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3496 (G > T)

MT-ND3_5xtc_s_j_AA64S_SB45T MT-ND3_5xtc_s_j_AA64S_SB45F MT-ND3_5xtc_s_j_AA64S_SB45Y MT-ND3_5xtc_s_j_AA64S_SB45A MT-ND3_5xtc_s_j_AA64S_SB45P MT-ND3_5xtc_s_j_AA64S_SB45C

General info

Chr
chrM
Start
3496
End
3496
Ref
G
Alt
T
Mitimpact ID
MI.11154
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
190
AA pos
64
AA ref
A
AA alt
S
Codon substitution
Gcc/Tcc
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Powered by MitoWheel

Conservation

PhyloP 100v
-2.80228 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
Benign Score and details of the meta-predictor
CAROL
Neutral 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
Neutral Score and details of the meta-predictor
DEOGEN2
Neutral Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
High impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Low 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
3496G>T
MITOMAP Disease Het/Hom
+/-
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported / secondary
MITOMAP Disease GenBank Freq
0.019%(0.000%)
MITOMAP Disease GenBank Seqs
11 (0)
MITOMAP Disease GenBank Curated refs
3
MITOMAP General GenBank Freq
0.00019
MITOMAP General GenBank Seqs
11
MITOMAP General GenBank Curated refs
4
Gnomad31 filter
Npg
Gnomad31 AC hom
0
Gnomad31 AC het
0
Gnomad31 AF hom
0
Gnomad31 AF het
0
Gnomad31 AN
56429
HelixMTdb AC hom
16.0
HelixMTdb AF hom
8.163974e-05
HelixMTdb AC het
0.0
HelixMTdb AF het
0.0
HelixMTdb mean ARF
.
HelixMTdb max ARF
.
COSMIC 90
.
dbSNP 155
rs1603218984

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
.

3496 (G > A)

MT-ND3_5xtc_s_j_AA64T_SB45P

General info

Chr
chrM
Start
3496
End
3496
Ref
G
Alt
A
Mitimpact ID
MI.11153
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
190
AA pos
64
AA ref
A
AA alt
T
Codon substitution
Gcc/Acc
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Powered by MitoWheel

Conservation

PhyloP 100v
-2.80228 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
Benign Score and details of the meta-predictor
CAROL
Neutral 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
Neutral Score and details of the meta-predictor
DEOGEN2
Neutral Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
High impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Low 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
0.00013
MITOMAP General GenBank Seqs
8
MITOMAP General GenBank Curated refs
1
Gnomad31 filter
Pass
Gnomad31 AC hom
3
Gnomad31 AC het
1
Gnomad31 AF hom
0.000053165095
Gnomad31 AF het
0.000017721699
Gnomad31 AN
56428
HelixMTdb AC hom
6.0
HelixMTdb AF hom
3.06149e-05
HelixMTdb AC het
1.0
HelixMTdb AF het
5.1024836e-06
HelixMTdb mean ARF
0.86726
HelixMTdb max ARF
0.86726
COSMIC 90
COSM5653110
dbSNP 155
rs1603218984

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
.

3496 (G > C)

