10197 (G > A)

General info

Chr
chrM
Start
10197
End
10197
Ref
G
Alt
A
Mitimpact ID
MI.15259
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
139
AA pos
47
AA ref
A
AA alt
T
Codon substitution
Gcc/Acc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-20 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
Deleterious 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
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 July2022 CLNSIG
.
ClinVar July2022 CLNDN
.
ClinVar July2022 Variation ID
ClinVar July2022 CLNDISDB
.
MITOMAP Allele
MITOMAP Disease Het/Hom
+/+
MITOMAP Disease Clinical info
Leigh disease / dystonia / stroke / ldyt
MITOMAP Disease Status
Cfrm
MITOMAP Disease GenBank Freq
0.000%
MITOMAP Disease GenBank Seqs
4 (0)
MITOMAP Disease GenBank Curated refs
23
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
56422
HelixMTdb AC hom
0
HelixMTdb AF hom
0
HelixMTdb AC het
7
HelixMTdb AF het
3.5717385e-05
HelixMTdb mean ARF
0.15194
HelixMTdb max ARF
0.25
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
.

10197 (G > T)

General info

Chr
chrM
Start
10197
End
10197
Ref
G
Alt
T
Mitimpact ID
MI.15258
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
139
AA pos
47
AA ref
A
AA alt
S
Codon substitution
Gcc/Tcc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-20 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
Deleterious Score and details of the predictor
Mutation Assessor
Low 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
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
Neutral 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
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
Meta SNP
Neutral 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
High 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 July2022 CLNSIG
.
ClinVar July2022 CLNDN
.
ClinVar July2022 Variation ID
ClinVar July2022 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
.
HelixMTdb AC hom
.
HelixMTdb AF hom
.
HelixMTdb AC het
.
HelixMTdb AF het
.
HelixMTdb mean ARF
.
HelixMTdb max ARF
.
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
.

10197 (G > C)

