14495 (A > G)

General info

Chr
chrM
Start
14495
End
14495
Ref
A
Alt
G
Mitimpact ID
MI.23813
Gene symbol
MT-ND6
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
179
AA pos
60
AA ref
L
AA alt
S
Codon substitution
tTa/tCa
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Conservation

PhyloP 100v
-4.86 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
FatHmm
Deleterious Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Deleterious Score and details of the predictor
Mutation Assessor
High impact Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
.
CADD
Deleterious Score and details of the predictor
SNAP
Disease Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor

Pathogenicity meta-predictors

APOGEE
Pathogenic Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
Meta SNP
Disease Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Deleterious Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar March2020 ClinSig
Pathogenic
ClinVar March2020 ClnDBN
Leber's optic atrophy
ClinVar March2020 ClnAllele ID
24730
ClinVar March2020 ClnDSDB
Human phenotype ontology:hp:0001112, medgen:c0917796, omim:535000, orphanet:orpha104, snomed ct:58610003
MITOMAP Allele
MITOMAP Phenotype
Lhon
MITOMAP Homoplasmy
-
MITOMAP Heteroplasmy
+
MITOMAP Status
Cfrm
MITOMAP NRef
8
COSMIC 90
.
dbSNP 153

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

14495 (A > C)

General info

Chr
chrM
Start
14495
End
14495
Ref
A
Alt
C
Mitimpact ID
MI.23812
Gene symbol
MT-ND6
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
179
AA pos
60
AA ref
L
AA alt
W
Codon substitution
tTa/tGa
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-4.86 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
FatHmm
Deleterious Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Deleterious Score and details of the predictor
Mutation Assessor
High impact Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
.
CADD
Deleterious Score and details of the predictor
SNAP
Disease Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor

Pathogenicity meta-predictors

APOGEE
Neutral Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
Meta SNP
Disease Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Deleterious Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
High impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar March2020 ClinSig
.
ClinVar March2020 ClnDBN
.
ClinVar March2020 ClnAllele ID
.
ClinVar March2020 ClnDSDB
.
MITOMAP Allele
.
MITOMAP Phenotype
.
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
.
MITOMAP NRef
.
COSMIC 90
.
dbSNP 153

