Gene Page: SLC9A3
Summary ?
| GeneID | 6550 |
| Symbol | SLC9A3 |
| Synonyms | NHE-3|NHE3 |
| Description | solute carrier family 9 member A3 |
| Reference | MIM:182307|HGNC:HGNC:11073|Ensembl:ENSG00000066230|HPRD:01660|Vega:OTTHUMG00000090315 |
| Gene type | protein-coding |
| Map location | 5p15.3 |
| Pascal p-value | 0.745 |
| Fetal beta | 0.223 |
| DMG | 1 (# studies) |
| eGene | Anterior cingulate cortex BA24 Caudate basal ganglia Cerebellar Hemisphere Cerebellum Cortex Frontal Cortex BA9 Hippocampus Hypothalamus Nucleus accumbens basal ganglia Putamen basal ganglia Meta |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:Wockner_2014 | Genome-wide DNA methylation analysis | This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). | 2 |
| 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,schizophrenias | Click to show details |
Section I. Genetics and epigenetics annotation
DNM table
| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| SLC9A3 | chr5 | 480017 | A | C | NM_004174 | . | silent | Schizophrenia | DNM:Gulsuner_2013 |
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg17778888 | 5 | 510421 | SLC9A3 | 3.43E-5 | 0.568 | 0.019 | DMG:Wockner_2014 |
| cg25925473 | 5 | 502920 | SLC9A3 | 3.28E-4 | 0.443 | 0.041 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs2561666 | 5 | 463898 | SLC9A3 | ENSG00000066230.6 | 2.186E-10 | 0 | 60549 | gtex_brain_ba24 |
| rs10474780 | 5 | 466075 | SLC9A3 | ENSG00000066230.6 | 2.186E-10 | 0 | 58372 | gtex_brain_ba24 |
| rs10475262 | 5 | 466113 | SLC9A3 | ENSG00000066230.6 | 2.186E-10 | 0 | 58334 | gtex_brain_ba24 |
| rs9313086 | 5 | 466125 | SLC9A3 | ENSG00000066230.6 | 2.186E-10 | 0 | 58322 | gtex_brain_ba24 |
| rs2434696 | 5 | 466458 | SLC9A3 | ENSG00000066230.6 | 2.186E-10 | 0 | 57989 | gtex_brain_ba24 |
| rs2278254 | 5 | 477968 | SLC9A3 | ENSG00000066230.6 | 4.174E-7 | 0 | 46479 | gtex_brain_ba24 |
| rs72717418 | 5 | 431538 | SLC9A3 | ENSG00000066230.6 | 1.405E-6 | 0 | 92909 | gtex_brain_putamen_basal |
| rs72717419 | 5 | 431996 | SLC9A3 | ENSG00000066230.6 | 1.406E-6 | 0 | 92451 | gtex_brain_putamen_basal |
| rs72717420 | 5 | 432905 | SLC9A3 | ENSG00000066230.6 | 1.086E-6 | 0 | 91542 | gtex_brain_putamen_basal |
| rs35664198 | 5 | 433258 | SLC9A3 | ENSG00000066230.6 | 1.414E-6 | 0 | 91189 | gtex_brain_putamen_basal |
| rs72717421 | 5 | 434998 | SLC9A3 | ENSG00000066230.6 | 2.686E-7 | 0 | 89449 | gtex_brain_putamen_basal |
| rs72717423 | 5 | 435259 | SLC9A3 | ENSG00000066230.6 | 2.026E-7 | 0 | 89188 | gtex_brain_putamen_basal |
| rs10060385 | 5 | 446730 | SLC9A3 | ENSG00000066230.6 | 7.304E-7 | 0 | 77717 | gtex_brain_putamen_basal |
| rs72717442 | 5 | 450079 | SLC9A3 | ENSG00000066230.6 | 1.093E-6 | 0 | 74368 | gtex_brain_putamen_basal |
| rs72717445 | 5 | 453086 | SLC9A3 | ENSG00000066230.6 | 1.12E-6 | 0 | 71361 | gtex_brain_putamen_basal |
| rs11134054 | 5 | 458841 | SLC9A3 | ENSG00000066230.6 | 1.391E-6 | 0 | 65606 | gtex_brain_putamen_basal |
| rs72698506 | 5 | 460002 | SLC9A3 | ENSG00000066230.6 | 1.406E-6 | 0 | 64445 | gtex_brain_putamen_basal |
| rs12188597 | 5 | 460119 | SLC9A3 | ENSG00000066230.6 | 1.406E-6 | 0 | 64328 | gtex_brain_putamen_basal |
| rs56218301 | 5 | 460603 | SLC9A3 | ENSG00000066230.6 | 1.409E-6 | 0 | 63844 | gtex_brain_putamen_basal |
