3460 (G > A)

General info

Chr
chrM
Start
3460
End
3460
Ref
G
Alt
A
Mitimpact ID
MI.11080
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
154
AA pos
52
AA ref
A
AA alt
T
Codon substitution
Gcc/Acc
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Conservation

PhyloP 100v
-7.82 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
Neutral Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Neutral Score and details of the predictor
Mutation Assessor
Medium impact Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
Neutral Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
Disease causing automatic Score and details of the predictor
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
Neutral 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
Neutral 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
Mitochondrial complex i deficiency, mitochondrial type 3;

leber's optic atrophy;

leigh syndrome;

not provided
ClinVar March2020 ClnAllele ID
24761
ClinVar March2020 ClnDSDB
.;

human phenotype ontology:hp:0001112, medgen:c0917796, omim:535000, orphanet:orpha104, snomed ct:58610003;

medgen:c0023264, omim:256000, orphanet:orpha506, snomed ct:29570005;

medgen:cn517202
MITOMAP Allele
MITOMAP Phenotype
Lhon
MITOMAP Homoplasmy
+
MITOMAP Heteroplasmy
+
MITOMAP Status
Cfrm
MITOMAP NRef
160
COSMIC 90
COSM6716713
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
.

3460 (G > T)

General info

Chr
chrM
Start
3460
End
3460
Ref
G
Alt
T
Mitimpact ID
MI.11078
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
154
AA pos
52
AA ref
A
AA alt
S
Codon substitution
Gcc/Tcc
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Powered by MitoWheel

Conservation

PhyloP 100v
-7.82 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
Neutral Score and details of the predictor
FatHMMW
Neutral Score and details of the predictor
PROVEAN
Neutral Score and details of the predictor
Mutation Assessor
Medium impact Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
Neutral Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
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
Neutral 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
.
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
.

3460 (G > C)

General info

Chr
chrM
Start
3460
End
3460
Ref
G
Alt
C
Mitimpact ID
MI.11079
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
154
AA pos
52
AA ref
A
AA alt
P
Codon substitution
Gcc/Ccc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-7.82 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
Pathogenic Score and details of the predictor
PANTHER
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
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
Neutral 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
.
~ 3460 (G/A) 3460 (G/T) 3460 (G/C)
~ 3460 (Gcc/Acc) 3460 (Gcc/Tcc) 3460 (Gcc/Ccc)
Chr chrM chrM chrM
Start 3460 3460 3460
End 3460 3460 3460
Ref G G G
Alt A T C
MitImpact id MI.11080 MI.11078 MI.11079
Gene symbol MT-ND1 MT-ND1 MT-ND1
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198888 ENSG00000198888 ENSG00000198888
Ensembl protein id ENSP00000354687 ENSP00000354687 ENSP00000354687
Ensembl transcript id ENST00000361390 ENST00000361390 ENST00000361390
Uniprot name NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN
Uniprot id P03886 P03886 P03886
Ncbi gene id 4535 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1 YP_003024026.1
Gene position 154 154 154
AA position 52 52 52
AA ref A A A
AA alt T S P
Codon substitution Gcc/Acc Gcc/Tcc Gcc/Ccc
PhyloP 100V -7.82 -7.82 -7.82
PhastCons 100V 0 0 0
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1 1 1
SIFT neutral neutral neutral
SIFT score 0.54 0.6 0.31
FatHmm neutral neutral deleterious
FatHmm score -1.54 -2.08 -3.8
FatHmmW neutral neutral neutral
FatHmmW score 2.62 2.64 2.56
PROVEAN neutral neutral deleterious
PROVEAN score -2.36 -0.79 -2.62
MutationAssessor medium impact medium impact high impact
MutationAssessor score 3.08 3.36 4.05
EFIN SP damaging neutral damaging
EFIN SP score 0.29 0.75 0.52
EFIN HD neutral neutral damaging
EFIN HD score 0.45 0.49 0.27
CADD deleterious deleterious deleterious
CADD score 4.24 3.6 3.77
CADD phred 23.9 23.2 23.4
VEST pvalue 0.13 0.2 0.02
VEST FDR 0.4 0.45 0.35
PANTHER neutral neutral disease
PANTHER score 0.26 0.35 0.6
PhD-SNP disease disease disease
PhD-SNP score 0.72 0.75 0.93
SNAP disease disease disease
SNAP score 0.65 0.65 0.76
Meta-SNP disease disease disease
Meta-SNP score 0.7 0.7 0.83
Meta-SNP RI 4 4 7
CAROL deleterious deleterious deleterious
CAROL score 1 1 1
Condel neutral neutral neutral
Condel score 0.27 0.3 0.16
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 1 1 2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.76 0.8 0.9
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.57 -3.57 -3.57
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.31 0.37 0.08
MutationAssessor transf medium impact medium impact high impact
MutationAssessor transf score 1.5 1.75 2.35
CHASM pvalue 0.78 0.48 0.56
CHASM FDR 0.85 0.8 0.8
APOGEE Pathogenic Neutral Neutral
APOGEE score 0.86 0.37 0.46
SNPDryad score 0.7 0.93 0.96
MutationTaster disease_causing_automatic polymorphism polymorphism
MutationTaster score 0 1 1
DEOGEN2 score 0.13 0.09 0.23
Mitoclass.1 damaging damaging damaging
dbSNP 153 id rs199476118 . .
ClinVar March2020 ClinSig Pathogenic . .
ClinVar March2020 ClnDBN MITOCHONDRIAL_COMPLEX_I_DEFICIENCY,_MITOCHONDRIAL_TYPE_3|Leber's_optic_atrophy|Leigh_syndrome|not_provided . .
ClinVar March2020 ClnAllele id 24761 . .
ClinVar March2020 ClnDSDB .|Human_Phenotype_Ontology:HP:0001112,MedGen:C0917796,OMIM:535000,Orphanet:ORPHA104,SNOMED_CT:58610003|MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005|MedGen:CN517202 . .
COSMIC 90 COSM6716713 . .
CPD Frequency . . .
MITOMAP Allele G3460A . .
MITOMAP Phenotype LHON . .
MITOMAP Homoplasmy + . .
MITOMAP Heteroplasmy + . .
MITOMAP Status Cfrm . .
MITOMAP NRef 160 . .
EVmutation MT-ND1_52A|56F:0.158649;221A:0.15824;57T:0.151346;225M:0.115603;119S:0.100308;55L:0.094289;81I:0.086307;83L:0.083706;110S:0.075964;218G:0.065091 MT-ND1_52A|56F:0.158649;221A:0.15824;57T:0.151346;225M:0.115603;119S:0.100308;55L:0.094289;81I:0.086307;83L:0.083706;110S:0.075964;218G:0.065091 MT-ND1_52A|56F:0.158649;221A:0.15824;57T:0.151346;225M:0.115603;119S:0.100308;55L:0.094289;81I:0.086307;83L:0.083706;110S:0.075964;218G:0.065091
Site A InterP ND1_52 ND1_52 ND1_52
Site B InterP ND5_194 ND5_194 ND5_194
Covariation Score InterP mfDCA_26.26 mfDCA_26.26 mfDCA_26.26
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