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4171 (C > A)

General info

Chr
chrM
Start
4171
End
4171
Ref
C
Alt
A
Mitimpact ID
MI.12561
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
865
AA pos
289
AA ref
L
AA alt
M
Codon substitution
Cta/Ata
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Powered by MitoWheel

Conservation

PhyloP 100v
-0.89852 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
SIFT4G
Damaging 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
Low 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
Neutral 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
Neutral 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

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-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
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
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 July2022 CLNSIG
.
ClinVar July2022 CLNDN
.
ClinVar July2022 Variation ID
.
ClinVar July2022 CLNDISDB
.
MITOMAP Allele
4171C>A
MITOMAP Disease Het/Hom
+/+
MITOMAP Disease Clinical info
Lhon / leigh-like phenotype
MITOMAP Disease Status
Cfrm [vus*]
MITOMAP Disease GenBank Freq
0.003%(0.000%)
MITOMAP Disease GenBank Seqs
2 (0)
MITOMAP Disease GenBank Curated refs
17
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
0.0
HelixMTdb AF hom
0.0
HelixMTdb AC het
1.0
HelixMTdb AF het
5.1024836e-06
HelixMTdb mean ARF
0.16872
HelixMTdb max ARF
0.16872
COSMIC 90
.
dbSNP 155
rs28616230

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
.

4171 (C > G)

General info

Chr
chrM
Start
4171
End
4171
Ref
C
Alt
G
Mitimpact ID
MI.12560
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
865
AA pos
289
AA ref
L
AA alt
V
Codon substitution
Cta/Gta
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.89852 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
SIFT4G
Tolerated 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
Neutral 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
Neutral Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
CADD
Neutral Score and details of the predictor
SNAP
Neutral Score and details of the predictor
MitoClass 1
Neutral Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Likely-benign 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
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
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 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
.
~ 4171 (C/A) 4171 (C/G)
~ 4171 (Cta/Ata) 4171 (Cta/Gta)
Chr chrM chrM
Start 4171 4171
End 4171 4171
Ref C C
Alt A G
MitImpact id MI.12561 MI.12560
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 865 865
AA position 289 289
AA ref L L
AA alt M V
Codon substitution Cta/Ata Cta/Gta
PhyloP 100V -0.89852 -0.89852
PhastCons 100V 0 0
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0
SIFT neutral neutral
SIFT score 0.24 0.49
SIFT4G Damaging Tolerated
SIFT4G score 0.029 0.278
FatHmm neutral neutral
FatHmm score -1.96 -0.82
FatHmmW neutral neutral
FatHmmW score 2.7 2.79
PROVEAN neutral neutral
PROVEAN score -0.98 -0.28
MutationAssessor low impact neutral impact
MutationAssessor score 1.76 0.46
EFIN SP neutral neutral
EFIN SP score 0.75 0.88
EFIN HD neutral neutral
EFIN HD score 0.56 0.71
CADD deleterious neutral
CADD score 3.81 1.77
CADD phred 23.4 14.81
VEST pvalue 0.22 0.22
VEST FDR 0.45 0.45
PANTHER neutral neutral
PANTHER score 0.32 0.17
PhD-SNP neutral neutral
PhD-SNP score 0.32 0.17
SNAP neutral neutral
SNAP score 0.18 0.16
Meta-SNP neutral neutral
Meta-SNP score 0.48 0.29
Meta-SNP RI 1 4
CAROL deleterious deleterious
CAROL score 1.0 1.0
Condel neutral neutral
Condel score 0.12 0.25
COVEC WMV neutral neutral
COVEC WMV score -2 -2
MtoolBox deleterious deleterious
MtoolBox DS 0.68 0.65
PolyPhen2 transf low impact low impact
PolyPhen2 transf score -3.57 -3.57
SIFT_transf medium impact medium impact
SIFT transf score -0.01 0.27
MutationAssessor transf medium impact medium impact
MutationAssessor transf score 0.35 -0.79
CHASM pvalue 0.44 0.52
CHASM FDR 0.8 0.8
APOGEE1 Pathogenic Neutral
APOGEE1 score 0.6 0.47
APOGEE2 Likely-pathogenic Likely-benign
APOGEE2 score 0.804645407958101 0.151989972386368
SNPDryad score 0.89 0.84
MutationTaster disease_causing_automatic polymorphism
MutationTaster score 0 1
DEOGEN2 score 0.03 0.02
Mitoclass.1 damaging neutral
dbSNP 155 id rs28616230 .
ClinVar July2022 Variation id . .
ClinVar July2022 CLNSIG . .
ClinVar July2022 CLNDN . .
ClinVar July2022 CLNDISDB . .
COSMIC 90 . .
MITOMAP Allele C4171A .
MITOMAP Disease Het/Hom +/+ .
MITOMAP Disease Clinical info LHON / Leigh-like phenotype .
MITOMAP Disease Status Cfrm [VUS*] .
MITOMAP Disease GenBank Freq 0.003%(0.000%) .
MITOMAP Disease GenBank Seqs 2 (0) .
MITOMAP Disease GenBank Curated refs 17 .
MITOMAP General GenBank Freq . .
MITOMAP General GenBank Seqs . .
MITOMAP General Curated refs . .
gnomAD 3.1 filter . .
gnomAD 3.1 AC Homo . .
gnomAD 3.1 AC Het . .
gnomAD 3.1 AF Hom . .
gnomAD 3.1 AF Het . .
gnomAD 3.1 AN . .
HelixMTdb AC Hom 0.0 .
HelixMTdb AF Hom 0.0 .
HelixMTdb AC Het 1.0 .
HelixMTdb AF Het 5.1024836e-06 .
HelixMTdb mean ARF 0.16872 .
HelixMTdb max ARF 0.16872 .
EVmutation MT-ND1_289L|297T:0.091596;292N:0.085219;293F:0.076007 MT-ND1_289L|297T:0.091596;292N:0.085219;293F:0.076007
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 <= 0.7
  • 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