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Gene Report
| Basic information | Related studies | Functional annotation | Related other genetic factors | Overlap with SZ and MDD | ADD to My Gene Set | Comment on Gene | View All Comments on Gene |
| Approved Symbol | CACNA1C |
|---|---|
| Previous Symbol | CCHL1A1, CACNL1A1 |
| Symbol Alias | Cav1.2, CACH2, CACN2, TS, LQT8 |
| Approved Name | calcium channel, voltage-dependent, L type, alpha 1C subunit |
| Location | 12p13.3 |
| Position | chr12:1970786-2697950, 1 |
| External Links |
HGNC: 1390 Entrez Gene: 775 Ensembl: ENSG00000151067 UCSC: uc001qjy.3 |
| No. of Studies | 20 (Positive: 17; Negative: 3; trend: 0) |
| Overlap with SZ? | YES |
| Overlap with MDD? | YES |
Gene related studies (count: 20)
| Reference | Tested Markers | Statistical Values/Author Comments | Result Category | Comment on Study |
|---|---|---|---|---|
| Ament, S. A., 2015 | Coding P-value=0.038, q-value=0.22, Regulatory P-value<1.0e-5, q-value=0.00026. The gene has significant rare variant associations to BD. | Positive | Comment on Study | |
| Ruderfer, D. M., 2013 | SNP: rs1006737 | The most significant SNP falls within the gene CACNA1C that was first found to be significant in BP, subsequently in SCZ. | Positive | Comment on Study |
| Zhang X, 2013 | SNP: rs723672, rs215976, rs1051375 | Our initial findings support a potential association of CACNA1C as a genetic risk factor for BD susceptibility. | Positive | Comment on Study |
| Green, E. K.,2012 | SNP: rs1006737, rs4765913 | SNPs in CACNA1C were significantly associated with BD. | Positive | Comment on Study |
| Soeiro-de-Souza, M. G.,2012 | SNP: rs1006737 | CACNA1C genotype frequency was similar in both groups. | Negative | Comment on Study |
| Lett, T. A.,2011 | SNP: rs1006737 | No significant association was observed in CACNA1C gene for BPD. | Negative | Comment on Study |
| Chen, D. T.,2011 | SNP: rs10848642 | No significant association was observed. | Negative | Comment on Study |
| Soeiro-de-Souza, M. G.,2013(b) | SNP: rs1006737 | Our data indicate for the first time that the CACNA1C risk allele is likely associated with executive dysfunction as a trait in BD, as this association was found regardless the presence of mood symptoms. Larger studies should evaluate the potential influence of CACNA1C on other cognitive domains in BD. | Positive | Comment on Study |
| Cross-Disorder Group of the Psychiatric Genomics Consortium,2013 | SNP: rs1024582, rs4765914 | Significant association was observed in cross-disorder analysis. | Positive | Comment on Study |
| Gonzalez, S.,2013 | SNP: rs769087, rs1006737, rs2159100, rs4765905, rs2370413, rs7297582, rs758170, rs1860002 Haplotype: rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(G-G-G-C-A-G-G-A), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(A-A-A-G-G-A-A-G), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(G-G-G-C-G-G-G-G), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(G-G-G-C-G-G-G-A), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(G-G-G-C-G-A-G-G), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(A-A-A-G-G-G-A-G), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(G-G-G-C-A-G-G-G), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(G-G-G-C-G-A-G-A), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(A-A-A-G-G-G-G-G), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(G-G-G-C-G-G-A-G), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(A-A-A-G-G-A-A-A), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(G-G-G-C-A-A-G-A), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(A-A-A-G-A-G-G-A), rs769087 - rs1006737 - rs2159100 - rs4765905 - rs2370413 - rs7297582 - rs758170 - rs1860002(G-A-A-G-G-A-A-G) |
