Gene Page: NLRC5

Summary ?
GeneID84166
SymbolNLRC5
SynonymsCLR16.1|NOD27|NOD4
DescriptionNLR family, CARD domain containing 5
ReferenceMIM:613537|HGNC:HGNC:29933|Ensembl:ENSG00000140853|HPRD:14831|Vega:OTTHUMG00000133470
Gene typeprotein-coding
Map location16q13
Pascal p-value0.061
TADA p-value0.005
Fetal beta-1.074
DMG1 (# studies)
SupportCompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWAScatGenome-wide Association StudiesThis data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 1
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
DNM:Xu_2012Whole Exome Sequencing analysisDe novo mutations of 4 genes were identified by exome sequencing of 795 samples in this study

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
NLRC5chr1657054730CTNM_032206p.36L>FmissenseSchizophreniaDNM:Fromer_2014
NLRC5chr1657074615GANM_032206p.975S>NmissenseSchizophreniaDNM:Fromer_2014
NLRC5chr1657095444GNNM_032206
NM_032206		.
.		intronic
splice-donor-in2		SchizophreniaDNM:Xu_2012

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg061815311657023355NLRC52.386E-4-0.3770.037DMG:Wockner_2014


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 V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
REACTOME NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING 3119All SZGR 2.0 genes in this pathway
REACTOME RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 7357All SZGR 2.0 genes in this pathway
REACTOME INNATE IMMUNE SYSTEM 279178All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM 933616All SZGR 2.0 genes in this pathway
WATANABE ULCERATIVE COLITIS WITH CANCER DN 149All SZGR 2.0 genes in this pathway
ROYLANCE BREAST CANCER 16Q COPY NUMBER UP 6344All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS DN 261155All SZGR 2.0 genes in this pathway
SANA RESPONSE TO IFNG UP 7850All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP 487303All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN 409268All SZGR 2.0 genes in this pathway
FUJII YBX1 TARGETS UP 4328All SZGR 2.0 genes in this pathway
LEE EARLY T LYMPHOCYTE DN 5736All SZGR 2.0 genes in this pathway
YOSHIOKA LIVER CANCER EARLY RECURRENCE UP 4023All SZGR 2.0 genes in this pathway
SENGUPTA EBNA1 ANTICORRELATED 17385All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP 430288All SZGR 2.0 genes in this pathway
DUAN PRDM5 TARGETS 7952All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION DN 321200All SZGR 2.0 genes in this pathway