Table 1.
Selected single nucleotide polymorphisms (SNPs) in DNA repair genes, with a minor allele frequency of a > 0.10 in the European population.
| Genomic Annotation | Functional Genomics | Comparative Genomics | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene ID | DNA Repair Pathway | UniProtKB | SNP ID | Base Change | Amino Acid Change | MAF in EUR a | LD with Other SNPs Associated with CRC | LD within the Same Gene | F-SNP Prediction Result (on Protein Coding) | ELASPIC (∆∆G) | DUET (∆∆G) | Element GERP RS Score >800 | SIPHYs |
| EME1 | DSB | Q96AY2 | rs12450550 | T > C | Ile350Thr | 0.24 | no | no | deleterious | Destabilizing (Core 1.646) | Destabilizing (−3.002 Kcal/mol) | ||
| FAAP24 | DSB | Q9BTP7 | rs3816032 b | T > C | Ile192Thr | 0.11 | no | no | deleterious | Destabilizing (Core 1.133) | Destabilizing (−1.653 Kcal/mol) | X | |
| FANCI | DSB | Q9NVI1 | rs2283432 | C > G | Cys742Ser | 0.38 | no | no | deleterious | NA | NA | X | X |
| MUS81 | DSB | Q96NY9 | rs545500 b | C > G | Arg180Pro | 0.33 | no | no | deleterious | NA | NA | X | |
| NEIL3 | BER | Q8TAT5 | rs7689099 | C > G | Pro117Arg | 0.12 | no | no | deleterious | NA | NA | X | X |
| POLE | BER, DSB, NER | Q07864 | rs5744934 | A > G | Asn1396Ser | 0.13 | no | no | deleterious | NA | NA | X | |
| POLN | DSB | Q7Z5Q5 | rs2353552 | C > A | Gln121His | 0.13 | no | no | deleterious | NA | NA | ||
| rs9328764 | A > G | Arg425Cys | 0.12 | no | no | deleterious | NA | Destabilizing (−1.765 Kcal/mol) | X | ||||
| POLQ | DSB | O75417 | rs1381057 | C > T | Gln2513Arg | 0.33 | no | no | deleterious | Destabilizing (Core 1.648) | NA | X | |
| rs3218649 | C > G | Thr982Arg | 0.39 | no | no | deleterious | NA | NA | X | ||||
| rs3218651 | T > C | His1201Arg | 0.15 | no | no | damaging | NA | NA | X | ||||
| RAD51D | DSB | O75771 | rs4796033 | C > T | Arg165Gln | 0.13 | no | no | deleterious | Destabilizing (Core 1.843) | NA | X | |
| REV1 | DSB | Q9UBZ9 | rs3087386 | G > A | Phe257Ser | 0.43 | no | no | deleterious | NA | NA | X | |
| rs3087399 | A > G | Asn373Ser | 0.12 | no | no | deleterious | NA | Destabilizing (−0.596 Kcal/mol) | X | X | |||
| REV3L | DSB | O60673 | rs3204953 | G > A | Val2986Ile | 0.17 | no | no | deleterious | Destabilizing (Core 1.965) | NA | X | X |
| RPA1 | BER, DSB, NER | P27694 | rs5030755 | A > G | Thr351Ala | 0.10 | no | no | deleterious | NA | Destabilizing (−1.037 Kcal/mol) | X | |
SNP—single nucleotide polymorphism; MAF—minor allele frequency; EUR—European population; LD—linkage disequilibrium; CRC—colorectal cancer; GERP—Genomic Evolutionary Rate Profiling; DSB—double strand break repair pathway; BER—base excision repair pathway; NER—nucleotide excision repair pathway; NA—not applicable; X—evolutionary conserved position. a https://www.ensembl.org/index.html. b Data for SNPs were not available in the Austrian cohort.