These results provide additional evidence that CACNA1C is associated with BP and provides the first evidence that variations in this gene might play a role in the pathogenesis of this disorder in the Latino population. | Positive | Comment on Study |
| Tesli, M.,2013 | SNP: rs1006737 | The risk allele of rs1006737 in CACNA1C was significantly associated with enhanced activity in the left amygdala ( in the BD group. | Positive | Comment on Study |
| Green, E. K., 2010 | SNP: rs1006737 | rs1006737 in this gene showed strong significance with BD | Positive | Comment on Study |
| Uemura, T., 2015 | SNP: rs1006737 | Our study further supports the association of SNP rs1006737 with BD-I and suggests that CACNA1C SNP rs1006737 and Bcl-2 SNP rs956572, or specific causal variants in LD with these proxies, act independently to increase risk and ICDH in BD-I. | Positive | Comment on Study |
| Moskvina, V.,2009 | In BP:Smallest P-value per gene=0.03798, Product of P truncation <=0.01=0.0007, Product of P truncation <=0.001=0.00225. It showed evidence for association with BD. | Positive | Comment on Study | |
| Fiorentino A., 2014 | SNP: rs723672, rs75639014, rs190532500, rs181910852, rs55792866, rs113414207, rs79398153, rs116947827, rs73033311, rs117222543, rs1016388, rs12424245, rs2283290, rs11062159, rs11062161, rs10774034, rs3922316, rs2190771, rs10848642, rs11062162, rs4765904, rs1108222, rs1108074, rs1108073, rs2239030, rs2283291, rs2239033, rs3794297, rs144110899, rs112312080, rs73033370, rs148008322, rs180949249, rs146482058, rs138855206, rs2283295, rs191953785, rs2238061, rs112532048, rs10848683, rs10774053, rs10774054, rs11062319, rs67257957, rs3518, rs143803992, rs7316246, rs12809807, rs10466907, rs4765975, rs188226168, rs7957163, rs184753996, rs4765976, rs181496343 Other variant: CACNA1C_Chr12:2161733 _G/C, CACNA1C_Chr12:2161930 _C/T, CACNA1C_Chr12:2161934 _G/A, CACNA1C_Chr12:2161984 _C/A, CACNA1C_Chr12:2162059 _-/GGGG/CGGG/AGGG, CACNA1C_Chr12:2162201 _-/CGGCG, CACNA1C_Chr12:2162217 _G/A, CACNA1C_Chr12:2272007 _C/T, CACNA1C_Chr12:2284208 _-/TGTTCAAACCTGTGT, CACNA1C_Chr12:2286800 _-/TCTTTCTT, CACNA1C_Chr12:2286819 _-/TT, CACNA1C_Chr12:2286820 _-/T, CACNA1C_Chr12:2291321 _-/AT, CACNA1C_Chr12:2292413 _-/A, CACNA1C_Chr12:2292742 _-/C, CACNA1C_Chr12:2296694 _-/T, CACNA1C_Chr12:2296695 _GG/TGG, CACNA1C_Chr12:2297340 _-/CT, CACNA1C_Chr12:2297530 _-/CT, CACNA1C_Chr12:2300919 _-/CA, CACNA1C_Chr12:2300934 _-/CTCCACAGGCACAT, CACNA1C_Chr12:2301013 _-/CACT, CACNA1C_Chr12:2301016 _-/T, CACNA1C_Chr12:2301048 _-/G, CACNA1C_Chr12:2301049 _-/T, CACNA1C_Chr12:2301051 _-/C, CACNA1C_Chr12:2301188 _-/ATAC/ACAC, CACNA1C_Chr12:2302620 _-/A, CACNA1C_Chr12:2302621 _-/A/AA, CACNA1C_Chr12:2308364 _-/GG, CACNA1C_Chr12:2308644 _-/C, CACNA1C_Chr12:2314099 _AAAGTATAA/-, CACNA1C_Chr12:2314103 _-/A, CACNA1C_Chr12:2317001 _-/AA/AAA, CACNA1C_Chr12:2317010 _A/C, CACNA1C_Chr12:2317010 _AC/CC, CACNA1C_Chr12:2321310 _-/C, CACNA1C_Chr12:2323140 _-/T, CACNA1C_Chr12:2323807 _A/C, CACNA1C_Chr12:2328828 _A/T, CACNA1C_Chr12:2329069 _G/T, CACNA1C_Chr12:2332571 _T/-, CACNA1C_Chr12:2334223 _-/G, CACNA1C_Chr12:2335287 _-/CG, CACNA1C_Chr12:2335288 _-/CG/CGCG, CACNA1C_Chr12:2335298 _-/A/C, CACNA1C_Chr12:2335301 _-/G/A, CACNA1C_Chr12:2335333 _-/ACACACAG/ACACACAC, CACNA1C_Chr12:2335340 _-/G/C, CACNA1C_Chr12:2336695 _G/A, CACNA1C_Chr12:2338101 _-/TA/TATG, CACNA1C_Chr12:2338102 _-/TG, CACNA1C_Chr12:2338946 _G/A, CACNA1C_Chr12:2339781 _G/C, CACNA1C_Chr12:2341084 _-/T, CACNA1C_Chr12:2341393 _-/G, CACNA1C_Chr12:2341397 _G/T, CACNA1C_Chr12:2347245 _-/TT, CACNA1C_Chr12:2349920 _-/TGGCCTCCTCA, CACNA1C_Chr12:2349920 _GTGGCCTCCTCAT/GT, CACNA1C_Chr12:2352902 _G/A, CACNA1C_Chr12:2354984 _C/T, CACNA1C_Chr12:2362014 _G/C, CACNA1C_Chr12:2365088 _G/T, CACNA1C_Chr12:2365131 _C/T, CACNA1C_Chr12:2370397 _-/A, CACNA1C_Chr12:2370911 _-/ACACAC, CACNA1C_Chr12:2375362 _-/TT, CACNA1C_Chr12:2381652 _G/A, CACNA1C_Chr12:2385027 _-/A, CACNA1C_Chr12:2385246 _G/T, CACNA1C_Chr12:2389778 _G/A, CACNA1C_Chr12:2391029 _-/T, CACNA1C_Chr12:2392186 _-/T, CACNA1C_Chr12:2418658 _-/AC, CACNA1C_Chr12:2418658 _-/T/TAC, CACNA1C_Chr12:2418659 _AC/ACAC, CACNA1C_Chr12:2419508 _-/A, CACNA1C_Chr12:2419516 _A/T/AAT, CACNA1C_Chr12:2421980 _-/T, CACNA1C_Chr12:2423175 _G/C, CACNA1C_Chr12:2694668 _G/A, CACNA1C_Chr12:2788668 _C/G, CACNA1C_Chr12:2800689 _A/G, CACNA1C_Chr12:2800954 _GCACGGGCCACGCCGAGCTCCCGGCCA/-, CACNA1C_Chr12:2801016 _C/G/CGCCGCCGGGAAGGG, CACNA1C_Chr12:2801133 _T/A, CACNA1C_Chr12:2803097 _T/G, CACNA1C_Chr12:2804191 _T/G, CACNA1C_Chr12:2804268 _T/-, CACNA1C_Chr12:2804832 _G/-, CACNA1C_Chr12:2806546 _G/A, rs113329024 |
Genetic markers in the genes a-calcium channel subunit (CACNA1C) is associated with bipolar disorder (BP). | Positive | Comment on Study |
| Sklar, P.,2011 | SNP: rs4765913 | Significant association was found in combined analysis . | Positive | Comment on Study |
| Jogia, J.,2011 | SNP: rs1006737 | The present findings suggest that the CACNA1C rs1006737 polymorphism impacts on vlPFC activation during fear processing in BD carriers of the risk allele but not their unaffected relatives. | Positive | Comment on Study |
| Liu, Y.,2011 | SNP: rs1006737, rs7297582 | In conclusion, this analysis provides support for a role of CACNA1C risk variants for both bipolar and unipolar major mood disorders. | Positive | Comment on Study |
| Jan, W. C., 2014 | SNP: rs1006737, rs10848635 | Weak associations for CACNA1C (rs10848635) genes were observed. | Positive | Comment on Study |
| Perrier, E.,2011 | SNP: rs1006737 | An interaction between genotype and diagnosis was observed in the left putamen.Our results suggest that genetic variation may be an additional and important source of variability and reinforce the role of striatal changes for disease expression in BD. | Positive | Comment on Study |
Gene functional annotation
Gene related GO terms (count: 40)
GO terms by PBA (count: 7)
| ID | Name | Type | Evidence[PMID] | No. of Genes in BDgene |
|---|---|---|---|---|
| GO:0007268 | synaptic transmission | biological process | IEA | 116 |
| GO:0016021 | integral component of membrane | cellular component | IDA[8392192] | 219 |
| GO:0005886 | plasma membrane | cellular component | IDA[11206130]; TAS | 360 |
| GO:0005245 | voltage-gated calcium channel activity | molecular function | IDA[12130699] | 14 |
| GO:0007411 | axon guidance | biological process | TAS | 60 |
| GO:0005516 | calmodulin binding | molecular function | IPI[15140941] | 20 |
| GO:0005891 | voltage-gated calcium channel complex | cellular component | IDA[12130699] | 13 |
GO terms by database search (count: 33)
Gene related KEGG pathways (count: 5)
KEGG pathways by PBA (count: 3)
| ID | Name | No. of Genes in BDgene | Brief Description |
