3697 (G > A)

General info

Chr
chrM
Start
3697
End
3697
Ref
G
Alt
A
Mitimpact ID
MI.11568
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
391
AA pos
131
AA ref
G
AA alt
S
Codon substitution
Ggc/Agc
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Conservation

PhyloP 100v
-8.05 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
Medium impact Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
VEST
Pathogenic 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
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
Pathogenic
ClinVar October2021 CLNDN
Leber hereditary optic neuropathy;

leber optic atrophy and dystonia;

juvenile myopathy, encephalopathy, lactic acidosis and stroke
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:0010772, medgen:c1839040, omim:500001;

mondo:mondo:0010789, medgen:c0162671, omim:540000, orphanet:orpha550, snomed ct:39925003
MITOMAP Allele
MITOMAP Disease Het/Hom
+/+
MITOMAP Disease Clinical info
Melas / leigh syndrome / ldyt / bsn
MITOMAP Disease Status
Cfrm
MITOMAP Disease GenBank Freq
0.000%
MITOMAP Disease GenBank Seqs
0 (0)
MITOMAP Disease GenBank Curated refs
18
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
Gnomad31 filter
Npg
Gnomad31 AC hom
0
Gnomad31 AC het
0
Gnomad31 AF hom
0
Gnomad31 AF het
0
Gnomad31 AN
56428
COSMIC 90
COSM6119904
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
.

3697 (G > C)

General info

Chr
chrM
Start
3697
End
3697
Ref
G
Alt
C
Mitimpact ID
MI.11567
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
391
AA pos
131
AA ref
G
AA alt
R
Codon substitution
Ggc/Cgc
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Powered by MitoWheel

Conservation

PhyloP 100v
-8.05 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
Neutral 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
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
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
.

3697 (G > T)

General info

Chr
chrM
Start
3697
End
3697
Ref
G
Alt
T
Mitimpact ID
MI.11566
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
391
AA pos
131
AA ref
G
AA alt
C
Codon substitution
Ggc/Tgc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-8.05 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
Neutral 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
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
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
0.000%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
1
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
.
~ 3697 (G/A) 3697 (G/C) 3697 (G/T)
~ 3697 (Ggc/Agc) 3697 (Ggc/Cgc) 3697 (Ggc/Tgc)
Chr chrM chrM chrM
Start 3697 3697 3697
End 3697 3697 3697
Ref G G G
Alt A C T
MitImpact id MI.11568 MI.11567 MI.11566
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 391 391 391
AA position 131 131 131
AA ref G G G
AA alt S R C
Codon substitution Ggc/Agc Ggc/Cgc Ggc/Tgc
PhyloP 100V -8.05 -8.05 -8.05
PhastCons 100V 0 0 0
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1 1 1
SIFT neutral neutral neutral
SIFT score 0.59 0.32 0.16
FatHmm deleterious deleterious deleterious
FatHmm score -5.32 -8.91 -8.74
FatHmmW neutral neutral neutral
FatHmmW score 1.99 1.92 1.9
PROVEAN deleterious deleterious deleterious
PROVEAN score -5.44 -7.26 -8.18
MutationAssessor medium impact high impact high impact
MutationAssessor score 3.36 4.94 4.94
EFIN SP neutral neutral neutral
EFIN SP score 0.63 0.77 0.67
EFIN HD damaging damaging damaging
EFIN HD score 0.14 0.13 0.09
CADD deleterious deleterious deleterious
CADD score 4.16 3.86 4.1
CADD phred 23.8 23.5 23.7
VEST pvalue 0.02 0.02 0.01
VEST FDR 0.35 0.35 0.35
PANTHER neutral disease disease
PANTHER score 0.46 0.85 0.86
PhD-SNP disease disease disease
PhD-SNP score 0.89 0.9 0.92
SNAP disease disease disease
SNAP score 0.64 0.78 0.67
Meta-SNP disease disease disease
Meta-SNP score 0.7 0.72 0.67
Meta-SNP RI 4 4 3
CAROL deleterious deleterious deleterious
CAROL score 1 1 1
Condel neutral neutral neutral
Condel score 0.3 0.16 0.08
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 1 2 2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.85 0.91 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 0.36 0.09 -0.13
MutationAssessor transf medium impact high impact high impact
MutationAssessor transf score 1.75 3.13 3.13
CHASM pvalue 0.56 0.52 0.24
CHASM FDR 0.8 0.8 0.8
APOGEE Neutral Pathogenic Pathogenic
APOGEE score 0.36 0.66 0.52
SNPDryad score 0.99 0.99 0.98
MutationTaster disease_causing_automatic polymorphism polymorphism
MutationTaster score 0 1 1
DEOGEN2 score 0.26 0.49 0.49
Mitoclass.1 damaging damaging damaging
dbSNP 155 id rs199476122 . .
ClinVar October2021 Variation id 9733 . .
ClinVar October2021 CLNSIG Pathogenic . .
ClinVar October2021 CLNDN Leber_hereditary_optic_neuropathy|Leber_optic_atrophy_and_dystonia|Juvenile_myopathy,_encephalopathy,_lactic_acidosis_AND_stroke . .
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:0010772,MedGen:C1839040,OMIM:500001|MONDO:MONDO:0010789,MedGen:C0162671,OMIM:540000,Orphanet:ORPHA550,SNOMED_CT:39925003 . .
COSMIC 90 COSM6119904 . .
MITOMAP Allele G3697A . .
MITOMAP Disease Het/Hom +/+ . .
MITOMAP Disease Clinical info MELAS / Leigh Syndrome / LDYT / BSN . .
MITOMAP Disease Status Cfrm . .
MITOMAP Disease GenBank Freq 0.000% . .
MITOMAP Disease GenBank Seqs 0 (0) . .
MITOMAP Disease GenBank Curated refs 18 . .
MITOMAP General GenBank Freq . . 0.000%
MITOMAP General GenBank Seqs . . 0
MITOMAP General Curated refs . . 1
gnomAD 3.1 filter npg . .
gnomAD 3.1 AC Homo 0 . .
gnomAD 3.1 AC Het 0 . .
gnomAD 3.1 AF Hom 0 . .
gnomAD 3.1 AF Het 0 . .
gnomAD 3.1 AN 56428 . .
EVmutation MT-ND1_131G|201A:0.172594;135A:0.150774;203G:0.086072;137A:0.073318;217A:0.066632;213I:0.064892 MT-ND1_131G|201A:0.172594;135A:0.150774;203G:0.086072;137A:0.073318;217A:0.066632;213I:0.064892 MT-ND1_131G|201A:0.172594;135A:0.150774;203G:0.086072;137A:0.073318;217A:0.066632;213I:0.064892
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 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