Common ALDH3A1 Gene Variant Associated with Keratoconus Risk in the Polish Population
Abstract
:1. Introduction
2. Results
2.1. Patient Characteristics
2.2. Sequencing and SNP Calling
3. Discussion
4. Materials and Methods
4.1. Participants and Clinical Data
4.2. Sequencing and SNP Calling
4.3. Statistical Analyses
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
#Uploaded Variation | Location | Consequence | EXON | INTRON | HGVSc | HGVSp | cDNA Position | CDS Position | Protein Position | Amino Acids | Codons | SIFT | PolyPhen | AF | EUR AF | gnomAD AF | gnomAD NFE AF |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
rs56234923 | 17:19744906-19744906 | intron variant | - | 1 | c.162 + 62A > G | - | - | - | - | - | - | - | - | - | - | - | - |
rs59102760 | 17:19743437-19743437 | synonymous variant | 2 | - | c.189G > A | p.Glu63= | 519 | 189 | 63 | E | gaG/gaA | - | - | 0.0116 | 0.0268 | 0.01945 | 0.02135 |
rs887241 | 17:19742625-19742625 | missense variant | 3 | - | c.400T > G | p.Ser134Ala | 730 | 400 | 134 | S/A | Tca/Gca | Tolerated (0.88) | Benign (0) | - | 0.6441 | 0.7057 | 0.6638 |
rs2072328 | 17:19742310-19742310 | intron variant | - | 3 | c.481−98C > T | - | - | - | - | - | - | - | - | 0.0429 | 0.008 | - | - |
rs2072330 | 17:19741159-19741159 | synonymous variant | 5 | - | c.741T > A | p.Pro247= | 1071 | 741 | 247 | P | ccT/ccA | - | - | 0.2907 | 0.3907 | 0.3577 | 0.4023 |
rs3826507 | 17:19740497-19740497 | intron variant | - | 5 | c.808−20C > T | - | - | - | - | - | - | - | - | 0.2941 | 0.3917 | 0.359 | 0.3993 |
rs141568499 | 17:19740476-19740476 | missense variant, splice region variant | 6 | - | c.809A > C | p.Glu270Ala | 1139 | 809 | 270 | E/A | gAg/gCg | Deleterious (0.03) | Benign (0.076) | 0.0004 | 0.001 | 0.004717 | 0.006718 |
rs2228100 | 17:19739639-19739639 | missense variant | 7 | - | c.985C > G | p.Pro329Ala | 1315 | 985 | 329 | P/A | Ccg/Gcg | Tolerated (0.17) | Benign (0) | 0.3800 | 0.2396 | 0.3115 | 0.249 |
rs4646791 | 17:19738956-19738956 | intron variant | - | 8 | c.1216 + 40_1216 + 41insC | - | - | - | - | - | - | - | - | - | 0.4006 | 0.3846 | 0.4093 |
rs57555435 | 17:19738431-19738431 | synonymous variant | 9 | - | c.1239C > T | p.Tyr413= | 1569 | 1239 | 413 | Y | taC/taT | - | - | 0.0369 | 0.0089 | 0.02118 | 0.007902 |
rs1042183 | 17:19738008-19738008 | 3 prime UTR variant | 10 | - | c.*213G > A | - | 1905 | - | - | - | - | - | - | 0.2965 | 0.3917 | - | - |
Exon | Primer F | Primer R |
---|---|---|
promoter region | AAACAGCCCGGGACCTAAT | AGGAATGCAGGGAAGAGGAT |
promoter region | TTTCGTGTATTGGTAGCAGGA | GTCCTGCCCGAGCTGAAG |
1 | CCAGGGAAGTCCCTTCCTAT | CCCAAGTCCTTCCTGAACCT |
2 | ATCACCCTGGCAGCTGAG | ATCCTGGCTTGGCTCCAC |
3 + 4 | AGAGCCTCTGGTGAAGTACCC | CCCCTACCCCCATGTAAGTT |
5 | GTCTGCAAAACGAGATGCAA | CCAAGGGGTCAACACTCACT |
6 | CTGTGTCTGTGCAGCCTTTG | CTGTGCTCTTCAGGGGTCAC |
7 | AGGTGCTTGCACTTTCCATC | CCTGAATTTGCTGGGTGAGT |