General info

Chr
chrM
Start
10197
End
10197
Ref
G
Alt
C
Mitimpact ID
MI.15260
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
139
AA pos
47
AA ref
A
AA alt
P
Codon substitution
Gcc/Ccc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-20 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
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
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 July2022 CLNSIG
.
ClinVar July2022 CLNDN
.
ClinVar July2022 Variation ID
ClinVar July2022 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
Npg
Gnomad31 AC hom
0
Gnomad31 AC het
0
Gnomad31 AF hom
0
Gnomad31 AF het
0
Gnomad31 AN
56433
HelixMTdb AC hom
.
HelixMTdb AF hom
.
HelixMTdb AC het
.
HelixMTdb AF het
.
HelixMTdb mean ARF
.
HelixMTdb max ARF
.
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
.
~ 10197 (G/A) 10197 (G/T) 10197 (G/C)
~ 10197 (Gcc/Acc) 10197 (Gcc/Tcc) 10197 (Gcc/Ccc)
Chr chrM chrM chrM
Start 10197 10197 10197
End 10197 10197 10197
Ref G G G
Alt A T C
MitImpact id MI.15259 MI.15258 MI.15260
Gene symbol MT-ND3 MT-ND3 MT-ND3
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198840 ENSG00000198840 ENSG00000198840
Ensembl protein id ENSP00000355206 ENSP00000355206 ENSP00000355206
Ensembl transcript id ENST00000361227 ENST00000361227 ENST00000361227
Uniprot name NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN
Uniprot id P03897 P03897 P03897
Ncbi gene id 4537 4537 4537
Ncbi protein id YP_003024033.1 YP_003024033.1 YP_003024033.1
Gene position 139 139 139
AA position 47 47 47
AA ref A A A
AA alt T S P
Codon substitution Gcc/Acc Gcc/Tcc Gcc/Ccc
PhyloP 100V -20 -20 -20
PhastCons 100V 0 0 0
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1 1 1
SIFT neutral neutral neutral
SIFT score 0.52 1 0.32
FatHmm neutral neutral deleterious
FatHmm score -1.8 -1.42 -3.08
FatHmmW neutral neutral neutral
FatHmmW score 0.89 0.98 0.82
PROVEAN deleterious deleterious deleterious
PROVEAN score -3.52 -2.76 -4.73
MutationAssessor medium impact low impact medium impact
MutationAssessor score 2.54 1.77 2.73
EFIN SP damaging damaging damaging
EFIN SP score 0.09 0.46 0.39
EFIN HD neutral neutral damaging
EFIN HD score 0.38 0.37 0.24
CADD deleterious deleterious deleterious
CADD score 4.2 3.72 3.87
CADD phred 23.9 23.3 23.5
VEST pvalue 0.17 0.26 0.04
VEST FDR 0.45 0.45 0.35
PANTHER neutral neutral disease
PANTHER score 0.31 0.17 0.58
PhD-SNP disease disease disease
PhD-SNP score 0.74 0.69 0.77
SNAP disease disease disease
SNAP score 0.74 0.71 0.74
Meta-SNP disease neutral disease
Meta-SNP score 0.58 0.36 0.7
Meta-SNP RI 2 3 4
CAROL deleterious deleterious deleterious
CAROL score 1 1 1
Condel neutral deleterious neutral
Condel score 0.26 0.5 0.16
COVEC WMV deleterious neutral deleterious
COVEC WMV score 1 -2 1
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.79 0.75 0.84
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.43 -3.43 -3.43
SIFT_transf medium impact high impact medium impact
SIFT transf score 0.21 1.85 0.01
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 1.22 0.51 1.39
CHASM pvalue 0.76 0.21 0.31
CHASM FDR 0.85 0.8 0.8
APOGEE Pathogenic Neutral Neutral
APOGEE score 0.88 0.39 0.46
SNPDryad score 0.93 0.98 0.96
MutationTaster disease_causing_automatic polymorphism polymorphism
MutationTaster score 0 1 1
DEOGEN2 score 0.53 0.5 0.54
Mitoclass.1 damaging neutral damaging
dbSNP 155 id rs267606891 . .
ClinVar October2021 Variation id . . .
ClinVar October2021 CLNSIG . . .
ClinVar October2021 CLNDN . . .
ClinVar October2021 CLNDISDB . . .
COSMIC 90 . . .
MITOMAP Allele G10197A . .
MITOMAP Disease Het/Hom +/+ . .
MITOMAP Disease Clinical info Leigh Disease / Dystonia / Stroke / LDYT . .
MITOMAP Disease Status Cfrm . .
MITOMAP Disease GenBank Freq 0.000% . .
MITOMAP Disease GenBank Seqs 4 (0) . .
MITOMAP Disease GenBank Curated refs 23 . .
MITOMAP General GenBank Freq . . .
MITOMAP General GenBank Seqs . . .
MITOMAP General Curated refs . . .
gnomAD 3.1 filter npg . npg
gnomAD 3.1 AC Homo 0 . 0
gnomAD 3.1 AC Het 0 . 0
gnomAD 3.1 AF Hom 0 . 0
gnomAD 3.1 AF Het 0 . 0
gnomAD 3.1 AN 56422 . 56433
HelixMTdb AC Hom 0 . .
HelixMTdb AF Hom 0 . .
HelixMTdb AC Het 7 . .
HelixMTdb AF Het 3.5717385e-05 . .
HelixMTdb mean ARF 0.15194 . .
HelixMTdb max ARF 0.25 . .
EVmutation MT-ND3_47A|48R:0.529134;51F:0.204156;60I:0.185266;70A:0.161734;49V:0.124035;64L:0.101053;57L:0.084193;50P:0.081725;52S:0.069404;73L:0.064072 MT-ND3_47A|48R:0.529134;51F:0.204156;60I:0.185266;70A:0.161734;49V:0.124035;64L:0.101053;57L:0.084193;50P:0.081725;52S:0.069404;73L:0.064072 MT-ND3_47A|48R:0.529134;51F:0.204156;60I:0.185266;70A:0.161734;49V:0.124035;64L:0.101053;57L:0.084193;50P:0.081725;52S:0.069404;73L:0.064072
Site A InterP ND3_47 ND3_47 ND3_47
Site B InterP ND6_68 ND6_68 ND6_68
Covariation Score InterP cMI_13.9282 cMI_13.9282 cMI_13.9282
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