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 October2021 CLNSIG
Pathogenic
ClinVar October2021 CLNDN
Mitochondrial complex i deficiency, mitochondrial type 3;

leber hereditary optic neuropathy;

leigh syndrome;

not provided
ClinVar October2021 Variation ID
ClinVar October2021 CLNDISDB
.;

human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:orpha104, snomed ct:58610003;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:orpha506, snomed ct:29570005;

medgen:cn517202
MITOMAP Allele
MITOMAP Disease Het/Hom
+/+
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Cfrm
MITOMAP Disease GenBank Freq
0.000%
MITOMAP Disease GenBank Seqs
31 (0)
MITOMAP Disease GenBank Curated refs
201
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
Gnomad31 filter
Pass
Gnomad31 AC hom
0
Gnomad31 AC het
1
Gnomad31 AF hom
0
Gnomad31 AF het
1.7722326e-05
Gnomad31 AN
56426
COSMIC 90
COSM6716713
dbSNP 155

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
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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
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 October2021 CLNSIG
.
ClinVar October2021 CLNDN
.
ClinVar October2021 Variation ID
ClinVar October2021 CLNDISDB
.
MITOMAP Allele
.
MITOMAP Disease Het/Hom
.
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease GenBank Freq
.
MITOMAP Disease GenBank Seqs
.
MITOMAP Disease GenBank Curated refs
.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
Gnomad31 filter
.
Gnomad31 AC hom
.
Gnomad31 AC het
.
Gnomad31 AF hom
.
Gnomad31 AF het
.
Gnomad31 AN
.
COSMIC 90
.
dbSNP 155

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 October2021 CLNSIG
.
ClinVar October2021 CLNDN
.
ClinVar October2021 Variation ID
ClinVar October2021 CLNDISDB
.
MITOMAP Allele
.
MITOMAP Disease Het/Hom
.
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease GenBank Freq
.
MITOMAP Disease GenBank Seqs
.
MITOMAP Disease GenBank Curated refs
.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
Gnomad31 filter
.
Gnomad31 AC hom
.
Gnomad31 AC het
.
Gnomad31 AF hom
.
Gnomad31 AF het
.
Gnomad31 AN
.
COSMIC 90
.
dbSNP 155

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/C) 3460 (G/T)
~ 3460 (Gcc/Acc) 3460 (Gcc/Ccc) 3460 (Gcc/Tcc)
Chr chrM chrM chrM
Start 3460 3460 3460
End 3460 3460 3460
Ref G G G
Alt A C T
MitImpact id MI.11080 MI.11079 MI.11078
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 P S
Codon substitution Gcc/Acc Gcc/Ccc Gcc/Tcc
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 0.31 0.6
FatHmm neutral deleterious neutral
FatHmm score -1.54 -3.8 -2.08
FatHmmW neutral neutral neutral
FatHmmW score 2.62 2.56 2.64
PROVEAN neutral deleterious neutral
PROVEAN score -2.36 -2.62 -0.79
MutationAssessor medium impact high impact medium impact
MutationAssessor score 3.08 4.05 3.36
EFIN SP damaging damaging neutral
EFIN SP score 0.29 0.52 0.75
EFIN HD neutral damaging neutral
EFIN HD score 0.45 0.27 0.49
CADD deleterious deleterious deleterious
CADD score 4.24 3.77 3.6
CADD phred 23.9 23.4 23.2
VEST pvalue 0.13 0.02 0.2
VEST FDR 0.4 0.35 0.45
PANTHER neutral disease neutral
PANTHER score 0.26 0.6 0.35
PhD-SNP disease disease disease
PhD-SNP score 0.72 0.93 0.75
SNAP disease disease disease
SNAP score 0.65 0.76 0.65
Meta-SNP disease disease disease
Meta-SNP score 0.7 0.83 0.7
Meta-SNP RI 4 7 4
CAROL deleterious deleterious deleterious
CAROL score 1 1 1
Condel neutral neutral neutral
Condel score 0.27 0.16 0.3
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 1 2 1
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.76 0.9 0.8
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 0.08 0.37
MutationAssessor transf medium impact high impact medium impact
MutationAssessor transf score 1.5 2.35 1.75
CHASM pvalue 0.78 0.56 0.48
CHASM FDR 0.85 0.8 0.8
APOGEE Pathogenic Neutral Neutral
APOGEE score 0.86 0.46 0.37
SNPDryad score 0.7 0.96 0.93
MutationTaster disease_causing_automatic polymorphism polymorphism
MutationTaster score 0 1 1
DEOGEN2 score 0.13 0.23 0.09
Mitoclass.1 damaging damaging damaging
dbSNP 155 id rs199476118 . .
ClinVar October2021 Variation id 9722 . .
ClinVar October2021 CLNSIG Pathogenic . .
ClinVar October2021 CLNDN MITOCHONDRIAL_COMPLEX_I_DEFICIENCY,_MITOCHONDRIAL_TYPE_3|Leber_hereditary_optic_neuropathy|Leigh_syndrome|not_provided . .
ClinVar October2021 CLNDISDB .|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:ORPHA104,SNOMED_CT:58610003|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005|MedGen:CN517202 . .
COSMIC 90 COSM6716713 . .
MITOMAP Allele G3460A . .
MITOMAP Disease Het/Hom +/+ . .
MITOMAP Disease Clinical info LHON . .
MITOMAP Disease Status Cfrm . .
MITOMAP Disease GenBank Freq 0.000% . .
MITOMAP Disease GenBank Seqs 31 (0) . .
MITOMAP Disease GenBank Curated refs 201 . .
MITOMAP General GenBank Freq . . .
MITOMAP General GenBank Seqs . . .
MITOMAP General Curated refs . . .
gnomAD 3.1 filter PASS . .
gnomAD 3.1 AC Homo 0 . .
gnomAD 3.1 AC Het 1 . .
gnomAD 3.1 AF Hom 0 . .
gnomAD 3.1 AF Het 1.7722326e-05 . .
gnomAD 3.1 AN 56426 . .
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 Frequency . . .
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