|---|---|---|---|
| hsa04720 | Long-term potentiation | 13 | |
| hsa04020 | Calcium signaling pathway | 53 | |
| hsa04010 | MAPK signaling pathway | 39 |
KEGG pathways by database search (count: 2)
| ID | Name | No. of Genes in BDgene | Brief Description |
|---|---|---|---|
| hsa04930 | Type II diabetes mellitus | 11 | |
| hsa04912 | GnRH signaling pathway | 17 |
Gene related BioCarta pathways (count: 0)
Gene related interactors from protein-protein interactions data in HPRD (count: 8)
| Gene | Interactor | Interactor in BDgene? | Experiment Type | PMID |
|---|---|---|---|---|
| CACNA1C | CABP1 | NO | in vitro;in vivo | 15140941 |
| CACNA1C | PPM1A | YES | in vitro;in vivo | 15728831 |
| CACNA1C | PRKACA | NO | in vitro;in vivo | 8612821 , 9247274 , 8664319 |
| CACNA1C | RIMS1 | NO | in vitro | 11438519 |
| CACNA1C | SRI | NO | in vitro | 9668070 |
| CACNA1C | RYR2 | YES | in vitro | 11576544 |
| CACNA1C | CACNB3 | YES | in vitro | 15170217 |
| CACNA1C | GNB1 | NO | yeast 2-hybrid | 15953418 |
Related other genetic factors
Gene related SNPs (count: 167)
Literature-origin SNPs (count: 72)
| rs_ID | Location | Functional Annotation | No. of Studies (Positive/Negative/Trend)  |
|---|---|---|---|
| rs1024582 | chr12:2293080 - 2293080(1) | downstream_gene_variant; intron_variant | 2(2/0/0) |
| rs1016388 | chr12:2212702 - 2212702(1) | downstream_gene_variant; intron_variant | 1(0/1/0) |
| rs4765975 | chr12:2696030 - 2696030(1) | 3_prime_UTR_variant; downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant | 1(0/1/0) |
| rs143803992 | chr12:2692499 - 2692499(1) | 3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant | 1(0/1/0) |
| rs12809807 | chr12:2695498 - 2695498(1) | 3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant | 1(0/1/0) |
| rs191953785 | chr12:2315931 - 2315931(1) | intron_variant | 1(0/1/0) |
| rs11062161 | chr12:2220804 - 2220804(1) | intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant | 1(0/1/0) |
| rs7972947 | chr12:2061267 - 2061267(1) | intron_variant | 1(1/0/0) |
| rs7316246 | chr12:2695289 - 2695289(1) | 3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant | 1(0/1/0) |
| rs2239037 | chr12:2254550 - 2254550(1) | intron_variant | 1(1/0/0) |
| rs3794297 | chr12:2229230 - 2229230(1) | intron_variant | 1(0/1/0) |
| rs73033311 | chr12:2199631 - 2199631(1) | intron_variant | 1(0/1/0) |
| rs146482058 | chr12:2293911 - 2293911(1) | downstream_gene_variant; intron_variant | 1(0/1/0) |
| rs10848683 | chr12:2681964 - 2681964(1) | downstream_gene_variant; intron_variant; missense_variant; non_coding_transcript_variant | 1(0/1/0) |
| rs3518 | chr12:2692067 - 2692067(1) | 3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant | 1(0/1/0) |
| rs10848642 | chr12:2222406 - 2222406(1) | intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant | 2(0/2/0) |
| rs723672 | chr12:2052395 - 2052395(1) | downstream_gene_variant; intron_variant; upstream_gene_variant | 2(0/2/0) |
| rs67257957 | chr12:2691852 - 2691851(1) | 3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant | 1(0/1/0) |
| rs4765913 | chr12:2310730 - 2310730(1) | intron_variant | 2(2/0/0) |
| rs181910852 | chr12:2052882 - 2052882(1) | downstream_gene_variant; intron_variant; upstream_gene_variant | 1(0/1/0) |
| rs11062162 | chr12:2222938 - 2222938(1) | intron_variant; non_coding_transcript_variant | 1(0/1/0) |
| rs79398153 | chr12:2185990 - 2185990(1) | intron_variant | 1(1/0/0) |
