Legend of the output


    General info

  1. Chr: Genomic coordinate according to the Revised Cambridge Reference Sequence; Ncbi accession number: NC_012920.1
  2. Start: Genomic start position for the variant
  3. End: Genomic end position for the variant
  4. Ref: Reference nucleotide, as of the Revised Cambridge Reference Sequence; Ncbi accession number: NC_012920.1
  5. Alt: Alternative nucleotide
  6. MitImpact id: MitImpact database identifier for the variant
  7. Gene symbol: Official gene symbol
  8. OXPHOS complex: Respiratory Chain Complex which the mitochondrial protein belongs to
  9. Ensembl gene id: Accession number in Ensembl Gene
  10. Ensembl protein id: Accession number in Ensembl Protein
  11. Ensembl transcript id: Accession number in Ensembl transcript
  12. Uniprot name: Gene symbol in Uniprot
  13. Uniprot id: Protein accession number in Uniprot
  14. NCBI gene id: Gene identifier from Ncbi (PMID:21115458)<
  15. NCBI protein id: Protein accession number for NCBI Gene Database
  16. Gene position: Variant position relative to the coordinate of the gene
  17. AA position: Amino acid position
  18. AA ref: Reference amino acid
  19. AA alt: Alternative amino acid
  20. Codon substitution: Codon substitution corresponding to the nucleotide change

  21. Conservation

  22. PhyloP 100V: PhyloP conservation index, from UCSC Table Browser 2015. See Pollard et at. 2010 for details.
  23. PhastCons 100V: PhastCons conservation index, from UCSC Table Browser 2015. See Pollard et at. 2010 for details.
  24. SiteVar: SiteVar conservation index, from Hmtdb 2014

  25. Pathogenicity predictors

  26. PolyPhen2: Categorical prediction for PolyPhen ver. 2.2.2 (HumDiv dataset). See Adzhubei et al. 2013 for details
  27. PolyPhen2 score: Score for PolyPhen ver. 2.2.2 (HumDiv dataset). See Adzhubei et al. 2013 for details
  28. SIFT: Categorical prediction for SIFT ver. 5.0.3. See Ng and Henikoff 2003 for details
  29. SIFT score: Score for SIFT ver. 5.0.3. See Ng and Henikoff 2003 for details
  30. FatHmm: Categorical prediction for FatHmm ver. 2.2 (unweighted version). See Shihab et al. 2013 for details.
  31. FatHmm score: Score for FatHmm ver. 2.2 (unweighted version). See Shihab et al. 2013 for details.
  32. FatHmmW: Categorical prediction for FatHmm ver. 2.3 (weighted version)
  33. FatHmmW score: Score for FatHmm ver. 2.3 (weighted version)
  34. PROVEAN: Categorical prediction for PROVEAN ver. 1.3. See Choi et al. 2012 for details
  35. PROVEAN score: Score for PROVEAN ver. 1.3. See Choi et al. 2012 for details
  36. MutationAssessor: Categorical prediction for MutationAssessor ver. 2.0. See Reva et al. 2011 for details
  37. MutationAssessor score: Score for MutationAssessor ver. 2.0. See Reva et al. 2011 for details
  38. EFIN SP: Categorical prediction for EFIN SP (trained with SwissProt dataset). See Zheng et al. 2014 for details
  39. EFIN SP score: Score for EFIN SP
  40. EFIN HD: Categorical prediction for EFIN HD (trained with HumDiv dataset)
  41. EFIN HD score: Score for EFIN HD
  42. MutationTaster: Categorical prediction (disease_causing, disease_causing_automatic, polymorphism) (PMID: 24681721)
  43. MutationTaster score: Confidence score for the prediction.
  44. CADD: Categorical prediction for CADD ver. 1.2
  45. CADD score: Score for CADD ver. 1.2. See Kircher et al. 2014 for details
  46. CADD phred: Phred-scaled score for CADD ver. 1.2
  47. VEST pvalue: Score-associated p-value (as computed by CRAVAT ver. 3.2). See Carter et al. 2013 for details
  48. VEST FDR: Score-associated False Discovery Rate
  49. PANTHER: Categorical prediction for PANTHER
  50. PANTHER score: Score (Thomas et al. 2003) as computed by the Meta-SNP tool (Capriotti et al. 2013)
  51. PhD-SNP: Categorical prediction for PhD-SNP
  52. PhD-SNP score: Score for PhD-SNP (Capriotti et al. 2006) as computed by the Meta-SNP tool (Capriotti et al. 2013)
  53. SNAP: Categorical prediction for SNAP
  54. SNAP score: Score for SNAP (Bromberg and Rost 2007) as computed by the Meta-SNP tool (Capriotti et al. 2013)
  55. SNPDryad score: Higher scores associate to more pathogenic variants (read the publication)
  56. Mitoclass.1: Categorical prediction (neutral, damaging) of the SVM classifier. See Martin-Navarro et al. 2017 for details

