Gene Page: LRPPRC

Summary ?
GeneID10128
SymbolLRPPRC
SynonymsCLONE-23970|GP130|LRP130|LSFC
Descriptionleucine rich pentatricopeptide repeat containing
ReferenceMIM:607544|HGNC:HGNC:15714|Ensembl:ENSG00000138095|HPRD:06343|Vega:OTTHUMG00000152782
Gene typeprotein-coding
Map location2p21
Pascal p-value0.99
Sherlock p-value0.167
Fetal beta0.032
DMG2 (# studies)
eGeneAnterior cingulate cortex BA24
Caudate basal ganglia
Cerebellar Hemisphere
Cerebellum
Cortex
Frontal Cortex BA9
Hippocampus
Hypothalamus
Nucleus accumbens basal ganglia
Putamen basal ganglia
Meta
SupportG2Cdb.humanPSD
G2Cdb.humanPSP
CompositeSet

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
DMG:Nishioka_2013Genome-wide DNA methylation analysisThe authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls. 2
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.0113 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg26538116244223328LRPPRC-0.020.85DMG:Nishioka_2013
cg01913188244223249LRPPRC5.68E-8-0.0091.46E-5DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs6720846244123073LRPPRCENSG00000138095.147.419E-70.02100071gtex_brain_ba24
rs201507883244123356LRPPRCENSG00000138095.146.232E-70.0299788gtex_brain_ba24
rs3839036244123672LRPPRCENSG00000138095.149.063E-70.0299472gtex_brain_ba24
rs4953032244128912LRPPRCENSG00000138095.141.03E-60.0294232gtex_brain_ba24
rs397870554244135775LRPPRCENSG00000138095.142.164E-60.0287369gtex_brain_ba24
rs13384238244155986LRPPRCENSG00000138095.141.069E-60.0267158gtex_brain_ba24
rs4507144244164481LRPPRCENSG00000138095.141.172E-60.0258663gtex_brain_ba24
rs9309111244165733LRPPRCENSG00000138095.141.301E-60.0257411gtex_brain_ba24
rs28394191244172444LRPPRCENSG00000138095.141.948E-60.0250700gtex_brain_ba24
rs9309111244165733LRPPRCENSG00000138095.141.647E-6057411gtex_brain_putamen_basal
rs7594526244173422LRPPRCENSG00000138095.141.244E-6049722gtex_brain_putamen_basal
rs200897097244209046LRPPRCENSG00000138095.141.775E-6014098gtex_brain_putamen_basal
rs6752841244209048LRPPRCENSG00000138095.141.464E-7014096gtex_brain_putamen_basal
rs6753293244235472LRPPRCENSG00000138095.145.928E-70-12328gtex_brain_putamen_basal
rs6544735244235780LRPPRCENSG00000138095.148.664E-70-12636gtex_brain_putamen_basal
rs6544736244236967LRPPRCENSG00000138095.147.778E-70-13823gtex_brain_putamen_basal
rs9678931244237335LRPPRCENSG00000138095.145.261E-70-14191gtex_brain_putamen_basal
rs4131367244237874LRPPRCENSG00000138095.143.108E-70-14730gtex_brain_putamen_basal
rs10203839244239095LRPPRCENSG00000138095.142.966E-70-15951gtex_brain_putamen_basal
rs10186873244241147LRPPRCENSG00000138095.142.522E-60-18003gtex_brain_putamen_basal
rs11687002244248383LRPPRCENSG00000138095.142.429E-60-25239gtex_brain_putamen_basal
rs11683522244249687LRPPRCENSG00000138095.143.02E-60-26543gtex_brain_putamen_basal
rs11683574244249811LRPPRCENSG00000138095.149.302E-70-26667gtex_brain_putamen_basal
rs11684838244250155LRPPRCENSG00000138095.141.685E-60-27011gtex_brain_putamen_basal
rs11688286244252765LRPPRCENSG00000138095.142.024E-60-29621gtex_brain_putamen_basal
rs13007140244258817LRPPRCENSG00000138095.144.28E-70-35673gtex_brain_putamen_basal
rs7598793244259490LRPPRCENSG00000138095.141.928E-60-36346gtex_brain_putamen_basal
rs7598912244259626LRPPRCENSG00000138095.141.077E-60-36482gtex_brain_putamen_basal
rs6744602244261185LRPPRCENSG00000138095.142.652E-60-38041gtex_brain_putamen_basal
rs3853704244261528LRPPRCENSG00000138095.141.308E-60-38384gtex_brain_putamen_basal