| rs11062159 | chr12:2217058 - 2217058(1) | downstream_gene_variant; intron_variant | 1(0/1/0) |
| rs117222543 | chr12:2201448 - 2201448(1) | intron_variant | 1(0/1/0) |
| rs1006737 | chr12:2236129 - 2236129(1) | intron_variant | 15(9/4/2) |
| rs2159100 | chr12:2237227 - 2237227(1) | intron_variant | 1(0/1/0) |
| rs180949249 | chr12:2276079 - 2276079(1) | intron_variant; non_coding_transcript_variant | 1(0/1/0) |
| rs138855206 | chr12:2303899 - 2303899(1) | intron_variant | 1(0/1/0) |
| rs10848635 | chr12:2207029 - 2207029(1) | intron_variant | 1(1/0/0) |
| rs11062319 | chr12:2691483 - 2691483(1) | 3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant | 1(0/1/0) |
| rs10774053 | chr12:2681966 - 2681966(1) | downstream_gene_variant; intron_variant; missense_variant; non_coding_transcript_variant | 1(0/1/0) |
| rs2239033 | chr12:2228580 - 2228580(1) | intron_variant | 1(0/1/0) |
| rs75639014 | chr12:2052476 - 2052476(1) | downstream_gene_variant; intron_variant; upstream_gene_variant | 1(0/1/0) |
| rs112312080 | chr12:2245344 - 2245344(1) | intron_variant | 1(0/1/0) |
| rs2370413 | chr12:2245704 - 2245704(1) | intron_variant | 1(0/1/0) |
| rs4765914 | chr12:2311211 - 2311211(1) | intron_variant | 1(1/0/0) |
| rs112532048 | chr12:2585485 - 2585485(1) | missense_variant | 1(0/1/0) |
| rs3922316 | chr12:2221978 - 2221978(1) | intron_variant; non_coding_transcript_variant; upstream_gene_variant | 1(0/1/0) |
| rs4765976 | chr12:2697169 - 2697169(1) | 3_prime_UTR_variant; intron_variant; non_coding_transcript_variant | 1(0/1/0) |
| rs190532500 | chr12:2052702 - 2052702(1) | downstream_gene_variant; intron_variant; upstream_gene_variant | 1(0/1/0) |
| rs2283290 | chr12:2214455 - 2214455(1) | downstream_gene_variant; intron_variant | 1(0/1/0) |
| rs2283295 | chr12:2314745 - 2314745(1) | intron_variant | 1(0/1/0) |
| rs215976 | chr12:2585472 - 2585472(1) | synonymous_variant | 1(0/1/0) |
| rs10774037 | chr12:2311360 - 2311360(1) | intron_variant | 1(1/0/0) |
| rs1108074 | chr12:2224318 - 2224318(1) | intron_variant; upstream_gene_variant | 1(0/1/0) |
| rs2283291 | chr12:2228294 - 2228294(1) | intron_variant; upstream_gene_variant | 1(0/1/0) |
| rs1860002 | chr12:2304637 - 2304637(1) | intron_variant | 1(0/1/0) |
| rs73033370 | chr12:2245364 - 2245364(1) | intron_variant | 1(0/1/0) |
| rs2190771 | chr12:2222026 - 2222026(1) | intron_variant; non_coding_transcript_variant; upstream_gene_variant | 1(0/1/0) |
| rs113414207 | chr12:2183578 - 2183577(1) | intron_variant | 1(0/1/0) |
| rs144110899 | chr12:2242385 - 2242385(1) | intron_variant | 1(0/1/0) |
| rs1051375 | chr12:2679713 - 2679713(1) | downstream_gene_variant; intron_variant; non_coding_transcript_variant; synonymous_variant | 1(1/0/0) |
| rs2238061 | chr12:2316622 - 2316622(1) | intron_variant | 1(0/1/0) |
| rs181496343 | chr12:2697732 - 2697732(1) | 3_prime_UTR_variant; intron_variant; non_coding_transcript_variant | 1(0/1/0) |
| rs10774034 | chr12:2221292 - 2221292(1) | intron_variant; non_coding_transcript_variant; upstream_gene_variant | 1(0/1/0) |
| rs184753996 | chr12:2697167 - 2697167(1) | 3_prime_UTR_variant; intron_variant; non_coding_transcript_variant | 1(0/1/0) |
| rs12424245 | chr12:2213347 - 2213347(1) | downstream_gene_variant; intron_variant | 1(0/1/0) |
| rs148008322 | chr12:2263770 - 2263770(1) | intron_variant | 1(0/1/0) |
| rs4765904 | chr12:2223227 - 2223227(1) | intron_variant; non_coding_transcript_variant | 1(0/1/0) |
| rs4765905 | chr12:2240418 - 2240418(1) | intron_variant | 1(0/1/0) |
