Gene Page: SMTNL1
Summary ?
| GeneID | 219537 |
| Symbol | SMTNL1 |
| Synonyms | CHASM |
| Description | smoothelin-like 1 |
| Reference | MIM:613664|HGNC:HGNC:32394|Ensembl:ENSG00000214872|Vega:OTTHUMG00000167046 |
| Gene type | protein-coding |
| Map location | 11q12.1 |
| Pascal p-value | 0.005 |
| Fetal beta | 0.295 |
| eGene | Caudate basal ganglia Cerebellar Hemisphere Cerebellum Cortex Frontal Cortex BA9 Putamen basal ganglia |
| Support | CompositeSet |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DNM:Fromer_2014 | Whole Exome Sequencing analysis | This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA. |
Section I. Genetics and epigenetics annotation
DNM table
| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| SMTNL1 | chr11 | 57313454 | C | T | NM_001105565 | p.340R>W | missense | Schizophrenia | DNM:Fromer_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs2581930 | 11 | 57282482 | SMTNL1 | ENSG00000214872.4 | 9.043E-7 | 0 | -26497 | gtex_brain_putamen_basal |
| rs2649666 | 11 | 57283056 | SMTNL1 | ENSG00000214872.4 | 2.243E-6 | 0 | -25923 | gtex_brain_putamen_basal |
| rs514385 | 11 | 57306011 | SMTNL1 | ENSG00000214872.4 | 3.053E-6 | 0 | -2968 | gtex_brain_putamen_basal |
| rs2729382 | 11 | 57309933 | SMTNL1 | ENSG00000214872.4 | 1.632E-6 | 0 | 954 | gtex_brain_putamen_basal |
| rs2848638 | 11 | 57311754 | SMTNL1 | ENSG00000214872.4 | 1.169E-6 | 0 | 2775 | gtex_brain_putamen_basal |
| rs2848639 | 11 | 57312717 | SMTNL1 | ENSG00000214872.4 | 1.127E-6 | 0 | 3738 | gtex_brain_putamen_basal |
| rs2649659 | 11 | 57312754 | SMTNL1 | ENSG00000214872.4 | 1.122E-6 | 0 | 3775 | gtex_brain_putamen_basal |
| rs12223229 | 11 | 57313469 | SMTNL1 | ENSG00000214872.4 | 1.023E-6 | 0 | 4490 | gtex_brain_putamen_basal |
| rs2649658 | 11 | 57313659 | SMTNL1 | ENSG00000214872.4 | 1.004E-6 | 0 | 4680 | gtex_brain_putamen_basal |
| rs2729367 | 11 | 57315521 | SMTNL1 | ENSG00000214872.4 | 8.269E-7 | 0 | 6542 | gtex_brain_putamen_basal |
| rs2729368 | 11 | 57315639 | SMTNL1 | ENSG00000214872.4 | 8.225E-7 | 0 | 6660 | gtex_brain_putamen_basal |
| rs2729369 | 11 | 57315927 | SMTNL1 | ENSG00000214872.4 | 6.876E-6 | 0 | 6948 | gtex_brain_putamen_basal |
| rs1124942 | 11 | 57316916 | SMTNL1 | ENSG00000214872.4 | 7.263E-7 | 0 | 7937 | gtex_brain_putamen_basal |
| rs2729370 | 11 | 57318943 | SMTNL1 | ENSG00000214872.4 | 6.197E-7 | 0 | 9964 | gtex_brain_putamen_basal |
| rs2649656 | 11 | 57320350 | SMTNL1 | ENSG00000214872.4 | 6.036E-7 | 0 | 11371 | gtex_brain_putamen_basal |
| rs2649655 | 11 | 57321520 | SMTNL1 | ENSG00000214872.4 | 6.036E-7 | 0 | 12541 | gtex_brain_putamen_basal |
| rs2234409 | 11 | 57321811 | SMTNL1 | ENSG00000214872.4 | 6.036E-7 | 0 | 12832 | gtex_brain_putamen_basal |
| rs34002509 | 11 | 57322388 | SMTNL1 | ENSG00000214872.4 | 6.036E-7 | 0 | 13409 | gtex_brain_putamen_basal |
| rs2649654 | 11 | 57322939 | SMTNL1 | ENSG00000214872.4 | 5.347E-7 | 0 | 13960 | gtex_brain_putamen_basal |
| rs2649653 | 11 | 57322940 | SMTNL1 | ENSG00000214872.4 | 5.491E-7 | 0 | 13961 | gtex_brain_putamen_basal |
| rs2848621 | 11 | 57324158 | SMTNL1 | ENSG00000214872.4 | 6.036E-7 | 0 | 15179 | gtex_brain_putamen_basal |
| rs2729373 | 11 | 57325251 | SMTNL1 | ENSG00000214872.4 | 6.036E-7 | 0 | 16272 | gtex_brain_putamen_basal |
| rs2649651 | 11 | 57327103 | SMTNL1 | ENSG00000214872.4 | 6.036E-7 | 0 | 18124 | gtex_brain_putamen_basal |
| rs2848624 | 11 | 57327446 | SMTNL1 | ENSG00000214872.4 | 3.064E-7 | 0 | 18467 | gtex_brain_putamen_basal |
| rs2649649 | 11 | 57328713 | SMTNL1 | ENSG00000214872.4 | 6.473E-8 | 0 | 19734 | gtex_brain_putamen_basal |
| rs2729375 | 11 | 57330767 | SMTNL1 | ENSG00000214872.4 | 6.173E-8 | 0 | 21788 | gtex_brain_putamen_basal |
| rs2467330 | 11 | 57342952 | SMTNL1 | ENSG00000214872.4 | 6.516E-8 | 0 | 33973 | gtex_brain_putamen_basal |
| rs2848622 | 11 | 57344024 | SMTNL1 | ENSG00000214872.4 | 6.616E-8 | 0 | 35045 | gtex_brain_putamen_basal |
| rs2729359 | 11 | 57347801 | SMTNL1 | ENSG00000214872.4 | 1.686E-8 | 0 | 38822 | gtex_brain_putamen_basal |
| rs2649645 | 11 | 57349586 | SMTNL1 | ENSG00000214872.4 | 7.164E-8 | 0 | 40607 | gtex_brain_putamen_basal |
| rs2649644 | 11 | 57349652 | SMTNL1 | ENSG00000214872.4 | 7.133E-8 | 0 | 40673 | gtex_brain_putamen_basal |
| rs2729358 | 11 | 57350784 | SMTNL1 | ENSG00000214872.4 | 7.322E-8 | 0 | 41805 | gtex_brain_putamen_basal |
Section II. Transcriptome annotation
General gene expression (GTEx)
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 name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| YAUCH HEDGEHOG SIGNALING PARACRINE DN | 264 | 159 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN MEF ICP WITH H3K27ME3 | 206 | 108 | All SZGR 2.0 genes in this pathway |
| FOSTER KDM1A TARGETS UP | 266 | 142 | All SZGR 2.0 genes in this pathway |
| CHEMELLO SOLEUS VS EDL MYOFIBERS UP | 35 | 16 | All SZGR 2.0 genes in this pathway |