Ccmsa2 QTL Detail

Summary

• Symbol
  Ccmsa2
• Name
  corpus callosum midsagittal area 2

• Feature Type
  QTL
• IDs
  MGI:7314527
• Candidate Genes
  8 Genes

Location &
Maps

• Sequence Map
  Genome coordinates not available from the current reference assembly.

• Genetic Map
  Chromosome 14, cM position of peak correlated region/marker: Syntenic
• Mapping Data
  2 experiments

References

• Summaries
  All 1
• Earliest
  J:276654 Newbury AJ, et al., Genetic, morphometric, and behavioral factors linked to the midsagittal area of the corpus callosum. Front Genet. 2012;3:91

Candidate Genes for Ccmsa2:

Gene	Genome Location (GRCm39)	Reference	QTL Note
Dgkh	Chr14:78796789-78970169 (-)	J:276654	To evaluate candidate genes, the authors used the QTLMiner module of GeneNetwork (Alberts and Schughart, 2010), which evaluates all genes in an interval against neocortical gene expression databases within GeneNetwork. The authors used QTLMiner to rank potential candidates among the 48 genes in the Ccmsa2 interval based on the presence of non-synonymous SNPs, of expression levels in mRNA databases (in this case, three neocortical mRNA expression databases: P3, P14, and P60), and cis-eQTL. Using sequence data and QTLMiner, the authors were able to narrow down eight positional and plausible biological candidate genes within the Ccmsa2 interval: The authors first isolated those genes with non-synonymous SNPs or indels, reasoning that only genes with allelic differences between the two parent strains could account for the QTL. Of the 48 genes in the interval, 14 had SNPs between B6 and D2 (4921530L21Rik [Spertl; MGI:1913982], AU017455 [Zfp957; MGI:2145729], Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], EG629734 [Gm6999; MGI:3647443], Kiaa0564 [Vwa8; MGI:1919008], Klhl1 [MGI:2136335], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh8 [MGI:1306800], Pcdh9 [MGI:1306801], Pcdh20 [MGI:2443376], Tdrd3 [MGI:2444023], Tnfsf11 [MGI:1100089]). The authors next identified those genes that had moderate to high expression in forebrain at some stage of development - values above the average of 8 in at least one neocortical expression database (Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], Kiaa0564 [Vwa8; MGI:1919008], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh20 [MGI:2443376], Pcd8*, Pcdh9 [MGI:1306801], Tdrd3 [MGI:2444023]). Of these, seven were identified as having cis-eQTL in at least one of the expression databases: Dgkh (MGI:2444188), Kiaa0564 (Vwa8; MGI:1919008), Naa16 (MGI:1914147), Mtrf1 (MGI:2384815), Diap3 (Diaph3; MGI:1927222), Tdrd3 (MGI:2444023), and Pcdh9 (MGI:1306801). Finally, the authors examined the interval for genes without non-synonymous SNPs but with significant cis-eQTL, and identified Rgc32 (Rgcc; 1190002H23Rik; MGI:1913464) as another potential candidate (Table 1; Figure 3A). Gene expression of these candidates is highly intercorrelated and their expression correlates with MSACC (Figure 3B). * Curator Note: Pcd8 is not in MGD. The authors may have been referring to Pcdh8 (MGI:1306800).
Diaph3	Chr14:86892803-87378671 (-)	J:276654	To evaluate candidate genes, the authors used the QTLMiner module of GeneNetwork (Alberts and Schughart, 2010), which evaluates all genes in an interval against neocortical gene expression databases within GeneNetwork. The authors used QTLMiner to rank potential candidates among the 48 genes in the Ccmsa2 interval based on the presence of non-synonymous SNPs, of expression levels in mRNA databases (in this case, three neocortical mRNA expression databases: P3, P14, and P60), and cis-eQTL. Using sequence data and QTLMiner, the authors were able to narrow down eight positional and plausible biological candidate genes within the Ccmsa2 interval: The authors first isolated those genes with non-synonymous SNPs or indels, reasoning that only genes with allelic differences between the two parent strains could account for the QTL. Of the 48 genes in the interval, 14 