| rs769087 | chr12:2235478 - 2235478(1) | intron_variant | 1(0/1/0) |
| rs116947827 | chr12:2186095 - 2186095(1) | intron_variant | 1(0/1/0) |
| rs7297582 | chr12:2246640 - 2246640(1) | intron_variant | 2(0/1/1) |
| rs10774054 | chr12:2682039 - 2682039(1) | downstream_gene_variant; intron_variant; missense_variant; non_coding_transcript_variant | 1(0/1/0) |
| rs2239030 | chr12:2226775 - 2226775(1) | intron_variant; upstream_gene_variant | 1(0/1/0) |
| rs55792866 | chr12:2120310 - 2120310(1) | downstream_gene_variant; intron_variant | 1(0/1/0) |
| rs1108222 | chr12:2223690 - 2223690(1) | intron_variant; upstream_gene_variant | 1(0/1/0) |
| rs7957163 | chr12:2696466 - 2696466(1) | 3_prime_UTR_variant; downstream_gene_variant; intron_variant; non_coding_transcript_variant | 1(0/1/0) |
| rs10466907 | chr12:2695810 - 2695810(1) | 3_prime_UTR_variant; downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant | 1(0/1/0) |
| rs1108073 | chr12:2224472 - 2224472(1) | intron_variant; upstream_gene_variant | 1(0/1/0) |
| rs188226168 | chr12:2696346 - 2696346(1) | 3_prime_UTR_variant; downstream_gene_variant; intron_variant; non_coding_transcript_variant | 1(0/1/0) |
| rs758170 | chr12:2252294 - 2252294(1) | intron_variant | 1(0/1/0) |
LD-proxies (count: 95)
| rs_ID | Literature-origin SNPs with LD | Location | Functional Annotation |
|---|---|---|---|
| rs4298967 | chr12:2299028 - 2299028(1) | intron_variant | |
| rs10431348 | chr12:2675368 - 2675368(1) | downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant | |
| rs10848684 | chr12:2684312 - 2684312(1) | intron_variant; non_coding_transcript_variant | |
| rs12423277 | chr12:2205153 - 2205153(1) | intron_variant | |
| rs7306298 | chr12:2668145 - 2668145(1) | downstream_gene_variant; intron_variant; non_coding_transcript_variant | |
| rs1860056 | chr12:2202670 - 2202670(1) | intron_variant | |
| rs6489375 | chr12:2668602 - 2668602(1) | intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant | |
| rs6489353 | chr12:2229692 - 2229692(1) | intron_variant | |
| rs7138079 | chr12:2672138 - 2672138(1) | downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant | |
| rs2238056 | chr12:2218778 - 2218778(1) | downstream_gene_variant; intron_variant; upstream_gene_variant | |
| rs2302729 | chr12:2674806 - 2674806(1) | downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant | |
| rs2429150 | chr12:2043489 - 2043489(1) | intron_variant; upstream_gene_variant | |
| rs2429148 | chr12:2040658 - 2040658(1) | intron_variant | |
| rs765125 | chr12:2047041 - 2047041(1) | intron_variant; upstream_gene_variant | |
| rs2239023 | chr12:2201450 - 2201450(1) | intron_variant | |
| rs2239020 | chr12:2201286 - 2201286(1) | intron_variant | |
| rs2007044 | chr12:2235794 - 2235794(1) | intron_variant | |
| rs215990 | chr12:2606134 - 2606134(1) | intron_variant; non_coding_transcript_variant; upstream_gene_variant | |
| rs215988 | chr12:2604177 - 2604177(1) | intron_variant; non_coding_transcript_variant; upstream_gene_variant | |
| rs215989 | chr12:2604700 - 2604700(1) | intron_variant; non_coding_transcript_variant; upstream_gene_variant | |
| rs215981 | chr12:2596190 - 2596190(1) | 3_prime_UTR_variant; intron_variant | |
| rs215984 | chr12:2597746 - 2597746(1) | downstream_gene_variant; intron_variant | |
| rs215977 | chr12:2587051 - 2587051(1) | intron_variant | |
| rs2239052 | chr12:2343922 - 2343922(1) | intron_variant | |
| rs4765924 | chr12:2343810 - 2343810(1) | intron_variant | |