8 | ACCTGCTCCTGTCCTTGTG | CCTGAATTTGCTGGGTGAGT |
9 + 10, 3′UTR | ACACCCAACAAGGTGGAGAG | ATGAGAGGCCTTTGCTGGTA |
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rs141568499 | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Group | Genotypes | Alleles | Comparisons * | OR ** | 95%CI | p *** | |||||
AA | AC | CC | A | C | |||||||
Controls | n | 290 | 25 | 2 | 605 | 29 | CC + AC vs. AA | 1.04235 | 0.582431 | 1.865449 | 0.888909 |
% | 91.48 | 7.89 | 0.63 | 95.42 | 4.57 | CC vs. AC + AA | 0.608108 | 0.054832 | 6.744155 | 0.682313 | |
KC patients | n | 237 | 22 | 1 | 496 | 24 | C vs. A | 1.009455 | 0.580235 | 1.756183 | 0.973428 |
% | 91.15 | 8.46 | 0.38 | 95.38 | 4.61 | ||||||
rs2228100 | |||||||||||
Group | Genotypes | Alleles | Comparisons * | OR ** | 95%CI | p *** | |||||
GG | GC | CC | G | C | |||||||
Controls | n | 173 | 123 | 21 | 469 | 165 | CC + GC vs. GG | 1.013938 | 0.729489 | 1.409302 | 0.93433 |
% | 54.57 | 38.8 | 6.62 | 73.97 | 26.03 | CC vs. GC + GG | 1.302921 | 0.699627 | 2.426442 | 0.40317 | |
KC patients | n | 141 | 97 | 22 | 379 | 141 | C vs. G | 1.057472 | 0.813413 | 1.374759 | 0.676369 |
% | 54.23 | 37.31 | 8.46 | 72.88 | 27.12 | ||||||
rs1042183 | |||||||||||
Group | Genotypes | Alleles | Comparisons * | OR ** | 95%CI | p *** | |||||
GG | GA | AA | G | A | |||||||
Controls | n | 116 | 140 | 61 | 372 | 262 | AA + GA vs. GG | 2.055337 | 1.416549 | 2.982186 | 0.00013 |
% | 36.59 | 44.16 | 19.24 | 58.68 | 41.32 | AA vs. GA + GG | 0.76304 | 0.492615 | 1.181917 | 0.224944 | |
KC patients | n | 57 | 163 | 40 | 277 | 243 | A vs. G | 1.24557 | 0.985888 | 1.573652 | 0.065503 |
% | 21.92 | 62.69 | 15.38 | 53.27 | 46.73 |
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Berdyński, M.; Krawczyk, P.; Safranow, K.; Borzemska, B.; Szaflik, J.P.; Nowakowska-Żawrocka, K.; Żekanowski, C.; Giebułtowicz, J. Common ALDH3A1 Gene Variant Associated with Keratoconus Risk in the Polish Population. J. Clin. Med. 2022, 11, 8. https://doi.org/10.3390/jcm11010008
Berdyński M, Krawczyk P, Safranow K, Borzemska B, Szaflik JP, Nowakowska-Żawrocka K, Żekanowski C, Giebułtowicz J. Common ALDH3A1 Gene Variant Associated with Keratoconus Risk in the Polish Population. Journal of Clinical Medicine. 2022; 11(1):8. https://doi.org/10.3390/jcm11010008
Chicago/Turabian StyleBerdyński, Mariusz, Piotr Krawczyk, Krzysztof Safranow, Beata Borzemska, Jacek P. Szaflik, Karolina Nowakowska-Żawrocka, Cezary Żekanowski, and Joanna Giebułtowicz. 2022. "Common ALDH3A1 Gene Variant Associated with Keratoconus Risk in the Polish Population" Journal of Clinical Medicine 11, no. 1: 8. https://doi.org/10.3390/jcm11010008
APA StyleBerdyński, M., Krawczyk, P., Safranow, K., Borzemska, B., Szaflik, J. P., Nowakowska-Żawrocka, K., Żekanowski, C., & Giebułtowicz, J. (2022). Common ALDH3A1 Gene Variant Associated with Keratoconus Risk in the Polish Population. Journal of Clinical Medicine, 11(1), 8. https://doi.org/10.3390/jcm11010008