Gene Page: SCAP
Summary ?
| GeneID | 22937 |
| Symbol | SCAP |
| Synonyms | - |
| Description | SREBF chaperone |
| Reference | MIM:601510|HGNC:HGNC:30634|Ensembl:ENSG00000114650|HPRD:03300|Vega:OTTHUMG00000125539 |
| Gene type | protein-coding |
| Map location | 3p21.31 |
| Pascal p-value | 0.169 |
| Sherlock p-value | 0.083 |
| Fetal beta | -0.423 |
| DMG | 1 (# studies) |
| eGene | Anterior cingulate cortex BA24 Caudate basal ganglia Cortex Putamen basal ganglia Myers' cis & trans Meta |
| Support | CompositeSet Darnell FMRP targets Ascano FMRP targets |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:Montano_2016 | Genome-wide DNA methylation analysis | This dataset includes 172 replicated associations between CpGs with schizophrenia. | 1 |
| PMID:cooccur | High-throughput literature-search | Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included. | |
| Literature | High-throughput literature-search | Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias | Click to show details |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg21581415 | 3 | 47460784 | SCAP | 2.38E-5 | 0.006 | 0.067 | DMG:Montano_2016 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs4864466 | chr4 | 54403975 | SCAP | 22937 | 0.12 | trans | ||
| rs6835548 | chr4 | 140644143 | SCAP | 22937 | 0.18 | trans | ||
| rs13094438 | 3 | 47277885 | SCAP | ENSG00000114650.14 | 4.515E-6 | 0.03 | 240731 | gtex_brain_ba24 |
| rs11130123 | 3 | 47285912 | SCAP | ENSG00000114650.14 | 4.589E-6 | 0.03 | 232704 | gtex_brain_ba24 |
| rs11710013 | 3 | 47296921 | SCAP | ENSG00000114650.14 | 4.589E-6 | 0.03 | 221695 | gtex_brain_ba24 |
| rs807936 | 3 | 47322496 | SCAP | ENSG00000114650.14 | 5.392E-6 | 0.03 | 196120 | gtex_brain_ba24 |
| rs1638676 | 3 | 47327651 | SCAP | ENSG00000114650.14 | 5.392E-6 | 0.03 | 190965 | gtex_brain_ba24 |
| rs13072802 | 3 | 47346415 | SCAP | ENSG00000114650.14 | 5.384E-6 | 0.03 | 172201 | gtex_brain_ba24 |
| rs807932 | 3 | 47354241 | SCAP | ENSG00000114650.14 | 4.963E-6 | 0.03 | 164375 | gtex_brain_ba24 |
| rs295428 | 3 | 47359262 | SCAP | ENSG00000114650.14 | 5.899E-6 | 0.03 | 159354 | gtex_brain_ba24 |
| rs295461 | 3 | 47368010 | SCAP | ENSG00000114650.14 | 5.388E-6 | 0.03 | 150606 | gtex_brain_ba24 |
| rs295449 | 3 | 47375955 | SCAP | ENSG00000114650.14 | 5.283E-6 | 0.03 | 142661 | gtex_brain_ba24 |
| rs295458 | 3 | 47385585 | SCAP | ENSG00000114650.14 | 5.392E-6 | 0.03 | 133031 | gtex_brain_ba24 |
| rs807810 | 3 | 47403892 | SCAP | ENSG00000114650.14 | 5.398E-6 | 0.03 | 114724 | gtex_brain_ba24 |
| rs369122584 | 3 | 47431869 | SCAP | ENSG00000114650.14 | 3.008E-6 | 0.03 | 86747 | gtex_brain_ba24 |
| rs4241548 | 3 | 47439231 | SCAP | ENSG00000114650.14 | 6.412E-6 | 0.03 | 79385 | gtex_brain_ba24 |
| rs4858805 | 3 | 47444281 | SCAP | ENSG00000114650.14 | 5.379E-6 | 0.03 | 74335 | gtex_brain_ba24 |
| rs12487736 | 3 | 47459679 | SCAP | ENSG00000114650.14 | 5.599E-6 | 0.03 | 58937 | gtex_brain_ba24 |
| rs4858894 | 3 | 47484953 | SCAP | ENSG00000114650.14 | 5.505E-6 | 0.03 | 33663 | gtex_brain_ba24 |
| rs12492433 | 3 | 47515557 | SCAP | ENSG00000114650.14 | 3.641E-6 | 0.03 | 3059 | gtex_brain_ba24 |
| rs199740248 | 3 | 47517772 | SCAP | ENSG00000114650.14 | 4.283E-6 | 0.03 | 844 | gtex_brain_ba24 |
| rs11708770 | 3 | 47517774 | SCAP | ENSG00000114650.14 | 6.491E-6 | 0.03 | 842 | gtex_brain_ba24 |
| rs11914932 | 3 | 47558184 | SCAP | ENSG00000114650.14 | 3.696E-6 | 0.03 | -39568 | gtex_brain_ba24 |
| rs75815271 | 3 | 48405661 | SCAP | ENSG00000114650.14 | 2.204E-6 | 0.03 | -887045 | 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 III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0051082 | unfolded protein binding | NAS | 11726962 | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0008202 | steroid metabolic process | IEA | - | |
| GO:0008203 | cholesterol metabolic process | IEA | - | |
| GO:0006994 | positive regulation of sterol regulatory element binding protein target gene transcription involved in sterol depletion response | IMP | 11726962 | |
| GO:0006629 | lipid metabolic process | IEA | - | |
| GO:0019217 | regulation of fatty acid metabolic process | IEA | - | |
| GO:0045541 | negative regulation of cholesterol biosynthetic process | NAS | 11969205 | |
| GO:0045716 | positive regulation of low-density lipoprotein receptor biosynthetic process | NAS | 11726974 | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0000139 | Golgi membrane | IEA | - | |
| GO:0005794 | Golgi apparatus | NAS | 11726962 | |
| GO:0005789 | endoplasmic reticulum membrane | IEA | - | |
| GO:0005783 | endoplasmic reticulum | NAS | 11726962 | |
| GO:0016020 | membrane | IEA | - | |
| GO:0016021 | integral to membrane | IEA | - | |
| GO:0016021 | integral to membrane | NAS | 11726962 | |
| GO:0031410 | cytoplasmic vesicle | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| SA CASPASE CASCADE | 19 | 13 | All SZGR 2.0 genes in this pathway |
| ONKEN UVEAL MELANOMA DN | 526 | 357 | All SZGR 2.0 genes in this pathway |
| OSMAN BLADDER CANCER DN | 406 | 230 | All SZGR 2.0 genes in this pathway |
| LASTOWSKA NEUROBLASTOMA COPY NUMBER DN | 800 | 473 | All SZGR 2.0 genes in this pathway |
| SCHLOSSER SERUM RESPONSE UP | 134 | 93 | All SZGR 2.0 genes in this pathway |
| LIN APC TARGETS | 77 | 55 | All SZGR 2.0 genes in this pathway |
| TARTE PLASMA CELL VS PLASMABLAST DN | 309 | 206 | All SZGR 2.0 genes in this pathway |
| WELCSH BRCA1 TARGETS DN | 141 | 92 | All SZGR 2.0 genes in this pathway |
| MONNIER POSTRADIATION TUMOR ESCAPE UP | 393 | 244 | All SZGR 2.0 genes in this pathway |
| MUELLER COMMON TARGETS OF AML FUSIONS UP | 14 | 10 | All SZGR 2.0 genes in this pathway |
| KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP | 756 | 494 | All SZGR 2.0 genes in this pathway |
| KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP | 682 | 440 | All SZGR 2.0 genes in this pathway |