| rs7313708 | chr12:2341996 - 2341996(1) | intron_variant | |
| rs7959938 | chr12:2341299 - 2341299(1) | intron_variant | |
| rs2238074 | chr12:2347671 - 2347671(1) | intron_variant | |
| rs2238067 | chr12:2344171 - 2344171(1) | intron_variant | |
| rs2238064 | chr12:2333015 - 2333015(1) | intron_variant | |
| rs2051989 | chr12:2333145 - 2333145(1) | intron_variant | |
| rs11062194 | chr12:2335213 - 2335213(1) | intron_variant | |
| rs10848648 | chr12:2337350 - 2337350(1) | intron_variant | |
| rs7311382 | chr12:2338167 - 2338167(1) | intron_variant | |
| rs2239050 | chr12:2338248 - 2338248(1) | intron_variant | |
| rs11062195 | chr12:2340238 - 2340238(1) | intron_variant | |
| rs6489363 | chr12:2340672 - 2340672(1) | intron_variant | |
| rs2239049 | chr12:2329000 - 2329000(1) | intron_variant | |
| rs2238062 | chr12:2329099 - 2329099(1) | intron_variant | |
| rs2238063 | chr12:2329162 - 2329162(1) | intron_variant | |
| rs11062189 | chr12:2330538 - 2330538(1) | intron_variant | |
| rs11062190 | chr12:2331029 - 2331029(1) | intron_variant | |
| rs11062192 | chr12:2331534 - 2331534(1) | intron_variant | |
| rs11062193 | chr12:2331554 - 2331554(1) | intron_variant | |
| rs2051992 | chr12:2332160 - 2332160(1) | intron_variant | |
| rs2239043 | chr12:2320259 - 2320259(1) | intron_variant | |
| rs2239018 | chr12:2195191 - 2195191(1) | intron_variant | |
| rs2238049 | chr12:2196962 - 2196962(1) | intron_variant | |
| rs2239044 | chr12:2321012 - 2321012(1) | intron_variant | |
| rs2238046 | chr12:2190832 - 2190832(1) | intron_variant | |
| rs12317078 | chr12:2320846 - 2320846(1) | intron_variant | |
| rs2238048 | chr12:2191041 - 2191041(1) | intron_variant | |
| rs3819529 | chr12:2327493 - 2327493(1) | intron_variant | |
| rs10459125 | chr12:2200698 - 2200698(1) | intron_variant | |
| rs2283298 | chr12:2325612 - 2325612(1) | intron_variant | |
| rs2239019 | chr12:2201144 - 2201144(1) | intron_variant | |
| rs11062188 | chr12:2328978 - 2328978(1) | intron_variant | |
| rs2238050 | chr12:2197541 - 2197541(1) | intron_variant | |
| rs2239048 | chr12:2328551 - 2328551(1) | intron_variant | |
| rs2238052 | chr12:2198130 - 2198130(1) | intron_variant | |
| rs10774030 | chr12:2183524 - 2183524(1) | intron_variant | |
| rs758171 | chr12:2185097 - 2185097(1) | intron_variant | |
| rs2283287 | chr12:2189558 - 2189558(1) | intron_variant | |
| rs2283288 | chr12:2189882 - 2189882(1) | intron_variant | |
| rs11062145 | chr12:2188187 - 2188187(1) | intron_variant | |
| rs10744559 | chr12:2189132 - 2189132(1) | intron_variant | |
| rs10848637 | chr12:2207388 - 2207388(1) | intron_variant | |
| rs12315711 | chr12:2237664 - 2237664(1) | intron_variant | |
| rs10848636 | chr12:2207327 - 2207327(1) | intron_variant | |
| rs10744560 | chr12:2277933 - 2277933(1) | intron_variant; non_coding_transcript_variant | |
| rs11062156 | chr12:2208357 - 2208357(1) | intron_variant | |
| rs2238053 | chr12:2207930 - 2207930(1) | intron_variant | |
| rs10848632 | chr12:2206827 - 2206827(1) | intron_variant | |
| rs758174 | chr12:2206540 - 2206540(1) | intron_variant | |
| rs10848634 | chr12:2206961 - 2206961(1) | intron_variant | |
| rs10848633 | chr12:2206853 - 2206853(1) | intron_variant | |
| rs4765670 | chr12:2203960 - 2203960(1) | intron_variant | |
| rs4765902 | chr12:2203799 - 2203799(1) | intron_variant | |
| rs758173 | chr12:2206062 - 2206062(1) | intron_variant | |
| rs10774033 | chr12:2205260 - 2205260(1) | intron_variant | |