  57. Pathogenicity meta-predictors

  58. Meta-SNP: Categorical prediction for
  59. Meta-SNP score: Consensus score for Meta-SNP (Capriotti et al. 2013)
  60. Meta-SNP RI: Meta-SNP score Reliability Index
  61. CAROL: Categorical prediction for CAROL consensus method. See Lopes et al. 2012 for details
  62. CAROL score: Score for CAROL consensus method
  63. Condel: Categorical prediction for Condel consensus method. See González-Pérez and López-Bigas 2011 for details
  64. Condel score: Score for Condel consensus method
  65. COVEC WMV: Categorical prediction for COVEC ver. 0.4 Weighted Majority Rule consensus method
  66. COVEC WMV score: Score for COVEC ver. 0.4 Weighted Majority Rule consensus method. See Frousios et al. 2013 for details
  67. MtoolBox: Categorical prediction for MtoolBox consensus method
  68. MtoolBox DS: Disease score for MtoolBox consensus method. See Santorsola et al. 2016 for details
  69. APOGEE bootstrap consensus: Consensus assessment of all categorical predictions obtained during the bootstrap loop (July 2015 release)
  70. APOGEE bootstrap mean probability (mp): Mean probability of being harmful over all bootstrap runs (July 2015 release)
  71. DEOGEN: DEOGEN functional score (see http://deogen2.mutaframe.com/ for details).

  72. Cancer-specific predictors

  73. PolyPhen2 transf: Transformed PolyPhen2 categorical prediction by TransFIC ver. 1.0. See González-Pérez et al. 2013 for details
  74. PolyPhen2 transf score: Transformed PolyPhen2 score
  75. SIFT transf: Transformed SIFT categorical prediction by TransFIC ver. 1.0. See González-Pérez et al. 2013 for details
  76. SIFT transf score: Transformed SIFT score
  77. MutationAssessor transf: Transformed MutationAssessor categorical prediction by TransFIC ver. 1.0. See González-Pérez et al. 2013 for details
  78. MutationAssessor transf score: Transformed MutationAssessor score
  79. CHASM pvalue: CHASM score associated p-value (CRAVAT ver. 3.2). See Carter et al. 2009 for details
  80. CHASM FDR: CHASM score-associated False Discovery Rate

  81. Residue interaction

  82. MISTIC coevo sites: Proportion of significant coevolving sites for each amino acid site. Mutual information (MI) scores by MISTIC tool. See Simonetti et al. 2013 for details
  83. MISTIC mean MI score: Mean Mutual Information (MI) score for the amino acid site. See Simonetti et al. 2013 for details
  84. EV Mutation Variant A: Protein variant (“protein_residueNumber_referenceAminoacid”) A of EVmutation precomputed coupling scores. See https://marks.hms.harvard.edu/evmutation/downloads.html.
  85. EV Mutation Variant B: Protein variant (“protein_residueNumber_referenceAminoacid”) B of EVmutation precomputed coupling scores.
  86. EV Mutation Score: precomputed coupling score for Variant A – Variant B couple. Downloaded from “Evolutionary couplings (.csv)” dataset.
  87. Site A-B InterP: Inter-protein covariation analysis between "Site A" and "Site B" residues (in the form of "GeneSymbol_residueNumber"). The covariation score for each site couple is expressed as "method:value".
  88. Site A-B IntraP: Intra-protein covariation analysis between "Site A" and "Site B" residues (in the form of "GeneSymbol_residueNumber"). The covariation score for each site couple is expressed as "method:value".
  89. ΔΔG intra: Free energy change of folding (ΔΔG, Kcal/mol) due to a mutation. See Schymkowitz et al., 2005 for details. ( 1. ΔΔG for both sites combined; 2. ΔΔG for first coevolving site; 3. ΔΔG for second coevolving site).
  90. ΔΔG intra interface: ΔΔG of interaction energy upon mutation calculated for interfaces with one member of the complex carrying both mutations. (1. ΔΔGbind for both coevolving sites; 2. ΔΔGbind for first coevolving site in first protein; 2. ΔΔGbind for second coevolving site in the same protein).
  91. ΔΔG inter: Interaction energy change (ΔΔGbind, Kcal/mol) used to quantify the magnitude of mutational effects on protein–protein interactions and calculated through comparison of wild-type and mutant ΔΔG. See Schymkowitz et al., 2005 for details. (1. ΔΔGbind for coevolving sites in both proteins forming complex; 2. ΔΔGbind for first coevolving site in first protein; 3. ΔΔGbind for second coevolving site in second protein)

