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3733 (G > A)

General info

Chr
chrM
Start
3733
End
3733
Ref
G
Alt
A
Mitimpact ID
MI.11638
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot name
NU1M_HUMAN
Uniprot ID
P03886
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Gene position
427
AA pos
143
AA ref
E
AA alt
K
Codon substitution
Gaa/Aaa
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Powered by MitoWheel

Conservation

PhyloP 100v
6.02898 Conservation Score
PhastCons 100v
1 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging 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
Neutral 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
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

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Pathogenic Score and details of the meta-predictor
CAROL
Neutral 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 July2022 CLNSIG
.
ClinVar July2022 CLNDN
.
ClinVar July2022 Variation ID
.
ClinVar July2022 CLNDISDB
.
MITOMAP Allele
3733G>A
MITOMAP Disease Het/Hom
+/+
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Cfrm [vus*]
MITOMAP Disease GenBank Freq
0.003%(0.000%)
MITOMAP Disease GenBank Seqs
2 (0)
MITOMAP Disease GenBank Curated refs
10
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
56431
HelixMTdb AC hom
0.0
HelixMTdb AF hom
0.0
HelixMTdb AC het
1.0
HelixMTdb AF het
5.1024836e-06
HelixMTdb mean ARF
0.175
HelixMTdb max ARF
0.175
COSMIC 90
.
dbSNP 155
rs199476125

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
.

3733 (G > C)

General info

Chr
chrM
Start
3733
End
3733
Ref
G
Alt
C
Mitimpact ID
MI.11637
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot name
NU1M_HUMAN
Uniprot ID
P03886
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Gene position
427
AA pos
143
AA ref
E
AA alt
Q
Codon substitution
Gaa/Caa
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
6.02898 Conservation Score
PhastCons 100v
1 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging 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
Neutral 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
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

