Table 1 Nuclear-encoded genetic variation significantly associated with inferred mitochondrial RNA cleavage rates in discovery (CARTaGENE) data and statistics for the same associations in replication (GTEx) data. Variants are linked to genes either through functional (missense) mutations or via eQTL data
From: Identification of human mitochondrial RNA cleavage sites and candidate RNA processing factors
Cleavage Site | Peak nuclear SNP | Chr | Position | Annotation | eQTL | Nearest nuclear gene | CaG beta | CaG P-value | GTEx beta | GTEx P-value |
|---|---|---|---|---|---|---|---|---|---|---|
598 | rs707009 | 3 | 66372144 | Intron/NMD | LIPA, LRIG1, SIRT1, SLC25A26 | SLC25A26 | 0.012 | 9.8E−16 | −0.011 | 2.8E−02 |
598 | rs11156878 | 14 | 35735967 | Missense | NA | MRPP3 | −0.013 | 9.4E−11 | −0.011 | 1.2E−01 |
3246 | rs74422990 | 14 | 35726093 | Intron | MRPP3, PPP2R3C | MRPP3 | −0.036 | 4.3E−28 | −0.028 | 3.7E−04 |
3258 | rs11156878 | 14 | 35735967 | Missense | NA | MRPP3 | −0.010 | 4.3E−18 | −0.004 | 1.5E−01 |
4252 | rs74422990 | 14 | 35726093 | Intron | MRPP3, PPP2R3C | MRPP3 | −0.034 | 1.9E−14 | −0.032 | 4.3E−05 |
4261 | rs11156878 | 14 | 35735967 | Missense | NA | MRPP3 | −0.033 | 2.9E−19 | −0.045 | 5.4E−04 |
4411 | rs74422990 | 14 | 35726093 | Intron | MRPP3, PPP2R3C | MRPP3 | −0.064 | 1.0E−35 | −0.078 | 2.5E−09 |
4438 | rs11156878 | 14 | 35735967 | Missense | NA | MRPP3 | −0.013 | 1.2E−17 | −0.002 | 6.6E−01 |
5511 | rs11156878 | 14 | 35735967 | Missense | NA | MRPP3 | −0.037 | 3.2E−11 | −0.014 | 2.4E−01 |
5911 | rs35681402 | 20 | 3138626 | Intron | ITPA, UBOX5, PROSAPIP1, FASTKD5 | UBOX5/FASTKD5 | −0.050 | 3.5E−60 | −0.058 | 5.1E−07 |
7514 | rs74422990 | 14 | 35726093 | Intron | MRPP3, PPP2R3C | MRPP3 | −0.041 | 7.9E−13 | −0.015 | 3.3E−01 |
7543 | rs7158706 | 14 | 35736692 | Intron | MRPP3 | MRPP3 | −0.022 | 2.2E−17 | −0.033 | 2.0E−03 |
8321 | rs74422990 | 14 | 35726093 | Intron | MRPP3, PPP2R3C | MRPP3 | −0.019 | 5.4E−18 | −0.005 | 5.3E−01 |
9194 | rs75286457 | 20 | 3138134 | Intron | ITPA, UBOX5, PROSAPIP1, FASTKD5 | UBOX5/FASTKD5 | −0.016 | 8.6E−23 | −0.014 | 1.7E−02 |
9205 | rs75286457 | 20 | 3138134 | Intron | ITPA, UBOX5, PROSAPIP1, FASTKD5 | UBOX5/FASTKD5 | −0.031 | 8.0E−17 | −0.043 | 1.7E−03 |
9219 | rs35681402 | 20 | 3138626 | Intron | ITPA, UBOX5, PROSAPIP1, FASTKD5 | UBOX5/FASTKD5 | −0.040 | 6.9E−30 | −0.042 | 1.6E−04 |
9219 | rs113933961 | 7 | 45051924 | Intron | CCM2, RP4-647J21.1, MYO1G, SNHG15, NACAD, TBRG4, H2AFV | CCM2/TBRG4 | −0.023 | 6.5E−10 | 0.012 | 1.7E−01 |
9990 | rs11156878 | 14 | 35735967 | Missense | NA | MRPP3 | −0.037 | 4.2E−11 | −0.015 | 1.4E−01 |
10404 | rs11156878 | 14 | 35735967 | Missense | NA | MRPP3 | −0.039 | 8.1E−11 | −0.030 | 4.1E−03 |
10432 | rs11156878 | 14 | 35735967 | Missense | NA | MRPP3 | −0.039 | 1.2E−24 | −0.006 | 5.4E−01 |
12137 | rs11156878 | 14 | 35735967 | Missense | NA | MRPP3 | −0.033 | 5.0E−11 | −0.020 | 2.4E−02 |
12280 | rs11156878 | 14 | 35735967 | Missense | NA | MRPP3 | −0.019 | 2.5E−16 | −0.015 | 6.2E−02 |
14698 | rs113933961 | 7 | 45051924 | Intron | CCM2, RP4-647J21.1, MYO1G, SNHG15, NACAD, TBRG4, H2AFV | CCM2/TBRG4 | −0.009 | 5.8E−10 | 0.001 | 7.3E−01 |
14716 | rs73109897 | 7 | 45156242 | Upstream gene | CCM2, RP4-647J21.1, MYO1G, SNHG15, NACAD, TBRG4, H2AFV | TBRG4 | −0.013 | 8.9E−14 | −0.007 | 6.5E−02 |
14758 | rs4724362 | 7 | 45161303 | Intergenic | CCM2, RP4-647J21.1, MYO1G, SNHG15, NACAD, TBRG4, H2AFV | TBRG4 | −0.069 | 1.7E−10 | −0.013 | 2.7E−01 |
15968 | rs61988271 | 14 | 35741554 | Intron | MRPP3, SNX6 | MRPP3 | −0.024 | 3.6E−10 | −0.026 | 3.5E−02 |