MITOMAP: mtDNA Coding Region & RNA Sequence Variants (Blacklist)

_Last Edited: , _

The GB frequency data is derived from 2200 GenBank sequences with size greater than 15.4kbp and 71091 Control Region sequences with size 0.4-1.6kbp. These sequences have been pre-loaded into Mitomaster and represent almost all haplogroups known to date. We will be updating and refining this set of sequences on a regular basis. As a caveat, please note that GenBank sequences may not be of equal quality (Yao, et al, 2009), that some of these sequences are from individuals with past, current or future disease, and that this portion of our data set has not been hand-curated by Mitomap.

For more details about the current GenBank sequence set, please see http://www.mitomap.org/MITOMAP/GBFreqInfo

Locus Nucleotide Position Nucleotide Change Codon number Codon Position Amino Acid Change GB frequency Curated References
592 MT-TF C-A - - tRNA 1 1
829 MT-RNR1 C-CC - - rRNA 1 1
941 MT-RNR1 G-A - - rRNA 1 1
996 MT-RNR1 A-G - - rRNA 1 1
1149 MT-RNR1 G-A - - rRNA 1 1
1345 MT-RNR1 G-A - - rRNA 1 1
1374 MT-RNR1 A-G - - rRNA 1 1
1535 MT-RNR1 T-del - - rRNA 1 1
1569 MT-RNR1 G-A - - rRNA 1 1
1664 MT-TV G-C - - tRNA 1 1
1778 MT-RNR2 T-C - - rRNA 1 1
1798 MT-RNR2 A-G - - rRNA 1 1
1868 MT-RNR2 G-T - - rRNA 1 1
2040 MT-RNR2 G-A - - rRNA 1 1
2116 MT-RNR2 C-T - - rRNA 1 1
2160 MT-RNR2 A-T - - rRNA 1 1
2235 MT-RNR2 C-T - - rRNA 1 1
2300 MT-RNR2 G-A - - rRNA 1 1
2463 MT-RNR2 A-AA - - rRNA 1 1
2501 MT-RNR2 C-T - - rRNA 1 1
2630 MT-RNR2 T-C - - rRNA 1 1
2832 MT-RNR2 A-del - - rRNA 1 1
2832 MT-RNR2 A-G - - rRNA 1 1
2940 MT-RNR2 A-del - - rRNA 1 1
3097 MT-RNR2 T-C - - rRNA 1 1
3290 MT-TL1 T-G - - tRNA 1 1
3359 MT-ND1 C-T 18 2 non-syn:A-V 5 1
3392 MT-ND1 G-A 29 2 non-syn:G-D 1 1
3473 MT-ND1 T-C 56 2 non-syn:F-S 1 1
3571 MT-ND1 C-CC 89 1 frameshift 8 1
3892 MT-ND1 A-T 196 1 non-syn:T-S 1 1
3920 MT-ND1 C-T 205 2 non-syn:S-F 1 1
3949 MT-ND1 T-C 215 1 non-syn:Y-H 1 1
4036 MT-ND1 G-A 244 1 non-syn:G-TERM 2 1
4053 MT-ND1 A-C 249 3 syn:A-A 2 1
4110 MT-ND1 C-T 268 3 syn:S-S 2 1
4134 MT-ND1 A-G 276 3 syn:A-A 1 1
4138 MT-ND1 C-T 278 1 non-syn:P-S 1 1
4148 MT-ND1 G-A 281 2 non-syn:R-H 1 1
4159 MT-ND1 C-T 285 1 non-syn:L-F 1 1
4168 MT-ND1 C-T 288 1 non-syn:L-F 1 1
4222 MT-ND1 T-C 306 1 non-syn:S-P 1 1
4276 MT-TI A-G - - tRNA 1 1
4309 MT-TI G-A - - tRNA 1 1
4313 MT-TI T-del - - tRNA 3 1
4410 MT-TM C-T - - tRNA 1 1
4431 MT-TM C-T - - tRNA 1 1
4515 MT-ND2 G-A 16 1 non-syn:G-S 1 1
4560 MT-ND2 G-C 31 1 non-syn:V-L 1 1
4576 MT-ND2 A-G 36 2 non-syn:N-S 1 1
4650 MT-ND2 C-T 61 1 non-syn:L-F 1 1
4720 MT-ND2 G-A 84 2 non-syn:W-Term 1 1
4724 MT-ND2 C-T 85 3 syn:T-T 1 1
4753 MT-ND2 C-T 95 2 non-syn:S-L 1 1
4795 MT-ND2 C-T 109 2 non-syn:A-V 1 1
4831 MT-ND2 G-A 121 2 non-syn:G-D 1 1