| rs10848628 | chr12:2203323 - 2203323(1) | intron_variant | |
| rs10848627 | chr12:2203242 - 2203242(1) | intron_variant | |
| rs10848629 | chr12:2203731 - 2203731(1) | intron_variant | |
| rs10774036 | chr12:2277782 - 2277782(1) | intron_variant; non_coding_transcript_variant | |
| rs12422554 | chr12:2203454 - 2203454(1) | intron_variant | |
| rs11062170 | chr12:2239678 - 2239678(1) | intron_variant | |
| rs2238054 | chr12:2208478 - 2208478(1) | intron_variant | |
| rs7957545 | chr12:2214876 - 2214876(1) | downstream_gene_variant; intron_variant | |
| rs1108221 | chr12:2223629 - 2223629(1) | intron_variant; upstream_gene_variant | |
| rs10774035 | chr12:2259508 - 2259508(1) | intron_variant | |
| rs3794284 | chr12:2687905 - 2687905(1) | downstream_gene_variant; intron_variant; non_coding_transcript_variant | |
| rs4765970 | chr12:2683495 - 2683495(1) | intron_variant; non_coding_transcript_variant | |
| rs1861673 | chr12:2689968 - 2689968(1) | intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant | |
| rs11062314 | chr12:2683439 - 2683439(1) | intron_variant; non_coding_transcript_variant | |
| rs3794288 | chr12:2680055 - 2680055(1) | downstream_gene_variant; intron_variant; non_coding_transcript_variant |
Gene related CNVs (count: 0)
Gene related other variants (count: 93)
Gene related regions (count: 2)
| Region Name | Position | No. of Studies (Positive/Negative/Trend) |
|---|---|---|
| Chr 12 | chr12:0-133275309 | 3 (0/3/0) |
| 12p13 | chr12:0-14600000 | 1 (0/1/0) |
Overlap with schizophrenia (SZ) and major depressive disorder (MDD)
Gene relationship with SZ
Overlap with SZ from cross-disorder studies (count: 5)
| Reference | Description | Result Category |
|---|---|---|
| 24280982 | The most significant SNP falls within the gene CACNA1C that was first found to be significant in BP, subsequently in SCZ. | Negative |
| 23453885 | Significant association was observed in cross-disorder analysis. | Positive |
| 23437284 | There were no FWE-corrected significant findings in SZ individuals. | Negative |
| 19065143 | It showed no evidence for association with SZ. | Negative |
| 19621016 | The risk allele rs1006737 in this gene conferred increased risk for schizophrenia (P= 0.034) with similar effect sizes to those previously observed in BD (allelic odds ratio B1.15). | Positive |
Overlap with SZ from candidate gene intersection analysis (count: 2)
Gene relationship with MDD
Overlap with MDD from cross-disorder studies (count: 5)
| Reference | Description | Category in MDD |
|---|---|---|
| 20351715 | In conclusion, this analysis provides support for a role of CACNA1C risk variants for both bipolar and unipolar major mood disorders. | Positive |
| 19621016 | The risk allele rs1006737 in this gene conferred increased risk for recurrent major depression (P= 0.013) with similar effect sizes to those previously observed in BD (allelic odds ratio B1.15). | Positive |
| 23453885 | Significant association was observed in cross-disorder analysis. | Positive |
| 23680436 | No significant association was found between MDD and this gene. | Negative |
| 25843436 | no significant differences were observed in this study. | Negative |
Overlap with MDD from candidate gene intersection analysis (count: 0)
View in gBrowse
Region: chr12:1970786..2697950 View in gBrowse
Copyright: Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences Feedback
Acknowledgements
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Last update: March 31, 2016