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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
PHF60.970.94
PRPF40A0.970.96
FAM76B0.970.95
MSH60.960.96
PDCL0.960.93
NUP2050.960.95
PHF160.960.93
SMC30.960.96
DHX90.960.94
SP30.960.95
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
HLA-F-0.68-0.77
C5orf53-0.67-0.73
PTH1R-0.66-0.75
AIFM3-0.66-0.74
TNFSF12-0.66-0.68
AF347015.31-0.66-0.86
AF347015.27-0.65-0.84
FBXO2-0.65-0.66
FXYD1-0.65-0.86
MT-CO2-0.65-0.87

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003677DNA bindingIEA-
GO:0003723RNA bindingNAS12832482 
GO:0005515protein bindingIPI17050673 |17353931 
GO:0008017microtubule bindingTAS12762840 
GO:0051015actin filament bindingIDA12762840 
GO:0048487beta-tubulin bindingIDA12762840 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0006350transcriptionIEA-
GO:0006810transportIEA-
GO:0051028mRNA transportIEA-
GO:0047497mitochondrion transport along microtubuleTAS12762840 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0000794condensed nuclear chromosomeIDA12762840 
GO:0005856cytoskeletonIDA12762840 
GO:0005634nucleusIDA12832482 
GO:0005637nuclear inner membraneIEA-
GO:0005640nuclear outer membraneIEA-
GO:0005739mitochondrionIDA12832482 
GO:0016020membraneIEA-
GO:0048471perinuclear region of cytoplasmIDA12762840 

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
ARF6DKFZp564M0264ADP-ribosylation factor 6Affinity Capture-MSBioGRID17353931 
CECR2KIAA1740cat eye syndrome chromosome region, candidate 2-HPRD,BioGRID11827465 
GABARAPL2ATG8 | GATE-16 | GATE16 | GEF-2 | GEF2GABA(A) receptor-associated protein-like 2Affinity Capture-MSBioGRID17353931 
GSTK1GST13glutathione S-transferase kappa 1Affinity Capture-MSBioGRID17353931 
HEBP2C6ORF34B | C6orf34 | KIAA1244 | PP23 | SOULheme binding protein 2-HPRD,BioGRID11827465 
IKBKEIKK-i | IKKE | IKKI | KIAA0151 | MGC125294 | MGC125295 | MGC125297inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilonAffinity Capture-MSBioGRID17353931 
MAGEA6MAGE-3b | MAGE3B | MAGE6 | MGC52297melanoma antigen family A, 6Affinity Capture-MSBioGRID17353931 
MAGED1DLXIN-1 | NRAGEmelanoma antigen family D, 1Affinity Capture-MSBioGRID17353931 
MAP1SBPY2IP1 | C19orf5 | FLJ10669 | MAP8 | MGC133087 | VCY2IP-1 | VCY2IP1microtubule-associated protein 1S-HPRD,BioGRID11827465 
NEK6SID6-1512NIMA (never in mitosis gene a)-related kinase 6Affinity Capture-MSBioGRID17353931 
PHLDA3TIH1pleckstrin homology-like domain, family A, member 3Affinity Capture-MSBioGRID17353931 
PTP4A3PRL-3 | PRL-R | PRL3protein tyrosine phosphatase type IVA, member 3Affinity Capture-MSBioGRID17353931 
TNFRSF10DCD264 | DCR2 | TRAILR4 | TRUNDDtumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domainAffinity Capture-MSBioGRID17353931 
UXTART-27ubiquitously-expressed transcript-HPRD,BioGRID11827465 
WDR8FLJ20430 | MGC99569WD repeat domain 8Affinity Capture-MSBioGRID17353931 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
RHEIN ALL GLUCOCORTICOID THERAPY DN 362238All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 2HR DN 8853All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 6HR DN 167100All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR UP 557331All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN 1375806All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP 633376All SZGR 2.0 genes in this pathway
OUELLET OVARIAN CANCER INVASIVE VS LMP UP 11785All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN 855609All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN 483336All SZGR 2.0 genes in this pathway
KIM MYC AMPLIFICATION TARGETS UP 201127All SZGR 2.0 genes in this pathway
LIAO METASTASIS 539324All SZGR 2.0 genes in this pathway
SHIPP DLBCL CURED VS FATAL DN 4530All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN 546351All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY NO BLOOD DN 15093All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY DN 14588All SZGR 2.0 genes in this pathway
BACOLOD RESISTANCE TO ALKYLATING AGENTS DN 6045All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP 953554All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN 911527All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR DN 1011592All SZGR 2.0 genes in this pathway
WONG MITOCHONDRIA GENE MODULE 217122All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS 425261All SZGR 2.0 genes in this pathway
MOOTHA PGC 420269All SZGR 2.0 genes in this pathway
LEE RECENT THYMIC EMIGRANT 227128All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER POOR SURVIVAL A6 456285All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP 605377All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP 548370All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN 882538All SZGR 2.0 genes in this pathway
ROESSLER LIVER CANCER METASTASIS DN 5329All SZGR 2.0 genes in this pathway