4891 MT-ND2 T-C 141 2 non-syn:I-T 1 1
4946 MT-ND2 C-A 159 3 non-syn:I-M 1 1
4953 MT-ND2 A-G 162 1 non-syn:I-V 1 1
4971 MT-ND2 G-A 168 1 non-syn:G-S 1 1
4975 MT-ND2 G-A 169 2 non-syn:G-E 1 1
4996 MT-ND2 G-A 176 2 non-syn:R-H 1 1
5041 MT-ND2 T-C 191 2 non-syn:M-T 3 1
5106 MT-ND2 A-G 213 1 non-syn:T-A 1 1
5149 MT-ND2 C-T 227 2 non-syn:T-I 1 1
5185 MT-ND2 G-A 239 2 non-syn:W-Term 1 1
5236 MT-ND2 C-T 256 2 non-syn:P-L 1 1
5303 MT-ND2 C-G 278 3 non-syn:I-M 1 1
5309 MT-ND2 C-T 280 3 syn:T-T 1 1
5623 MT-TA G-A - - tRNA 1 1
5642 MT-TA T-TT - - tRNA 1 1
5668 MT-TN G-A - - tRNA 1 1
5713 MT-TN C-T - - tRNA 1 1
5746 MT-OLR G-GG - - non-coding 3 1
5780 MT-OLR G-C - - tRNA 1 1
5780 MT-TC G-C - - tRNA 1 1
6206 MT-CO1 C-T 101 3 syn:S-S 1 1
6283 MT-CO1 C-T 127 2 non-syn:T-M 1 1
6419 MT-CO1 A-C 172 3 non-syn:K-N 1 1
6457 MT-CO1 T-C 185 2 non-syn:V-A 1 1
6600 MT-CO1 C-T 233 1 non-syn:H-Y 1 1
6712 MT-CO1 A-G 270 2 non-syn:Y-C 1 1
6714 MT-CO1 A-C 271 1 non-syn:M-L 1 1
6820 MT-CO1 C-T 306 2 non-syn:T-I 1 1
6847 MT-CO1 C-T 315 2 non-syn:P-L 1 1
7060 MT-CO1 T-C 386 2 non-syn:V-A 1 1
7190 MT-CO1 C-T 429 3 syn:H-H 1 1
7297 MT-CO1 T-G 465 2 non-syn:V-G 1 1
7316 MT-CO1 G-C 471 3 non-syn:M-I 2 1
7441 MT-CO1 C-A 513 2 non-syn:S-Y 1 1
7441 MT-CO1 C-T 513 2 non-syn:S-F 1 1
7487 MT-TS1 C-T - - tRNA 1 1
7569 MT-TD A-del - - tRNA 1 1
7592 MT-CO2 C-T 3 1 non-syn:H-Y 1 1
7721 MT-CO2 C-T 46 1 non-syn:L-F 1 1
7758 MT-CO2 C-T 58 2 non-syn:A-V 1 1
7965 MT-CO2 T-C 127 2 non-syn:F-S 1 1
8276 MT-NC7 C-T - - non-coding 2 1
8596 MT-ATP6 A-T 24 1 non-syn:I-F 1 1
8598 MT-ATP6 T-A 24 3 non-syn:I-M 1 1
8601 MT-ATP6 A-T 25 3 syn:L-L 1 1
8602 MT-ATP6 T-A 26 1 non-syn:F-I 1 1
8608 MT-ATP6 CC-del 28 1 frameshift 1 1
8621 MT-ATP6 C-T 32 2 non-syn:P-L 1 1
8622 MT-ATP6 C-A 32 3 syn:P-P 1 1
8694 MT-ATP6 A-G 56 3 syn:Q-Q 1 1
8697 MT-ATP6 G-C 57 3 non-syn:M-I 1 1
8840 MT-ATP6 C-T 105 2 non-syn:A-V 2 1
8873 MT-ATP6 G-A 116 2 non-syn:G-D 1 1
8916 MT-ATP6 A-G 130 3 syn:P-P 2 1
8918 MT-ATP6 A-G 131 2 non-syn:Q-R 1 1
8926 MT-ATP6 C-T 134 1 non-syn:P-S 1 1
8943 MT-ATP6 C-G 139 3 syn:P-P 1 1
9001 MT-ATP6 C-T 159 1 non-syn:R-C 1 1
9215 MT-CO3 C-T 3 3 syn:H-H 1 1
9216 MT-CO3 C-T 4 1 non-syn:Q-TERM 1 1
9264 MT-CO3 G-A 20 1 non-syn:G-TERM 1 1
9341 MT-CO3 A-G 45 3 syn:L-L 1 1
9350 MT-CO3 A-C 48 3 syn:L-L 1 1
9388 MT-CO3 T-C 61 2 non-syn:V-A 1 1
9434 MT-CO3 A-G 76 3 syn:Q-Q 1 1
9437 MT-CO3 A-G 77 3 syn:K-K 2 1
9477 MT-CO3 G-del 91 1 frameshift 1 1
9478 MT-CO3 T-A 91 2 non-syn:V-D 1 1
9524 MT-CO3 A-T 106 3 syn:L-L 1 1
9550 MT-CO3 A-C 115 2 non-syn:H-P 1 1
9660 MT-CO3 A-T 152 1 non-syn:M-L 1 1
9964 MT-CO3 A-G 253 2 non-syn:Y-C 1 1
10116 MT-ND3 AT-del 20 1 frameshift 1 1
10187 MT-ND3 T-G 43 3 syn:P-P 2 1
10377 MT-ND3 C-T 107 1 syn:L-L 1 1
10416 MT-TR T-C - - tRNA 1 1