had SNPs between B6 and D2 (4921530L21Rik [Spertl; MGI:1913982], AU017455 [Zfp957; MGI:2145729], Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], EG629734 [Gm6999; MGI:3647443], Kiaa0564 [Vwa8; MGI:1919008], Klhl1 [MGI:2136335], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh8 [MGI:1306800], Pcdh9 [MGI:1306801], Pcdh20 [MGI:2443376], Tdrd3 [MGI:2444023], Tnfsf11 [MGI:1100089]). The authors next identified those genes that had moderate to high expression in forebrain at some stage of development - values above the average of 8 in at least one neocortical expression database (Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], Kiaa0564 [Vwa8; MGI:1919008], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh20 [MGI:2443376], Pcd8*, Pcdh9 [MGI:1306801], Tdrd3 [MGI:2444023]). Of these, seven were identified as having cis-eQTL in at least one of the expression databases: Dgkh (MGI:2444188), Kiaa0564 (Vwa8; MGI:1919008), Naa16 (MGI:1914147), Mtrf1 (MGI:2384815), Diap3 (Diaph3; MGI:1927222), Tdrd3 (MGI:2444023), and Pcdh9 (MGI:1306801). Finally, the authors examined the interval for genes without non-synonymous SNPs but with significant cis-eQTL, and identified Rgc32 (Rgcc; 1190002H23Rik; MGI:1913464) as another potential candidate (Table 1; Figure 3A). Gene expression of these candidates is highly intercorrelated and their expression correlates with MSACC (Figure 3B). * Curator Note: Pcd8 is not in MGD. The authors may have been referring to Pcdh8 (MGI:1306800).
Mtrf1	Chr14:79635212-79661027 (+)	J:276654	To evaluate candidate genes, the authors used the QTLMiner module of GeneNetwork (Alberts and Schughart, 2010), which evaluates all genes in an interval against neocortical gene expression databases within GeneNetwork. The authors used QTLMiner to rank potential candidates among the 48 genes in the Ccmsa2 interval based on the presence of non-synonymous SNPs, of expression levels in mRNA databases (in this case, three neocortical mRNA expression databases: P3, P14, and P60), and cis-eQTL. Using sequence data and QTLMiner, the authors were able to narrow down eight positional and plausible biological candidate genes within the Ccmsa2 interval: The authors first isolated those genes with non-synonymous SNPs or indels, reasoning that only genes with allelic differences between the two parent strains could account for the QTL. Of the 48 genes in the interval, 14 had SNPs between B6 and D2 (4921530L21Rik [Spertl; MGI:1913982], AU017455 [Zfp957; MGI:2145729], Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], EG629734 [Gm6999; MGI:3647443], Kiaa0564 [Vwa8; MGI:1919008], Klhl1 [MGI:2136335], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh8 [MGI:1306800], Pcdh9 [MGI:1306801], Pcdh20 [MGI:2443376], Tdrd3 [MGI:2444023], Tnfsf11 [MGI:1100089]). The authors next identified those genes that had moderate to high expression in forebrain at some stage of development - values above the average of 8 in at least one neocortical expression database (Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], Kiaa0564 [Vwa8; MGI:1919008], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh20 [MGI:2443376], Pcd8*, Pcdh9 [MGI:1306801], Tdrd3 [MGI:2444023]). Of these, seven were identified as having cis-eQTL in at least one of the expression databases: Dgkh (MGI:2444188), Kiaa0564 (Vwa8; MGI:1919008), Naa16 (MGI:1914147), Mtrf1 (MGI:2384815), Diap3 (Diaph3; MGI:1927222), Tdrd3 (MGI:2444023), and Pcdh9 (MGI:1306801). Finally, the authors examined the interval for genes without non-synonymous SNPs but with significant cis-eQTL, and identified Rgc32 (Rgcc; 1190002H23Rik; MGI:1913464) as another potential candidate (Table 1; Figure 3A). Gene expression of these candidates is highly intercorrelated and their expression correlates with MSACC (Figure 3B). * Curator Note: Pcd8 is not in MGD. The authors may have been referring to Pcdh8 (MGI:1306800).
