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.