10554 MT-ND4L T-C 29 1 non-syn:S-P 1 1
10573 MT-ND4L G-A 35 2 non-syn:G-E 1 1
10657 MT-ND4L T-G 63 2 non-syn:M-Term 1 1
10658 MT-ND4L A-T 63 3 non-syn:M-I 1 1
10684 MT-ND4L C-G 72 2 non-syn:A-G 1 1
10706 MT-ND4L C-T 79 3 syn:V-V 1 1
10768 MT-ND4 A-T 3 3 non-syn:K-N 1 1
10937 MT-ND4 C-T 60 1 non-syn:P-S 1 1
10952 MT-ND4 C-CC 65 1 frameshift 1 1
10977 MT-ND4 T-A 73 2 non-syn:L-Q 1 1
11032 MT-ND4 A-del 91 3 frameshift 7 1
11084 MT-ND4 AC-del 109 1 frameshift 1 1
11090 MT-ND4 A-C 111 1 non-syn:T-P 1 1
11177 MT-ND4 C-A 140 1 non-syn:P-T 1 1
11186 MT-ND4 C-T 143 1 syn:L-L 1 1
11195 MT-ND4 G-A 146 1 non-syn:G-S 1 1
11209 MT-ND4 A-G 150 3 syn:L-L 1 1
11403 MT-ND4 G-A 215 2 non-syn:W-Term 1 1
11475 MT-ND4 G-A 239 2 non-syn:G-D 1 1
11544 MT-ND4 T-C 262 2 non-syn:L-P 1 1
11602 MT-ND4 C-T 281 3 syn:D-D 1 1
11613 MT-ND4 T-C 285 2 non-syn:L-P 1 1
11889 MT-ND4 G-A 377 2 non-syn:G-E 1 1
11911 MT-ND4 C-T 384 3 syn:T-T 2 1
11935 MT-ND4 T-G 392 3 syn:T-T 1 1
11995 MT-ND4 C-G 412 3 syn:T-T 2 1
12010 MT-ND4 C-T 417 3 syn:G-G 2 1
12042 MT-ND4 C-T 428 2 non-syn:P-L 1 1
12056 MT-ND4 G-A 433 1 non-syn:E-K 1 1
12098 MT-ND4 C-G 447 1 non-syn:L-V 1 1
12105 MT-ND4 T-C 449 2 non-syn:L-P 1 1
12242 MT-TS2 A-C - - tRNA 1 1
12508 MT-ND5 G-A 58 1 non-syn:D-N 1 1
12555 MT-ND5 A-G 73 3 syn:T-T 3 1
12576 MT-ND5 C-T 80 3 syn:F-F 1 1
12594 MT-ND5 C-T 86 3 syn:S-S 1 1
12601 MT-ND5 T-C 89 1 non-syn:F-L 1 1
12731 MT-ND5 T-C 132 2 non-syn:V-A 1 1
12797 MT-ND5 T-C 154 2 non-syn:L-P 1 1
12875 MT-ND5 T-C 180 2 non-syn:I-T 1 1
13136 MT-ND5 C-T 267 2 non-syn:A-V 1 1
13166 MT-ND5 C-T 277 2 non-syn:T-M 1 1
13235 MT-ND5 A-AT 300 2 frameshift 1 1
13271 MT-ND5 T-C 312 2 non-syn:L-P 1 1
13302 MT-ND5 A-G 322 3 syn:P-P 1 1
13349 MT-ND5 T-C 338 2 non-syn:M-T 1 1
13374 MT-ND5 C-T 346 3 syn:I-I 1 1
13490 MT-ND5 T-A 385 2 non-syn:F-Y 1 1
13579 MT-ND5 G-A 415 1 non-syn:A-T 1 1
13745 MT-ND5 A-G 470 2 non-syn:N-S 4 1
13915 MT-ND5 G-A 527 1 non-syn:G-TERM 1 1
14046 MT-ND5 A-G 570 3 syn:Q-Q 1 1
14191 MT-ND6 A-T 161 3 non-syn:F-L 1 1
14339 MT-ND6 A-G 112 2 non-syn:V-A 3 1
14491 MT-ND6 C-T 61 3 syn:G-G 12 1
14513 MT-ND6 A-G 54 2 non-syn:M-T 1 1
14607 MT-ND6 G-A 23 1 non-syn:P-S 1 1
14623 MT-ND6 C-CC 17 3 frameshift 1 1
14656 MT-ND6 A-G 6 3 syn:F-F 1 1
14767 MT-CYB T-A 7 3 syn:T-T 1 1
14792 MT-CYB C-G 16 1 non-syn:H-D 1 1
14859 MT-CYB G-T 38 2 non-syn:G-V 1 1
14931 MT-CYB C-T 62 2 non-syn:A-V 1 1
14947 MT-CYB C-A 67 3 syn:A-A 1 1
14950 MT-CYB C-G 68 3 non-syn:H-Q 1 1
15390 MT-CYB C-G 215 2 non-syn:S-C 1 1
15469 MT-CYB A-G 241 3 syn:T-T 3 1
15557 MT-CYB G-A 271 1 non-syn:E-K 1 1
15692 MT-CYB ATA-del 316 1 frameshift 2 1
15813 MT-CYB T-G 356 2 non-syn:V-G 2 1
15843 MT-CYB T-C 366 2 non-syn:M-T 1 1
15898 MT-TT T-C - - tRNA 1 1
15943 MT-TT T-G - - tRNA 1 1
15961 MT-TP G-A - - tRNA 1 1


