Summary ?
GeneID79628
SymbolSH3TC2
SynonymsCMT4C|MNMN
DescriptionSH3 domain and tetratricopeptide repeats 2
ReferenceMIM:608206|HGNC:HGNC:29427|HPRD:10496|
Gene typeprotein-coding
Map location5q32
Pascal p-value0.644
TADA p-value0.018
Fetal beta0.26
SupportCompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_IGenome scan meta-analysisPsr: 0.0032 
GSMA_IIEGenome scan meta-analysis (European-ancestry samples)Psr: 0.01718 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.00459 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
SH3TC2chr5148407572ATNM_024577p.575L>MmissenseSchizophreniaDNM:Fromer_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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
MLF10.840.73
SPA170.840.75
C9orf980.810.71
C20orf260.810.74
C9orf1160.810.74
FBXO150.800.61
WDR690.800.78
FAM164C0.790.64
KIF90.790.72
MDH1B0.780.72
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.18-0.32-0.22
SCUBE1-0.30-0.31
SATB2-0.29-0.12
ANP32C-0.29-0.37
SLA-0.290.09
AF347015.2-0.29-0.14
AC010300.1-0.28-0.34
AF347015.26-0.27-0.16
AC100783.1-0.27-0.24
MPPED1-0.26-0.06

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005488bindingIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
SABATES COLORECTAL ADENOMA UP 14175All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS UP 292168All SZGR 2.0 genes in this pathway
LIN SILENCED BY TUMOR MICROENVIRONMENT 10873All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS MATURE CELL 293160All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP 395249All SZGR 2.0 genes in this pathway
MIKKELSEN ES ICP WITH H3K4ME3 718401All SZGR 2.0 genes in this pathway
CHYLA CBFA2T3 TARGETS DN 242146All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION DN 321200All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN 784464All SZGR 2.0 genes in this pathway
PEDRIOLI MIR31 TARGETS DN 418245All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-1/20624142420m8hsa-miR-1UGGAAUGUAAAGAAGUAUGUA
hsa-miR-206SZUGGAAUGUAAGGAAGUGUGUGG
hsa-miR-613AGGAAUGUUCCUUCUUUGCC
miR-125/3514094161A,m8hsa-miR-125bbrainUCCCUGAGACCCUAACUUGUGA
hsa-miR-125abrainUCCCUGAGACCCUUUAACCUGUG
miR-20816991169971Ahsa-miR-208AUAAGACGAGCAAAAAGCUUGU
miR-324-3p635163581A,m8hsa-miR-324-3pCCACUGCCCCAGGUGCUGCUGG
miR-409-3p24132419m8hsa-miR-409-3pCGAAUGUUGCUCGGUGAACCCCU
miR-43117892178991A,m8hsa-miR-431UGUCUUGCAGGCCGUCAUGCA
miR-4967167231A,m8hsa-miR-496AUUACAUGGCCAAUCUC
miR-49916990169971A,m8hsa-miR-499UUAAGACUUGCAGUGAUGUUUAA