Gene Page: SMNDC1

Summary ?
GeneID10285
SymbolSMNDC1
SynonymsSMNR|SPF30|TDRD16C
Descriptionsurvival motor neuron domain containing 1
ReferenceMIM:603519|HGNC:HGNC:16900|HPRD:04627|
Gene typeprotein-coding
Map location10q23
Pascal p-value0.447
Sherlock p-value0.863
Fetal beta0.506
DMG1 (# studies)
eGeneMyers' cis & trans

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. 1

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg2187239110112064057SMNDC11.23E-8-0.0135E-6DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs7629431chr3189336841SMNDC1102850.14trans
rs4491879chr3189373908SMNDC1102850.03trans
rs4505678chr3189374356SMNDC1102850.06trans

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
PCIF10.960.94
ZNF5740.950.96
ZC3H30.950.95
NUP620.950.95
GEMIN40.950.94
ZNF3190.940.94
MAPK70.940.92
NUP1880.940.94
ZNF8350.940.96
USP210.940.94
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
C5orf53-0.71-0.79
AF347015.31-0.70-0.87
MT-CO2-0.69-0.88
AF347015.27-0.69-0.86
AF347015.33-0.67-0.84
S100B-0.67-0.81
AF347015.8-0.66-0.86
MT-CYB-0.66-0.83
FXYD1-0.65-0.81
IFI27-0.65-0.78

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
CDK5RAP3C53 | HSF-27 | IC53 | LZAP | MST016 | OK/SW-cl.114CDK5 regulatory subunit associated protein 3Affinity Capture-MSBioGRID17353931 
DDX21DKFZp686F21172 | GUA | GURDB | RH-II/GU | RH-II/GuADEAD (Asp-Glu-Ala-Asp) box polypeptide 21Affinity Capture-MSBioGRID17353931 
EWSR1EWSEwing sarcoma breakpoint region 1Affinity Capture-MSBioGRID17353931 
FDFT1DGPT | ERG9 | SQS | SSfarnesyl-diphosphate farnesyltransferase 1Affinity Capture-MSBioGRID17353931 
PPANBXDC3 | MGC14226 | MGC45852 | SSF | SSF1 | SSF2peter pan homolog (Drosophila)Affinity Capture-MSBioGRID17353931 
RNMTL1FLJ10581 | HC90RNA methyltransferase like 1Affinity Capture-MSBioGRID17353931 
RPL3MGC104284 | TARBP-Bribosomal protein L3Affinity Capture-MSBioGRID17353931 
RUVBL1ECP54 | INO80H | NMP238 | PONTIN | Pontin52 | RVB1 | TIH1 | TIP49 | TIP49ARuvB-like 1 (E. coli)Affinity Capture-MSBioGRID17353931 
SF3A2PRP11 | PRPF11 | SAP62 | SF3a66splicing factor 3a, subunit 2, 66kDaAffinity Capture-MSBioGRID12234937 
SF3A3PRP9 | PRPF9 | SAP61 | SF3a60splicing factor 3a, subunit 3, 60kDaAffinity Capture-MSBioGRID17353931 
SF3B1PRP10 | PRPF10 | SAP155 | SF3b155splicing factor 3b, subunit 1, 155kDaAffinity Capture-MSBioGRID17353931 
SF3B2SAP145 | SF3B145 | SF3b1 | SF3b150splicing factor 3b, subunit 2, 145kDaAffinity Capture-MSBioGRID17353931 
SF3B3KIAA0017 | RSE1 | SAP130 | SF3b130 | STAF130splicing factor 3b, subunit 3, 130kDaAffinity Capture-MSBioGRID17353931 
SF3B4MGC10828 | SAP49 | SF3b49splicing factor 3b, subunit 4, 49kDaAffinity Capture-MSBioGRID17353931 
SNRNP200ASCC3L1 | BRR2 | HELIC2 | U5-200KDsmall nuclear ribonucleoprotein 200kDa (U5)-HPRD,BioGRID11331595 
TSR1FLJ10534 | KIAA1401 | MGC131829TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)Affinity Capture-MSBioGRID17353931 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG SPLICEOSOME 12872All SZGR 2.0 genes in this pathway
PRAMOONJAGO SOX4 TARGETS UP 5238All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
BORCZUK MALIGNANT MESOTHELIOMA UP 305185All SZGR 2.0 genes in this pathway
ENK UV RESPONSE EPIDERMIS DN 508354All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN 712443All SZGR 2.0 genes in this pathway
INAMURA LUNG CANCER SCC SUBTYPES UP 149All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779480All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS UP 769437All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX 795478All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS 882572All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION UP 314201All SZGR 2.0 genes in this pathway
DE YY1 TARGETS DN 9264All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP 973570All SZGR 2.0 genes in this pathway
ZHANG BREAST CANCER PROGENITORS UP 425253All SZGR 2.0 genes in this pathway
MUELLER PLURINET 299189All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER POOR SURVIVAL A6 456285All SZGR 2.0 genes in this pathway
SAKAI CHRONIC HEPATITIS VS LIVER CANCER UP 8363All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN 918550All SZGR 2.0 genes in this pathway