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.
~ 14495 (A/G) 14495 (A/C)
~ 14495 (tTa/tCa) 14495 (tTa/tGa)
Chr chrM chrM
Start 14495 14495
End 14495 14495
Ref A A
Alt G C
MitImpact id MI.23813 MI.23812
Gene symbol MT-ND6 MT-ND6
Respiratory Chain complex I I
Ensembl gene id ENSG00000198695 ENSG00000198695
Ensembl protein id ENSP00000354665 ENSP00000354665
Ensembl transcript id ENST00000361681 ENST00000361681
Uniprot name NU6M_HUMAN NU6M_HUMAN
Uniprot id P03923 P03923
Ncbi gene id 4541 4541
Ncbi protein id YP_003024037.1 YP_003024037.1
Gene position 179 179
AA position 60 60
AA ref L L
AA alt S W
Codon substitution tTa/tCa tTa/tGa
PhyloP 100V -4.86 -4.86
PhastCons 100V 0 0
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 1 1
SIFT neutral neutral
SIFT score 0.29 0.12
FatHmm deleterious deleterious
FatHmm score -6.14 -7.73
FatHmmW neutral neutral
FatHmmW score 2.17 2.1
PROVEAN deleterious deleterious
PROVEAN score -5.99 -5.99
MutationAssessor high impact high impact
MutationAssessor score 3.66 4
EFIN SP damaging damaging
EFIN SP score 0.23 0.5
EFIN HD damaging damaging
EFIN HD score 0.17 0.25
CADD deleterious deleterious
CADD score 3.77 3.29
CADD phred 23.4 22.8
VEST pvalue 0.19 0.15
VEST FDR 0.45 0.45
PANTHER disease disease
PANTHER score 0.82 0.9
PhD-SNP disease disease
PhD-SNP score 0.91 0.91
SNAP disease disease
SNAP score 0.75 0.78
Meta-SNP disease disease
Meta-SNP score 0.84 0.88
Meta-SNP RI 7 8
CAROL deleterious deleterious
CAROL score 1 1
Condel neutral neutral
Condel score 0.15 0.06
COVEC WMV deleterious deleterious
COVEC WMV score 2 2
MtoolBox deleterious deleterious
MtoolBox DS 0.86 0.87
PolyPhen2 transf low impact low impact
PolyPhen2 transf score -3.55 -3.55
SIFT_transf medium impact medium impact
SIFT transf score -0.01 -0.27
MutationAssessor transf medium impact high impact
MutationAssessor transf score 1.93 2.21
CHASM pvalue 0.64 0.68
CHASM FDR 0.8 0.85
APOGEE Pathogenic Neutral
APOGEE score 0.87 0.42
SNPDryad score 0.97 0.98
MutationTaster . .
MutationTaster score . .
DEOGEN2 score 0.84 0.84
Mitoclass.1 damaging damaging
dbSNP 153 id rs199476106 .
ClinVar March2020 ClinSig Pathogenic .
ClinVar March2020 ClnDBN Leber's_optic_atrophy .
ClinVar March2020 ClnAllele id 24730 .
ClinVar March2020 ClnDSDB Human_Phenotype_Ontology:HP:0001112,MedGen:C0917796,OMIM:535000,Orphanet:ORPHA104,SNOMED_CT:58610003 .
COSMIC 90 . .
CPD Frequency . .
MITOMAP Allele A14495G .
MITOMAP Phenotype LHON .
MITOMAP Homoplasmy - .
MITOMAP Heteroplasmy + .
MITOMAP Status Cfrm .
MITOMAP NRef 8 .
EVmutation MT-ND6_60L|74A:0.105229;73M:0.076548;165Y:0.076104;82W:0.074487 MT-ND6_60L|74A:0.105229;73M:0.076548;165Y:0.076104;82W:0.074487
Site A InterP . .
Site B InterP . .
Covariation Score InterP . .
Site A IntraP . .
Site B IntraP . .
Covariation Score IntraP . .
CPD AA ref . .
CPD AA alt . .
CPD Aln pos . .
CPD Species name . .
CPD RefSeq Protein ID . .
CPD Ncbi Taxon id . .
DDG intra . .
DDG intra interface . .
DDG inter . .
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
For more info, please check the output legend.
Score:  
0
  [min -20, max 10]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.9
  • Conserved:  score > 0.9 (soft threshold)
Score:  
0
  [min 0, max 1]
  • Neutral:  score <= 0.15
  • Possibly damaging:  0.15 < score <= 0.85
  • Probably damaging:  score > 0.85
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.05
  • Deleterious:  score <= 0.05
Score:  
0
  [min -15, max 10]
  • Neutral:  score > -3
  • Deleterious:  score <= -3
Score:  
0
  [min -3, max 6]
  • Neutral:  score > -1.5
  • Deleterious:  score <= -1.5
Score:  
0
  [min -14, max 14]
  • Neutral:  score > -2.5
  • Deleterious:  score <= -2.5 (soft threshold)
Score:  
0
  [min -6, max 6]
  • Neutral:  score <= 0.8
  • Low impact:  0.8 < score <= 1.9
  • Medium impact:  1.9 < score <= 3.5
  • High impact:  score > 3.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.6
  • Damaging:  score <= 0.6
Score:  
0
  [min 0, max 1]
  • Neutral:  score > 0.28
  • Damaging:  score <= 0.28
Phred score:  
0
  [min 0, max 35]
  • Neutral:  score < 20 (soft threshold)
  • Deleterious:  score >= 20
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Polymorphism:  score < 0.5
  • Disease causing:  score >= 0.5
P-value:  
0
  [min 0, max 1]
  • Neutral:  p-value > 0.05
  • Pathogenic:  p-value <= 0.05
Score:  
0
  [min 0, max 1]
No hard-thresholds were indicated by authors (ref). Indicatively:
  • Neutral:  score < 0.9
  • Pathogenic:  score >= 0.9
No score. Categorical only
Please refer to Additional File 14: Table S10 for further details.
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.98
  • Deleterious:  score >= 0.98
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Disease:  score >= 0.5
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
Score:  
0
  [min -6, max 6]
  • Neutral:  score < 0
  • Deleterious:  score > 0
  • Inaccurate prediction:  score = 0
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5
  • Deleterious:  score >= 0.5
DS score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.43
  • Deleterious:  score >= 0.43
Score:  
0
  [min 0, max 1]
  • Neutral:  score <= 0.5
  • Pathogenic:  score > 0.5
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1 (soft threshold)
  • Medium impact:  -1 < score < 1.5 (soft threshold)
  • High impact:  score >= 1.5 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
Score:  
0
  [min -5, max 5]
  • Low impact:  score <= -1
  • Medium impact:  -1 < score < 2 (soft threshold)
  • High impact:  score >= 2 (soft threshold)
P-value:  
0
  [min 0, max 1]
  • Neutral:  FDR > 0.2
  • Driver:  FDR <= 0.2
The frequency of a CPD variant is proportional to the
number of aligned orthologous sequences that
carry a specific human pathogenic variant as
wild-type amino acid on the total number of aligned
sequences.

For more info, please check the output legend