Gene Page: GGCX

Summary ?
GeneID2677
SymbolGGCX
SynonymsVKCFD1
Descriptiongamma-glutamyl carboxylase
ReferenceMIM:137167|HGNC:HGNC:4247|Ensembl:ENSG00000115486|HPRD:00665|Vega:OTTHUMG00000130173
Gene typeprotein-coding
Map location2p12
Pascal p-value0.265
Sherlock p-value0.04
Fetal beta-0.449
DMG1 (# studies)
eGeneAnterior cingulate cortex BA24
Caudate basal ganglia
Cerebellar Hemisphere
Cerebellum
Cortex
Hypothalamus
Nucleus accumbens basal ganglia

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 2
GSMA_IGenome scan meta-analysisPsr: 0.0004 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg13174083285788758GGCX2.73E-9-0.0251.95E-6DMG:Jaffe_2016
cg17127132285788382GGCX5.31E-8-0.0161.38E-5DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs6738009285737509GGCXENSG00000115486.71.759E-7051161gtex_brain_ba24
rs7591175285738374GGCXENSG00000115486.76.655E-7050296gtex_brain_ba24
rs2166529285742175GGCXENSG00000115486.71.3E-7046495gtex_brain_ba24
rs6750847285758144GGCXENSG00000115486.71.458E-6030526gtex_brain_ba24
rs6731005285760395GGCXENSG00000115486.75.769E-8028275gtex_brain_ba24
rs6705839285761279GGCXENSG00000115486.71.188E-7027391gtex_brain_ba24
rs6705971285761417GGCXENSG00000115486.72.759E-7027253gtex_brain_ba24
rs10175792285761654GGCXENSG00000115486.72.409E-7027016gtex_brain_ba24
rs10176176285762048GGCXENSG00000115486.75.893E-8026622gtex_brain_ba24
rs10179195285762761GGCXENSG00000115486.72.749E-7025909gtex_brain_ba24
rs6714157285763274GGCXENSG00000115486.72.028E-6025396gtex_brain_ba24
rs6743030285763520GGCXENSG00000115486.72.744E-7025150gtex_brain_ba24
rs3755014285764006GGCXENSG00000115486.75.769E-8024664gtex_brain_ba24
rs3755015285764041GGCXENSG00000115486.75.769E-8024629gtex_brain_ba24
rs1446668285764960GGCXENSG00000115486.79.1E-7023710gtex_brain_ba24
rs2028900285767735GGCXENSG00000115486.71.842E-7020935gtex_brain_ba24
rs1078004285769711GGCXENSG00000115486.75.769E-8018959gtex_brain_ba24
rs7605975285772548GGCXENSG00000115486.75.888E-8016122gtex_brain_ba24
rs12473819285773061GGCXENSG00000115486.72.064E-7015609gtex_brain_ba24
rs6547621285774676GGCXENSG00000115486.75.769E-8013994gtex_brain_ba24
rs5832649285776490GGCXENSG00000115486.77.418E-8012180gtex_brain_ba24
rs6738645285783128GGCXENSG00000115486.75.881E-805542gtex_brain_ba24
rs7568458285788175GGCXENSG00000115486.77.041E-80495gtex_brain_ba24
rs11891260285796101GGCXENSG00000115486.72.064E-70-7431gtex_brain_ba24
rs1561198285809989GGCXENSG00000115486.75.769E-80-21319gtex_brain_ba24
rs55971080285812746GGCXENSG00000115486.71.745E-80-24076gtex_brain_ba24

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0016874ligase activityIEA-
GO:0008488gamma-glutamyl carboxylase activityTAS1749935 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006464protein modification processTAS1749935 
GO:0007596blood coagulationTAS9845520 
GO:0017187peptidyl-glutamic acid carboxylationIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005789endoplasmic reticulum membraneIEA-
GO:0005624membrane fractionTAS1749935 
GO:0005783endoplasmic reticulumIEA-
GO:0016020membraneIEA-
GO:0016021integral to membraneTAS1749935 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
REACTOME PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION 2717All SZGR 2.0 genes in this pathway
REACTOME GAMMA CARBOXYLATION TRANSPORT AND AMINO TERMINAL CLEAVAGE OF PROTEINS 118All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF PROTEINS 518242All SZGR 2.0 genes in this pathway
REACTOME POST TRANSLATIONAL PROTEIN MODIFICATION 188116All SZGR 2.0 genes in this pathway
RODRIGUES DCC TARGETS DN 12184All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 8HR DN 12984All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN 848527All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN 637377All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS B LYMPHOCYTE UP 7851All SZGR 2.0 genes in this pathway
HSIAO LIVER SPECIFIC GENES 244154All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
ZHU CMV ALL UP 12089All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN 287208All SZGR 2.0 genes in this pathway
ZHU CMV 24 HR UP 9365All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP 973570All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP 491316All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A4 196124All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS DN 442275All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN 457302All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SURVIVAL DN 11376All SZGR 2.0 genes in this pathway
YAGI AML WITH T 8 21 TRANSLOCATION 368247All SZGR 2.0 genes in this pathway
GREGORY SYNTHETIC LETHAL WITH IMATINIB 14583All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE 1137655All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 NOT SATB1 DN 448282All SZGR 2.0 genes in this pathway