| rs55846849 | 5 | 460710 | SLC9A3 | ENSG00000066230.6 | 1.409E-6 | 0 | 63737 | gtex_brain_putamen_basal |
| rs36111336 | 5 | 463616 | SLC9A3 | ENSG00000066230.6 | 1.421E-6 | 0 | 60831 | gtex_brain_putamen_basal |
| rs2561666 | 5 | 463898 | SLC9A3 | ENSG00000066230.6 | 3.466E-17 | 0 | 60549 | gtex_brain_putamen_basal |
| rs72698510 | 5 | 464339 | SLC9A3 | ENSG00000066230.6 | 1.421E-6 | 0 | 60108 | gtex_brain_putamen_basal |
| rs10474780 | 5 | 466075 | SLC9A3 | ENSG00000066230.6 | 3.466E-17 | 0 | 58372 | gtex_brain_putamen_basal |
| rs10475262 | 5 | 466113 | SLC9A3 | ENSG00000066230.6 | 3.466E-17 | 0 | 58334 | gtex_brain_putamen_basal |
| rs9313086 | 5 | 466125 | SLC9A3 | ENSG00000066230.6 | 3.466E-17 | 0 | 58322 | gtex_brain_putamen_basal |
| rs2434696 | 5 | 466458 | SLC9A3 | ENSG00000066230.6 | 3.45E-17 | 0 | 57989 | gtex_brain_putamen_basal |
| rs72698512 | 5 | 467143 | SLC9A3 | ENSG00000066230.6 | 1.421E-6 | 0 | 57304 | gtex_brain_putamen_basal |
| rs72698513 | 5 | 467144 | SLC9A3 | ENSG00000066230.6 | 1.421E-6 | 0 | 57303 | gtex_brain_putamen_basal |
| rs148940020 | 5 | 468606 | SLC9A3 | ENSG00000066230.6 | 1.421E-6 | 0 | 55841 | gtex_brain_putamen_basal |
| rs72698514 | 5 | 468744 | SLC9A3 | ENSG00000066230.6 | 1.421E-6 | 0 | 55703 | gtex_brain_putamen_basal |
| rs115438441 | 5 | 469652 | SLC9A3 | ENSG00000066230.6 | 1.426E-6 | 0 | 54795 | gtex_brain_putamen_basal |
| rs149745538 | 5 | 470139 | SLC9A3 | ENSG00000066230.6 | 1.893E-6 | 0 | 54308 | gtex_brain_putamen_basal |
| rs11169 | 5 | 470663 | SLC9A3 | ENSG00000066230.6 | 1.44E-6 | 0 | 53784 | gtex_brain_putamen_basal |
| rs3315 | 5 | 470695 | SLC9A3 | ENSG00000066230.6 | 1.444E-6 | 0 | 53752 | gtex_brain_putamen_basal |
| rs72698516 | 5 | 472221 | SLC9A3 | ENSG00000066230.6 | 1.525E-6 | 0 | 52226 | gtex_brain_putamen_basal |
| rs72700688 | 5 | 474091 | SLC9A3 | ENSG00000066230.6 | 2.017E-6 | 0 | 50356 | gtex_brain_putamen_basal |
| rs199785534 | 5 | 474940 | SLC9A3 | ENSG00000066230.6 | 1.541E-7 | 0 | 49507 | gtex_brain_putamen_basal |
| rs2247114 | 5 | 475104 | SLC9A3 | ENSG00000066230.6 | 9.845E-7 | 0 | 49343 | gtex_brain_putamen_basal |
| rs2244240 | 5 | 476530 | SLC9A3 | ENSG00000066230.6 | 4.919E-7 | 0 | 47917 | gtex_brain_putamen_basal |
| rs2278254 | 5 | 477968 | SLC9A3 | ENSG00000066230.6 | 7.452E-11 | 0 | 46479 | gtex_brain_putamen_basal |
| rs3734137 | 5 | 478440 | SLC9A3 | ENSG00000066230.6 | 1.968E-6 | 0 | 46007 | gtex_brain_putamen_basal |
| rs3734138 | 5 | 478458 | SLC9A3 | ENSG00000066230.6 | 7.441E-7 | 0 | 45989 | gtex_brain_putamen_basal |
| rs3832380 | 5 | 478574 | SLC9A3 | ENSG00000066230.6 | 3.397E-8 | 0 | 45873 | gtex_brain_putamen_basal |
| rs890982 | 5 | 479454 | SLC9A3 | ENSG00000066230.6 | 1.75E-10 | 0 | 44993 | gtex_brain_putamen_basal |
| rs890983 | 5 | 479473 | SLC9A3 | ENSG00000066230.6 | 1.74E-10 | 0 | 44974 | gtex_brain_putamen_basal |
| rs6879351 | 5 | 481194 | SLC9A3 | ENSG00000066230.6 | 1.529E-9 | 0 | 43253 | gtex_brain_putamen_basal |
| rs11954611 | 5 | 481993 | SLC9A3 | ENSG00000066230.6 | 1.215E-6 | 0 | 42454 | gtex_brain_putamen_basal |
| rs13170444 | 5 | 488941 | SLC9A3 | ENSG00000066230.6 | 2.037E-7 | 0 | 35506 | gtex_brain_putamen_basal |
| rs56166334 | 5 | 489002 | SLC9A3 | ENSG00000066230.6 | 8.334E-7 | 0 | 35445 | 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.
