5 (UniProtKB/Swiss-Prot),   Q6Y2K6 (UniProtKB/Swiss-Prot),   Q2EZ43 (UniProtKB/Swiss-Prot),   Q0P630 (UniProtKB/Swiss-Prot),   Q8WTY2 (UniProtKB/Swiss-Prot),   Q8IVS8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001138423   ⟸   NM_001144951
- Peptide Label: isoform 2
- UniProtKB: Q8IVS8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_016861219   ⟸   XM_017005730
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_024309120   ⟸   XM_024453352
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_024309119   ⟸   XM_024453351
- Peptide Label: isoform X1
- UniProtKB: Q8TED2 (UniProtKB/Swiss-Prot),   Q8IVS8 (UniProtKB/Swiss-Prot),   Q86YR8 (UniProtKB/Swiss-Prot),   Q7Z6G5 (UniProtKB/Swiss-Prot),   Q6Y2K6 (UniProtKB/Swiss-Prot),   Q2EZ43 (UniProtKB/Swiss-Prot),   Q0P630 (UniProtKB/Swiss-Prot),   Q8WTY2 (UniProtKB/Swiss-Prot)
- Sequence:
MOFRL-associated

Name Modeler Protein Id AA Range Protein Structure
AF-Q8IVS8-F1-model_v2 AlphaFold Q8IVS8 1-523 view protein structure

RGD ID:6864630
Promoter ID:EPDNEW_H5480
Type:initiation region
Name:GLYCTK_1
Description:glycerate kinase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H5482  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,287,828 - 52,287,888EPDNEW
RGD ID:6864634
Promoter ID:EPDNEW_H5482
Type:initiation region
Name:GLYCTK_2
Description:glycerate kinase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H5480  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38352,290,066 - 52,290,126EPDNEW
RGD ID:6801079
Promoter ID:HG_KWN:45214
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_001144951,   NM_145262,   NR_026699,   NR_026700,   NR_026701,   NR_026702
Position:
Human AssemblyChrPosition (strand)Source
Build 36352,296,046 - 52,297,027 (+)MPROMDB
RGD ID:6801078
Promoter ID:HG_KWN:45216
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   Lymphoblastoid
Transcripts:UC003DDR.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36352,300,286 - 52,300,786 (+)MPROMDB


1 to 40 of 48 rows
Database
Acc Id
Source(s)
COSMIC GLYCTK COSMIC
Ensembl Genes ENSG00000168237 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000305690 ENTREZGENE
  ENST00000305690.12 UniProtKB/Swiss-Prot
  ENST00000436784 ENTREZGENE
  ENST00000436784.7 UniProtKB/Swiss-Prot
  ENST00000471180 ENTREZGENE
  ENST00000473032.5 UniProtKB/Swiss-Prot
  ENST00000477382 ENTREZGENE
  ENST00000477382.1 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.1480.10 UniProtKB/Swiss-Prot
  3.40.50.10180 UniProtKB/Swiss-Prot
GTEx ENSG00000168237 GTEx
HGNC ID HGNC:24247 ENTREZGENE
Human Proteome Map GLYCTK Human Proteome Map
InterPro GK-like_C_sf UniProtKB/Swiss-Prot
  GK_N_sf UniProtKB/Swiss-Prot
  MOFRL UniProtKB/Swiss-Prot
  MOFRL_assoc_dom UniProtKB/Swiss-Prot
  MOFRL_protein UniProtKB/Swiss-Prot
KEGG Report hsa:132158 UniProtKB/Swiss-Prot
NCBI Gene 132158 ENTREZGENE
OMIM 610516 OMIM
PANTHER GLYCERATE KINASE UniProtKB/Swiss-Prot
  PTHR12227 UniProtKB/Swiss-Prot
Pfam DUF4147 UniProtKB/Swiss-Prot
  MOFRL UniProtKB/Swiss-Prot
PharmGKB PA162389865 PharmGKB
Superfamily-SCOP GckA/TtuD-like UniProtKB/Swiss-Prot
UniProt A0A0C4DGA0_HUMAN UniProtKB/TrEMBL
  C9J3N5 ENTREZGENE, UniProtKB/TrEMBL
  C9JA32 ENTREZGENE, UniProtKB/TrEMBL
  GLCTK_HUMAN UniProtKB/Swiss-Prot
  Q0P630 ENTREZGENE
  Q2EZ43 ENTREZGENE
  Q6Y2K6 ENTREZGENE
  Q7Z6G5 ENTREZGENE
  Q86YR8 ENTREZGENE
  Q8IVS8 ENTREZGENE
  Q8TED2 ENTREZGENE
1 to 40 of 48 rows