Naa16	Chr14:79571947-79628228 (-)	J:276654	To evaluate candidate genes, the authors used the QTLMiner module of GeneNetwork (Alberts and Schughart, 2010), which evaluates all genes in an interval against neocortical gene expression databases within GeneNetwork. The authors used QTLMiner to rank potential candidates among the 48 genes in the Ccmsa2 interval based on the presence of non-synonymous SNPs, of expression levels in mRNA databases (in this case, three neocortical mRNA expression databases: P3, P14, and P60), and cis-eQTL. Using sequence data and QTLMiner, the authors were able to narrow down eight positional and plausible biological candidate genes within the Ccmsa2 interval: The authors first isolated those genes with non-synonymous SNPs or indels, reasoning that only genes with allelic differences between the two parent strains could account for the QTL. Of the 48 genes in the interval, 14 had SNPs between B6 and D2 (4921530L21Rik [Spertl; MGI:1913982], AU017455 [Zfp957; MGI:2145729], Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], EG629734 [Gm6999; MGI:3647443], Kiaa0564 [Vwa8; MGI:1919008], Klhl1 [MGI:2136335], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh8 [MGI:1306800], Pcdh9 [MGI:1306801], Pcdh20 [MGI:2443376], Tdrd3 [MGI:2444023], Tnfsf11 [MGI:1100089]). The authors next identified those genes that had moderate to high expression in forebrain at some stage of development - values above the average of 8 in at least one neocortical expression database (Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], Kiaa0564 [Vwa8; MGI:1919008], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh20 [MGI:2443376], Pcd8*, Pcdh9 [MGI:1306801], Tdrd3 [MGI:2444023]). Of these, seven were identified as having cis-eQTL in at least one of the expression databases: Dgkh (MGI:2444188), Kiaa0564 (Vwa8; MGI:1919008), Naa16 (MGI:1914147), Mtrf1 (MGI:2384815), Diap3 (Diaph3; MGI:1927222), Tdrd3 (MGI:2444023), and Pcdh9 (MGI:1306801). Finally, the authors examined the interval for genes without non-synonymous SNPs but with significant cis-eQTL, and identified Rgc32 (Rgcc; 1190002H23Rik; MGI:1913464) as another potential candidate (Table 1; Figure 3A). Gene expression of these candidates is highly intercorrelated and their expression correlates with MSACC (Figure 3B). * Curator Note: Pcd8 is not in MGD. The authors may have been referring to Pcdh8 (MGI:1306800).
Pcdh9	Chr14:93250846-94128115 (-)	J:276654	To evaluate candidate genes, the authors used the QTLMiner module of GeneNetwork (Alberts and Schughart, 2010), which evaluates all genes in an interval against neocortical gene expression databases within GeneNetwork. The authors used QTLMiner to rank potential candidates among the 48 genes in the Ccmsa2 interval based on the presence of non-synonymous SNPs, of expression levels in mRNA databases (in this case, three neocortical mRNA expression databases: P3, P14, and P60), and cis-eQTL. Using sequence data and QTLMiner, the authors were able to narrow down eight positional and plausible biological candidate genes within the Ccmsa2 interval: The authors first isolated those genes with non-synonymous SNPs or indels, reasoning that only genes with allelic differences between the two parent strains could account for the QTL. Of the 48 genes in the interval, 14 had SNPs between B6 and D2 (4921530L21Rik [Spertl; MGI:1913982], AU017455 [Zfp957; MGI:2145729], Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], EG629734 [Gm6999; MGI:3647443], Kiaa0564 [Vwa8; MGI:1919008], Klhl1 [MGI:2136335], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh8 [MGI:1306800], Pcdh9 [MGI:1306801], Pcdh20 [MGI:2443376], Tdrd3 [MGI:2444023], Tnfsf11 [MGI:1100089]). The authors next identified those genes that had moderate to high expression in forebrain at some stage of development - values above the average of 8 in at least one neocortical expression database (Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], Kiaa0564 [Vwa8; MGI:1919008], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh20 [MGI:2443376], Pcd8*, Pcdh9 [MGI:1306801], Tdrd3 [MGI:2444023]). Of these, seven were identified as having cis-eQTL in at least one of the expression databases: Dgkh (MGI:2444188), Kiaa0564 (Vwa8; MGI:1919008), Naa16 (MGI:1914147), Mtrf1 (MGI:2384815), Diap3 (Diaph3; MGI:1927222), Tdrd3 (MGI:2444023), and Pcdh9 (MGI:1306801). Finally, the authors examined the interval for genes without non-synonymous SNPs but with significant cis-eQTL, and identified Rgc32 (Rgcc; 1190002H23Rik; MGI:1913464) as another potential candidate (Table 1; Figure 3A). Gene expression of these candidates is highly intercorrelated and their expression correlates with MSACC (Figure 3B). * Curator Note: Pcd8 is not in MGD. The authors may have been referring to Pcdh8 (MGI:1306800).
Rgcc	Chr14:79526190-79539075 (-)	J:276654	To evaluate candidate genes, the authors used the QTLMiner module of GeneNetwork (Alberts and Schughart, 2010), which evaluates all genes in an interval against neocortical gene expression databases within GeneNetwork. The authors used QTLMiner to rank potential candidates among the 48 genes in the Ccmsa2 interval based on the presence of non-synonymous SNPs, of expression levels in mRNA databases (in this case, three neocortical mRNA expression databases: P3, P14, and P60), and cis-eQTL. Using sequence data and QTLMiner, the authors were able to narrow down eight positional and plausible biological candidate genes within the Ccmsa2 interval: The authors first isolated those genes with non-synonymous SNPs or indels, reasoning that only genes with allelic differences between the two parent strains could account for the QTL. Of the 48 genes in the interval, 14 had SNPs between B6 and D2 (4921530L21Rik [Spertl; MGI:1913982], AU017455 [Zfp957; MGI:2145729], Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], EG629734 [Gm6999; MGI:3647443], Kiaa0564 [Vwa8; MGI:1919008], Klhl1 [MGI:2136335], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh8 [MGI:1306800], Pcdh9 [MGI:1306801], Pcdh20 [MGI:2443376], Tdrd3 [MGI:2444023], Tnfsf11 [MGI:1100089]). The authors next identified those genes that had moderate to high expression in forebrain at some stage of development - values above the average of 8 in at least one neocortical expression database (Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], Kiaa0564 [Vwa8; MGI:1919008], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh20 [MGI:2443376], Pcd8*, Pcdh9 [MGI:1306801], Tdrd3 [MGI:2444023]). Of these, seven were identified as having cis-eQTL in at least one of the expression databases: Dgkh (MGI:2444188), Kiaa0564 (Vwa8; MGI:1919008), Naa16 (MGI:1914147), Mtrf1 (MGI:2384815), Diap3 (Diaph3; MGI:1927222), Tdrd3 (MGI:2444023), and Pcdh9 (MGI:1306801). Finally, the authors examined the interval for genes without non-synonymous SNPs but with significant cis-eQTL, and identified Rgc32 (Rgcc; 1190002H23Rik; MGI:1913464) as another potential candidate (Table 1; Figure 3A). Gene expression of these candidates is highly intercorrelated and their expression correlates with MSACC (Figure 3B). * Curator Note: Pcd8 is not in MGD. The authors may have been referring to Pcdh8 (MGI:1306800).
Tdrd3	Chr14:87654075-87782940 (+)	J:276654	To evaluate candidate genes, the authors used the QTLMiner module of GeneNetwork (Alberts and Schughart, 2010), which evaluates all genes in an interval against neocortical gene expression databases within GeneNetwork. The authors used QTLMiner to rank potential candidates among the 48 genes in the Ccmsa2 interval based on the presence of non-synonymous SNPs, of expression levels in mRNA databases (in this case, three neocortical mRNA expression databases: P3, P14, and P60), and cis-eQTL. Using sequence data and QTLMiner, the authors were able to narrow down eight positional and plausible biological candidate genes within the Ccmsa2 interval: The authors first isolated those genes with non-synonymous SNPs or indels, reasoning that only genes with allelic differences