Top co-expressed genes in brain regions
| Top 10 positively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| RPRM | 0.73 | 0.71 |
| VSTM2L | 0.69 | 0.69 |
| STK32B | 0.68 | 0.50 |
| SOSTDC1 | 0.68 | 0.64 |
| CLDN1 | 0.67 | 0.49 |
| RASGEF1C | 0.66 | 0.72 |
| CBLN2 | 0.66 | 0.51 |
| CSRP2 | 0.65 | 0.41 |
| TAL2 | 0.65 | 0.47 |
| LMO4 | 0.64 | 0.62 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| C11orf67 | -0.39 | -0.53 |
| MYH14 | -0.38 | -0.50 |
| ZBTB7B | -0.38 | -0.51 |
| BDH2 | -0.37 | -0.53 |
| HEPN1 | -0.37 | -0.47 |
| AIF1L | -0.37 | -0.47 |
| PHGDH | -0.36 | -0.51 |
| AIFM3 | -0.36 | -0.49 |
| NFE2L2 | -0.36 | -0.38 |
| AF347015.27 | -0.36 | -0.48 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| KEGG PROXIMAL TUBULE BICARBONATE RECLAMATION | 23 | 16 | All SZGR 2.0 genes in this pathway |
| PID ENDOTHELIN PATHWAY | 63 | 52 | All SZGR 2.0 genes in this pathway |
| PID RHOA PATHWAY | 45 | 33 | All SZGR 2.0 genes in this pathway |
| REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES | 413 | 270 | All SZGR 2.0 genes in this pathway |
| REACTOME SLC MEDIATED TRANSMEMBRANE TRANSPORT | 241 | 157 | All SZGR 2.0 genes in this pathway |
| REACTOME TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES | 94 | 65 | All SZGR 2.0 genes in this pathway |
| BENPORATH SUZ12 TARGETS | 1038 | 678 | All SZGR 2.0 genes in this pathway |
| BENPORATH EED TARGETS | 1062 | 725 | All SZGR 2.0 genes in this pathway |
| BENPORATH ES WITH H3K27ME3 | 1118 | 744 | All SZGR 2.0 genes in this pathway |
| BENPORATH PRC2 TARGETS | 652 | 441 | All SZGR 2.0 genes in this pathway |
| NIKOLSKY BREAST CANCER 5P15 AMPLICON | 26 | 15 | All SZGR 2.0 genes in this pathway |
| BROWNE HCMV INFECTION 18HR DN | 178 | 121 | All SZGR 2.0 genes in this pathway |
| LEIN CEREBELLUM MARKERS | 85 | 47 | All SZGR 2.0 genes in this pathway |
| MEISSNER NPC HCP WITH H3 UNMETHYLATED | 536 | 296 | All SZGR 2.0 genes in this pathway |
| MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 | 1069 | 729 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN MCV6 HCP WITH H3K27ME3 | 435 | 318 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN MEF HCP WITH H3K27ME3 | 590 | 403 | All SZGR 2.0 genes in this pathway |
| MARTENS BOUND BY PML RARA FUSION | 456 | 287 | All SZGR 2.0 genes in this pathway |