Table 2.
KIF23 mutations in cancer
| Position GRCh37 | DNA, amino acid change | rs ID | MAFa | Prediction | Genotype | Cancer type | References |
|---|---|---|---|---|---|---|---|
| 69,709,610, intron 2 | c.82–112C>G | rs150343049 | G=0.0004 (1000G) | No predictable effect | C/G, case 68 | NSCLC | This study |
| 69,709,686, intron 2 | c.82–36G>A | rs3759825 | G=0.0749 (ExAC) | Splicing changeb | A/A, all cases | NSCLC | This study |
| 69,714,651, intron 5 | c.454–14delT | rs769142360 | −=0.0186 (ExAC) | No predictable effect | −/T, all cases | NSCLC | This study |
| 69,714,707, exon 6 | c.496G>A, p.E166K | – | NA | Possibly damagingc Splicing changed |
Melanoma | Cifola et al 201324 | |
| 69,715,488, intron 6 | c.564–10C>T | rs7180624 | C=0.2610 (ExAC) | No predictable effect | T/T, all cases | NSCLC | This study van de Wetering et al 201525 |
| 69,715,488, intron 6 | c.564 10delC | rs199725995 | −=0.2552 (ExAC) | Splicing changee | −/−, all cases | NSCLC | This study |
| 69,715,495, intron 6 | c.564 3delT | – | NA | Splicing changef | −/T, all cases | NSCLC | This study |
| 69,728,530, exon 13 | c.1326A>C, p.(V442=) | rs11852675 | C=0.0481 (ExAC) | Splicing changeg | A/C, cases 16, 108 | NSCLC | This study |
| 69,728,949, exon 14 | c.1443A>G, p.(P481=) | rs3825858 | A=0.1097 (ExAC) | No predictable effect | G/G, all cases | NSCLC | This study |
| 69,729,001, exon 14 | c.1495G>A, p.E499K | – | NA | Benignc Splicing changeh |
Melanoma | Cifola et al 201324 | |
| 69,729,111, intron 14 | c.1555+50delT | rs72161188 | −=0.0044 (ExAC) | No predictable effect | −/T, all cases | NSCLC | This study |
| 69,732,736, exon 17 | c.1977C>T, p.(T659=) | rs937724 | C=0.1095 (ExAC) | Splicing changei | T/T, all cases | NSCLC | This study |
| 69,732,770, exon 17 | c.2011C>T, p.R671W | rs377162847 | T=7.7e-5 (EVS) | Probably damagingc Splicing changej |
Colorectal cancer | DeRycke et al 201323 |
Notes:
Allele frequencies for all variants were retrieved from http://www.ncbi.nlm.nih.gov/variation/view using data from Exome Variant Server (http://evs.gs.washington.edu), Exome Aggregation Consortium (http://exac.broadinstitute.org) and a Deep Catalog of Human Genetic Variation (http://browser.1000genomes.org).
Created splicing signal at branch point according to SpliceSiteFinder-like (from 0/100 to 72.3/100), and increased splicing signal according to Human Splicing Finder (from 71.2/100 to 79.5/100).
According to PolyPhen2.
Created splicing signal at intron 5 acceptor site according to NNSPLICE (from 0/1.0 to 1.0/1.0). Increased splicing signal in exon 6 according to MaxEntScan (from 2.9/12 to 5.2/12), and increased splicing signal nearby according to MaxEntScan (from 1.5/12 to 4.2/12). Abolished splicing binding site for splicing factor SF2/ASF in exon 6 according to ESE finder. Abolished splicing signal at intron 6 donor site according to NNSPLICE (from 1.0/1.0 to 0/1.0).
Decreased splicing signal at acceptor site according to MaxEntScan (from 9.0/16 to 6.4/16).
Decreased splicing signal at acceptor site according to MaxEntScan (from 9.0/16 to 7.6/16) and increased splicing signal according to GeneSplicer (from 7.8/15 to 8.5/15).
Splicing binding sites for SC35 and SRp55 are changed to SF2/ASF and SF2/ASF (IgM-BrCa1) according to ESE finder.
Created splicing binding sites for splicing binding factor SC35 and SRp40 in exon 14.
Created splicing signal according to Human Splicing Finder (from 0/100 to 66.4/100). Binding sites for splicing factor SF2/ASF (IgM-BrCa1) were changed to a binding site for SRp40.
Two splicing binding sites for each of splicing binding factor SF2/ASF, SF2/ASF (IgM-BrCa1), and SRp40 were abolished.
Abbreviation: NSCLC, non-small-cell lung cancer.