between the two parent strains could account for the QTL. Of the 48 genes in the interval, 14 had SNPs between B6 and D2 (4921530L21Rik [Spertl; MGI:1913982], AU017455 [Zfp957; MGI:2145729], Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], EG629734 [Gm6999; MGI:3647443], Kiaa0564 [Vwa8; MGI:1919008], Klhl1 [MGI:2136335], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh8 [MGI:1306800], Pcdh9 [MGI:1306801], Pcdh20 [MGI:2443376], Tdrd3 [MGI:2444023], Tnfsf11 [MGI:1100089]). The authors next identified those genes that had moderate to high expression in forebrain at some stage of development - values above the average of 8 in at least one neocortical expression database (Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], Kiaa0564 [Vwa8; MGI:1919008], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh20 [MGI:2443376], Pcd8*, Pcdh9 [MGI:1306801], Tdrd3 [MGI:2444023]). Of these, seven were identified as having cis-eQTL in at least one of the expression databases: Dgkh (MGI:2444188), Kiaa0564 (Vwa8; MGI:1919008), Naa16 (MGI:1914147), Mtrf1 (MGI:2384815), Diap3 (Diaph3; MGI:1927222), Tdrd3 (MGI:2444023), and Pcdh9 (MGI:1306801). Finally, the authors examined the interval for genes without non-synonymous SNPs but with significant cis-eQTL, and identified Rgc32 (Rgcc; 1190002H23Rik; MGI:1913464) as another potential candidate (Table 1; Figure 3A). Gene expression of these candidates is highly intercorrelated and their expression correlates with MSACC (Figure 3B). * Curator Note: Pcd8 is not in MGD. The authors may have been referring to Pcdh8 (MGI:1306800).
Vwa8	Chr14:79086492-79439750 (+)	J:276654	To evaluate candidate genes, the authors used the QTLMiner module of GeneNetwork (Alberts and Schughart, 2010), which evaluates all genes in an interval against neocortical gene expression databases within GeneNetwork. The authors used QTLMiner to rank potential candidates among the 48 genes in the Ccmsa2 interval based on the presence of non-synonymous SNPs, of expression levels in mRNA databases (in this case, three neocortical mRNA expression databases: P3, P14, and P60), and cis-eQTL. Using sequence data and QTLMiner, the authors were able to narrow down eight positional and plausible biological candidate genes within the Ccmsa2 interval: The authors first isolated those genes with non-synonymous SNPs or indels, reasoning that only genes with allelic differences between the two parent strains could account for the QTL. Of the 48 genes in the interval, 14 had SNPs between B6 and D2 (4921530L21Rik [Spertl; MGI:1913982], AU017455 [Zfp957; MGI:2145729], Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], EG629734 [Gm6999; MGI:3647443], Kiaa0564 [Vwa8; MGI:1919008], Klhl1 [MGI:2136335], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh8 [MGI:1306800], Pcdh9 [MGI:1306801], Pcdh20 [MGI:2443376], Tdrd3 [MGI:2444023], Tnfsf11 [MGI:1100089]). The authors next identified those genes that had moderate to high expression in forebrain at some stage of development - values above the average of 8 in at least one neocortical expression database (Dgkh [MGI:2444188], Diap3 [Diaph3; MGI:1927222], Kiaa0564 [Vwa8; MGI:1919008], Mtrf1 [MGI:2384815], Naa16 [MGI:1914147], Pcdh20 [MGI:2443376], Pcd8*, Pcdh9 [MGI:1306801], Tdrd3 [MGI:2444023]). Of these, seven were identified as having cis-eQTL in at least one of the expression databases: Dgkh (MGI:2444188), Kiaa0564 (Vwa8; MGI:1919008), Naa16 (MGI:1914147), Mtrf1 (MGI:2384815), Diap3 (Diaph3; MGI:1927222), Tdrd3 (MGI:2444023), and Pcdh9 (MGI:1306801). Finally, the authors examined the interval for genes without non-synonymous SNPs but with significant cis-eQTL, and identified Rgc32 (Rgcc; 1190002H23Rik; MGI:1913464) as another potential candidate (Table 1; Figure 3A). Gene expression of these candidates is highly intercorrelated and their expression correlates with MSACC (Figure 3B). * Curator Note: Pcd8 is not in MGD. The authors may have been referring to Pcdh8 (MGI:1306800).