Footnotes:

The GB frequency data is derived from 47412 GenBank sequences with size greater than 15.4kbp and 71091 Control Region sequences with size 0.4-1.6kbp. These sequences have been pre-loaded into Mitomaster and represent almost all haplogroups known to date. We will be updating and refining this set of sequences on a regular basis. As a caveat, please note that GenBank sequences may not be of equal quality (Yao, et al, 2009), that some of these sequences are from individuals with past, current or future disease, and that this portion of our data set has not been hand-curated by Mitomap.

For more details about the current GenBank sequence set, please see http://www.mitomap.org/MITOMAP/GBFreqInfo Polymorphic sequence variants identified from mtDNA sequence analysis. Nucleotide changes are indicated as L-strand substitutions. "MT-NC" indicates non-coding locus; "syn" = synonymous mutation.

For the corrections made in 1999 by Andrews et al to the original Cambridge sequence, please see this summary table. Due to rare polymorphisms in the reference sequence, some “variants” are present at more than 80% frequency in one or more of the three major mtDNA lineages. To see a listing of these common variants, please see Mitomap’s tabulation of the most prevalent mtDNA variants along with its companion table of top level phylogenetic branch markers.

Some variants listed in this table might also be found in the disease-associated mtDNA variants table if subsequent publications have reported a possible association with pathogenicity. However, no variants with a ‘Cfrm’ pathogenicity status are included in this table of general variants.
Topic revision: r13 - 08 Mar 2019, ShipingZhang

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