Table 4. SNPs in or near genes known to cause monogenic syndromes with abnormal magnesium metabolism or near known magnesium transport genes in association with serum magnesium in 15,366 participants from the CHARGE Consortium.
| Gene | # of SNPs† | Lead SNP | CAF | Coded/Other Allele | CHR | Location (base pairs) | Beta (mmol/L)‡ | SE | P | |
| Mendelian Genes | ||||||||||
| CLCNKB | 108 | rs848305 | 0.89 | T/A | 1 | 16316825 | −0.007 | 0.002 | 2.74E-03 | |
| CLDN19 | 62 | rs719676 | 0.76 | A/G | 1 | 43254108 | −0.002 | 0.001 | 5.51E-02 | |
| BSND | 174 | rs9326034 | 0.01 | A/G | 1 | 55530664 | −0.018 | 0.006 | 5.18E-03 | |
| CASR | 261 | rs17251221 | 0.86 | A/G | 3 | 121993247 | −0.004 | 0.001 | 1.31E-03 | |
| CLDN16 | 213 | rs9990270 | 0.42 | C/G | 3 | 190176606 | −0.002 | 9.00E-04 | 2.58E-02 | |
| EGF | 255 | rs11569033 | 0.96 | A/G | 4 | 110905803 | −0.013 | 0.004 | 1.39E-03 | |
| FXYD2 | 165 | rs948100 | 0.09 | G/A | 11 | 117660275 | −0.003 | 0.002 | 3.65E-02 | |
| KCNJ1 | 190 | rs496844 | 0.49 | G/C | 11 | 128650029 | −0.002 | 9.00E-04 | 2.49E-03 | |
| SLC12A1 | 100 | rs17428448 | 0.01 | G/T | 15 | 48551594 | −0.049 | 0.022 | 2.62E-02 | |
| SLC12A3 | 195 | rs8048695 | 0.02 | A/G | 16 | 56910986 | −0.023 | 0.007 | 7.64E-04 | |
| Magnesium Transport Genes § | ||||||||||
| SLC41A1 | 117 | rs17348507 | 0.05 | G/A | 1 | 205814735 | −0.004 | 0.002 | 5.39E-02 | |
| CNNM4 | 42 | rs6746896 | 0.66 | A/G | 2 | 97410949 | −0.004 | 0.001 | 7.01E-05 | |
| CNNM3 | 46 | rs994430 | 0.59 | A/T | 2 | 97439001 | −0.004 | 9.00E-04 | 1.53E-04 | |
| SLC41A3 | 277 | rs7617162 | 0.35 | T/C | 3 | 125755450 | −0.002 | 9.00E-04 | 2.03E-02 | |
| NIPAL1 (NPAL1) | 100 | rs17470528 | 0.83 | T/C | 4 | 48052003 | −0.003 | 0.001 | 1.73E-02 | |
| NIPAL4 (ICHTHYIN) | 124 | rs11134799 | 0.11 | C/T | 5 | 156958290 | −0.003 | 0.001 | 5.68E-02 | |
| BTBD9 | 536 | rs4714146 | 0.91 | G/A | 6 | 38287910 | −0.006 | 0.002 | 5.00E-04 | |
| ZDHHC13 | 228 | rs7116312 | 0.27 | G/A | 7 | 19079292 | −0.004 | 0.001 | 5.31E-04 | |
| TUSC3 | 557 | rs12681567 | 0.10 | A/C | 8 | 15657603 | −0.003 | 0.002 | 2.35E-02 | |
| CNNM1 | 211 | rs2490281 | 0.97 | G/C | 10 | 101192482 | −0.006 | 0.003 | 3.92E-02 | |
| CNNM2 | 222 | rs3740393 | 0.86 | G/C | 10 | 104636655 | −0.006 | 0.001 | 8.58E-07 | |
| ZDHHC17 | 170 | rs11115332 | 0.96 | C/G | 12 | 77171192 | −0.004 | 0.002 | 8.65E-02 | |
| SLC41A2 | 197 | rs2463021 | 0.88 | A/T | 12 | 105168431 | −0.003 | 0.002 | 3.99E-02 | |
| NIPA1 | 123 | rs4778439 | 0.95 | G/A | 15 | 23002053 | −0.005 | 0.002 | 3.23E-02 | |
| NIPA2 | 147 | rs4778439 | 0.95 | G/A | 15 | 23002053 | −0.005 | 0.002 | 3.23E-02 | |
| TRPM7 | 177 | rs2163098 | 0.03 | G/C | 15 | 50906498 | −0.005 | 0.003 | 6.01E-02 | |
CAF, coded allele frequency; SE, standard error; SNPs, single nucleotide polymorphisms.
SNP locations are based on the provisional NCBI Build 37.1.
†: Within 60 kb of the gene.
‡: Adjusted for age, sex, and study center (if applicable); the association reported is for the magnesium-lowering allele and p-values are adjusted for genomic control. Proportion of variance in serum magnesium levels explained by the listed SNPs ranged from 0.11% by rs17251221 to <0.001.
§: MAGT1 and MMGT1were not investigated because of their localization on the X chromosome.