Info for variant 3890G>A
MITOMAP: Reported Mitochondrial DNA Base Substitution Diseases: Coding and Control Region Variants
in 52633 FL Seqs
in 195983 seqs
|Disease Reports||Mitomap Status|
Encephalomyopathy / Leigh
Syndrome / Optic Atrophy
We have standardized our variant notation to follow the 3' rule of HGVS (see their statement below). For your reference, we also show previously reported alternative notations in red.
Quote from HGVS: "For deletions, duplications and insertions the most 3' position possible is arbitrarily assigned to have been changed. This rule also applies to variants in single residue stretches (mono-nucleotide or amino acid) or tandem repeats."
‡ Mitomap Frequency and High Frequency Haplogroup Flags:
The current haplogroup lineage distribution of Mitomap's 51836 sequences is N: 67%; L: 12%; M: 21%.
Variants found in haplogroups at 50% or higher are marked with . You may click a flagged link to see the high-scoring haplogroups. For detailed info about the high frequency haplogroup flag, please check the calculation criteria.
‡‡ gnomAD v3.1 Frequency:
The current haplogroup lineage distribution of gnomAD's 56434 sequences is N: 70%; L: 25%; M: 5%.
‡‡‡ Helix Frequency:
The current haplogroup lineage distribution of Helix's 195893 sequences is N: 91%; L+M: 9%.
♦ Amino Acid Change:
Amino acid changes for variants in protein genes are predicted according to the human mitochondrial genetic code.†† TOOLS:
If available, data in this column are from the tools MitoTIP, HmtVar and/or APOGEE.
|APOGEE Consensus||APOGEE Scoring||Mitomap Notation|
Full Length (FL) sequences are classified into three subsets: aDNA for ancient DNA, CancerCL for cancer, tumor, other abnormal tissues, or cell line studies, and Main for the rest. The total variant count is broken out into these three subsets in this column and shown in the format of Total: Main/aDNA/CancerCL (+CR seqs, if any). Clicking on the count link in the GB Sequences column will display a table with all sequence IDs and haplotypes. Each sequence has a further link to full SNP details provided by Mitomaster.
The current sequence counts are from two sets of human mitochondrial sequences collected from GenBank on Jul 15, 2021. These sets consist of:
All sequences are pre-loaded into Mitomaster and represent almost all haplogroups known to date. We update and refine 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, including haplogroup distribution with sequences and variants for each group, please see GenBank Frequency Info.
For the corrections made in 1999 by Andrews et al to the original Cambridge sequence, 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.
All nucleotide changes are reported as L-strand substitutions.
Variants reported in patients, but not assigned a "Cfrm" status of pathogenicity by Mitomap, may possibly be included in both the disease variants and general variants tables. Once Mitomap assigns a "Cfrm" status of pathogenicity to a variant, that variant will only be listed in the disease table.