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Pathogenic Score and details of the meta-predictor
CAROL
Neutral 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 July2022 CLNSIG
.
ClinVar July2022 CLNDN
.
ClinVar July2022 Variation ID
.
ClinVar July2022 CLNDISDB
.
MITOMAP Allele
3733G>C
MITOMAP Disease Het/Hom
-/+
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported
MITOMAP Disease GenBank Freq
0.000%(0.000%)
MITOMAP Disease GenBank Seqs
0 (0)
MITOMAP Disease GenBank Curated refs
1
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
0.000017719814
Gnomad31 AN
56434
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
.
~ 3733 (G/A) 3733 (G/C)
~ 3733 (Gaa/Aaa) 3733 (Gaa/Caa)
Chr chrM chrM
Start 3733 3733
End 3733 3733
Ref G G
Alt A C
MitImpact id MI.11638 MI.11637
Gene symbol MT-ND1 MT-ND1
Respiratory Chain complex I I
Ensembl gene id ENSG00000198888 ENSG00000198888
Ensembl protein id ENSP00000354687 ENSP00000354687
Ensembl transcript id ENST00000361390 ENST00000361390
Uniprot name NU1M_HUMAN NU1M_HUMAN
Uniprot id P03886 P03886
Ncbi gene id 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1
Gene position 427 427
AA position 143 143
AA ref E E
AA alt K Q
Codon substitution Gaa/Aaa Gaa/Caa
PhyloP 100V 6.02898 6.02898
PhastCons 100V 1 1
PolyPhen2 possibly_damaging probably_damaging
PolyPhen2 score 0.85 0.95
SIFT neutral neutral
SIFT score 0.23 0.6
SIFT4G Damaging Damaging
SIFT4G score 0.004 0.001
FatHmm deleterious deleterious
FatHmm score -6.28 -6.3
FatHmmW neutral neutral
FatHmmW score 1.77 1.75
PROVEAN deleterious deleterious
PROVEAN score -3.64 -2.73
MutationAssessor high impact high impact
MutationAssessor score 4.96 4.96
EFIN SP neutral neutral
EFIN SP score 0.63 0.67
EFIN HD neutral neutral
EFIN HD score 0.4 0.58
CADD deleterious deleterious
CADD score 4.47 3.35
CADD phred 24.2 22.9
VEST pvalue 0.03 0.06
VEST FDR 0.35 0.35
PANTHER disease disease
PANTHER score 0.82 0.84
PhD-SNP disease disease
PhD-SNP score 0.9 0.79
SNAP disease disease
SNAP score 0.78 0.74
Meta-SNP disease disease
Meta-SNP score 0.71 0.7
Meta-SNP RI 4 4
CAROL neutral neutral
CAROL score 0.9 0.95
Condel neutral neutral
Condel score 0.19 0.33
COVEC WMV deleterious deleterious
COVEC WMV score 1 2
MtoolBox deleterious deleterious
MtoolBox DS 0.84 0.87
PolyPhen2 transf low impact low impact
PolyPhen2 transf score -1.46 -1.95
SIFT_transf medium impact medium impact
SIFT transf score -0.02 0.37
MutationAssessor transf high impact high impact
MutationAssessor transf score 3.14 3.14
CHASM pvalue 0.7 0.49
CHASM FDR 0.85 0.8
APOGEE1 Pathogenic Pathogenic
APOGEE1 score 0.79 0.74
APOGEE2 Pathogenic Pathogenic
APOGEE2 score 0.980844581163991 0.930200911016243
SNPDryad score 0.99 0.91
MutationTaster disease_causing_automatic polymorphism
MutationTaster score 0 1
DEOGEN2 score 0.48 0.49
Mitoclass.1 damaging damaging
dbSNP 155 id rs199476125 .
ClinVar July2022 Variation id . .
ClinVar July2022 CLNSIG . .
ClinVar July2022 CLNDN . .
ClinVar July2022 CLNDISDB . .
COSMIC 90 . .
MITOMAP Allele G3733A G3733C
MITOMAP Disease Het/Hom +/+ -/+
MITOMAP Disease Clinical info LHON LHON
MITOMAP Disease Status Cfrm [VUS*] Reported
MITOMAP Disease GenBank Freq 0.003%(0.000%) 0.000%(0.000%)
MITOMAP Disease GenBank Seqs 2 (0) 0 (0)
MITOMAP Disease GenBank Curated refs 10 1
MITOMAP General GenBank Freq . .
MITOMAP General GenBank Seqs . .
MITOMAP General Curated refs . .
gnomAD 3.1 filter npg PASS
gnomAD 3.1 AC Homo 0 0
gnomAD 3.1 AC Het 0 1
gnomAD 3.1 AF Hom 0 0
gnomAD 3.1 AF Het 0 0.000017719814
gnomAD 3.1 AN 56431 56434
HelixMTdb AC Hom 0.0 .
HelixMTdb AF Hom 0.0 .
HelixMTdb AC Het 1.0 .
HelixMTdb AF Het 5.1024836e-06 .
HelixMTdb mean ARF 0.175 .
HelixMTdb max ARF 0.175 .
EVmutation MT-ND1_143E|202E:0.068401 MT-ND1_143E|202E:0.068401
Site A InterP ND1_143 ND1_143
Site B InterP ND4L_93;ND4L_94;ND4L_95;ND6_139 ND4L_93;ND4L_94;ND4L_95;ND6_139
Covariation Score InterP mfDCA_24.55;mfDCA_21.13;mfDCA_19.9;mfDCA_38.31 mfDCA_24.55;mfDCA_21.13;mfDCA_19.9;mfDCA_38.31
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 <= 0.7
  • Conserved:  score > 0.7 (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 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
Pathogenicity score:  
0
  [min 0, max 1]
  • Neutral:  score ≤ 0.5
  • Pathogenic:  score > 0.5


Pathogenicity score for this variant:  
0
  [min 0, max 1]
ACMG-AMP curations for mitochondrial variants should use the raw scores. Standalone probabilities are shown below:
  • Benign:  score ≤ 0.062 (prob. ≤ 0.001)
  • Likely-benign:  0.062 < score ≤ 0.265 (0.001 < prob. ≤ 0.1)
  • Low-scoring VUS (VUS-):  0.265 < score ≤ 0.396 (0.1 < prob. ≤ 0.33)
  • VUS:  0.396 < score ≤ 0.544 (0.33 < prob. ≤ 0.66)
  • High-scoring VUS (VUS+):  0.544 < score < 0.716 (0.66 < prob. < 0.9)
  • Likely-pathogenic:  0.716 ≤ score < 0.907 (0.9 ≤ prob. < 0.99)
  • Pathogenic:  score ≥ 0.907 (prob. ≥ 0.99)
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