  92. Frequency & Phenotype DBs

  93. ClinVar June2018 ClinSig: Variant's clinical significance, June 2018
  94. ClinVar June2018 ClnDBN: Variant’s associated disease name, June 2018
  95. ClinVar June2018 ClnAllele id: Variant allele, June 2018
  96. ClinVar June2018 ClnDSDB: Variant disease database name, June 2018
  97. Mitomap Allele: Allele description for variants reported in Mitomap Database (accessed at July 2017, https://www.mitomap.org//foswiki/bin/view/MITOMAP/MutationsCodingControl)
  98. Mitomap Phenotype: Phenotypes associated to the Mitomap variant
  99. Mitomap Homo: '+' indicates that the variant was found in homoplasmy
  100. Mitomap Het: '-' indicates that the variant was found in heteroplasmy
  101. Mitomap Status: Status of the Mitomap reported variants (see https://www.mitomap.org//foswiki/bin/view/MITOMAP/MutationsCodingControl for details)
  102. Mitomap NRef: Number of public references reporting a phenotype association
  103. Mitomap Dec2016 somatic occurrence: Cancer-associated variant according to MITOMAP (accessed on December 2016)
  104. COSMIC 87: COSMIC ver. 87 accession number if this is a cancer-associated variant
  105. Classification Clinvar: Clinical significance according to ClinVar (“N” for neutral, “P” for pathogenic, “.” for unobserved mutations)
  106. Classification Mitomap: Clinical significance according to Mitomap (“N” for neutral, “P” for pathogenic, “.” for unobserved mutations)
  107. Classification Global: Clinical significance according to ClinVar and Mitomap (“N” for neutral, “P” for pathogenic, “.” for unobserved mutations. “N,P” and “P,N” are used with discordant assessments)
  108. dbSNP id: dbSNP accession number, ver. 151

  109. Pathogenic variants, CPD

  110. CPD candidate: Marked with 'CPD' if a human amino acid variant can be considered as a reliable “Compensated Pathogenic Deviations”. See Jordan et al.2015 (PMID:26123021), Azevedo et al. 2017 (PMID:27703146) for details
  111. CPD frequency: Proportion of aligned orthologous sequences that carries a specific human pathogenic variant (homologous amino acid substitution). The total number of aligned orthologous sequences from mammalian reference mitochondrial genomes was 673 (for CYB, ND6), 674 (ND1, ND2, CO1, CO3), and 675 (all remaining genes) Sequences were downloaded from https://www.ncbi.nlm.nih.gov/genome/, October 2014). Frequencies have been calculated for all raw “CPDs” (column 85 represents a subset)
  112. CPD AA Ref: Indicates the reference amino acid for the CPD (‘Compensated Pathogenic Deviation’) mutation; reference: human protein sequence.
  113. CPD AA Alt: The alternate amino acid found in that position (“CPD – aln pos”), within non-human species (see “CPD – species name”, “CPD – RefSeq Protein ID”, “CPD – Ncbi Taxon ID”).
  114. CPD aln pos: Indicates the position of the CPD within the alignment of protein orthologous sequences.
  115. CPD RefSeq ProteinID: NCBI RefSeq Protein identifier for the protein.
  116. CPD Species name: Scientific species name associated to mutant protein (“CPD – aa alt”).
  117. CPD NCBI Taxon ID: Associated NCBI Taxonomy identifier for the species.