MT-ND3_5xtc_s_j_AA64P_SB45P

General info

Chr
chrM
Start
3496
End
3496
Ref
G
Alt
C
Mitimpact ID
MI.11155
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
190
AA pos
64
AA ref
A
AA alt
P
Codon substitution
Gcc/Ccc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-2.80228 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
Disease 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
Vus Score and details of the meta-predictor
CAROL
Neutral 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
Disease Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Neutral Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Medium 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
56431
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
.
~ 3496 (G/T) 3496 (G/A) 3496 (G/C)
~ 3496 (Gcc/Tcc) 3496 (Gcc/Acc) 3496 (Gcc/Ccc)
Chr chrM chrM chrM
Start 3496 3496 3496
End 3496 3496 3496
Ref G G G
Alt T A C
MitImpact id MI.11154 MI.11153 MI.11155
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 190 190 190
AA position 64 64 64
AA ref A A A
AA alt S T P
Codon substitution Gcc/Tcc Gcc/Acc Gcc/Ccc
PhyloP 100V -2.80228 -2.80228 -2.80228
PhastCons 100V 0 0 0
PolyPhen2 benign benign benign
PolyPhen2 score 0.0 0.0 0.11
SIFT neutral neutral neutral
SIFT score 0.81 0.72 0.35
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 1 0.23 0.051
FatHmm neutral neutral neutral
FatHmm score -0.3 -0.92 -2.44
FatHmmW neutral neutral neutral
FatHmmW score 2.79 2.71 2.65
PROVEAN neutral neutral neutral
PROVEAN score 1.31 0.01 -1.97
MutationAssessor neutral impact neutral impact low impact
MutationAssessor score -0.84 -0.51 1.13
EFIN SP neutral neutral neutral
EFIN SP score 0.68 0.76 0.67
EFIN HD neutral neutral neutral
EFIN HD score 0.95 0.74 0.37
CADD neutral neutral neutral
CADD score -1.03 0.9 0.76
CADD phred 0.01 10.05 9.24
VEST pvalue 0.42 0.34 0.17
VEST FDR 0.55 0.5 0.45
PANTHER neutral neutral neutral
PANTHER score 0.13 0.18 0.29
PhD-SNP neutral neutral disease
PhD-SNP score 0.06 0.17 0.77
SNAP neutral neutral neutral
SNAP score 0.11 0.14 0.28
Meta-SNP neutral neutral disease
Meta-SNP score 0.21 0.28 0.58
Meta-SNP RI 6 4 1
CAROL neutral neutral neutral
CAROL score 0.19 0.28 0.6
Condel deleterious deleterious deleterious
Condel score 0.91 0.86 0.62
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -6
MtoolBox neutral neutral neutral
MtoolBox DS 0.08 0.09 0.26
PolyPhen2 transf high impact high impact medium impact
PolyPhen2 transf score 2.07 2.07 0.1
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.63 0.51 0.12
MutationAssessor transf low impact low impact medium impact
MutationAssessor transf score -1.92 -1.63 -0.2
CHASM pvalue 0.39 0.55 0.37
CHASM FDR 0.8 0.8 0.8
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.44 0.46 0.38
APOGEE2 Benign Benign VUS
APOGEE2 score 0.0300959733751049 0.0252991649228041 0.483325502098256
SNPDryad score 0.07 0.34 0.74
MutationTaster polymorphism polymorphism polymorphism
MutationTaster score 1 1 1
DEOGEN2 score 0.0 0.01 0.03
Mitoclass.1 neutral neutral neutral
dbSNP 155 id rs1603218984 rs1603218984 .
ClinVar July2022 Variation id . . .
ClinVar July2022 CLNSIG . . .
ClinVar July2022 CLNDN . . .
ClinVar July2022 CLNDISDB . . .
COSMIC 90 . COSM5653110 .
MITOMAP Allele G3496T . .
MITOMAP Disease Het/Hom +/- . .
MITOMAP Disease Clinical info LHON . .
MITOMAP Disease Status Reported / Secondary . .
MITOMAP Disease GenBank Freq 0.019%(0.000%) . .
MITOMAP Disease GenBank Seqs 11 (0) . .
MITOMAP Disease GenBank Curated refs 3 . .
MITOMAP General GenBank Freq 0.00019 0.00013 .
MITOMAP General GenBank Seqs 11 8 .
MITOMAP General Curated refs 4 1 .
gnomAD 3.1 filter npg PASS npg
gnomAD 3.1 AC Homo 0 3 0
gnomAD 3.1 AC Het 0 1 0
gnomAD 3.1 AF Hom 0 0.000053165095 0
gnomAD 3.1 AF Het 0 0.000017721699 0
gnomAD 3.1 AN 56429 56428 56431
HelixMTdb AC Hom 16.0 6.0 .
HelixMTdb AF Hom 8.163974e-05 3.06149e-05 .
HelixMTdb AC Het 0.0 1.0 .
HelixMTdb AF Het 0.0 5.1024836e-06 .
HelixMTdb mean ARF . 0.86726 .
HelixMTdb max ARF . 0.86726 .
EVmutation MT-ND1_64A|65T:0.21755;118W:0.097737;183M:0.083952;69T:0.082342;110S:0.082298;305V:0.075737;99N:0.075659;87T:0.074904;302M:0.070495;70L:0.070242;266L:0.066295;247Y:0.065793 MT-ND1_64A|65T:0.21755;118W:0.097737;183M:0.083952;69T:0.082342;110S:0.082298;305V:0.075737;99N:0.075659;87T:0.074904;302M:0.070495;70L:0.070242;266L:0.066295;247Y:0.065793 MT-ND1_64A|65T:0.21755;118W:0.097737;183M:0.083952;69T:0.082342;110S:0.082298;305V:0.075737;99N:0.075659;87T:0.074904;302M:0.070495;70L:0.070242;266L:0.066295;247Y:0.065793
Site A InterP ND1_64 ND1_64 ND1_64
Site B InterP ND4_86;ND5_4;ND6_95;ND2_213;ND2_22;ND2_6;ND2_239;ND2_221;ND2_90;ND2_89;ND2_96;ND2_48;ND3_29;ND3_85;ND3_90;ND3_21;ND3_88;ND3_45;ND3_46;ND3_93;ND3_18;ND3_92;ND3_89;ND4_4;ND4_363;ND4_357;ND4_248;ND4L_19;ND5_420;ND6_86;ND6_150;ND6_165;ND6_142;ND6_139;ND6_102;ND6_140 ND4_86;ND5_4;ND6_95;ND2_213;ND2_22;ND2_6;ND2_239;ND2_221;ND2_90;ND2_89;ND2_96;ND2_48;ND3_29;ND3_85;ND3_90;ND3_21;ND3_88;ND3_45;ND3_46;ND3_93;ND3_18;ND3_92;ND3_89;ND4_4;ND4_363;ND4_357;ND4_248;ND4L_19;ND5_420;ND6_86;ND6_150;ND6_165;ND6_142;ND6_139;ND6_102;ND6_140 ND4_86;ND5_4;ND6_95;ND2_213;ND2_22;ND2_6;ND2_239;ND2_221;ND2_90;ND2_89;ND2_96;ND2_48;ND3_29;ND3_85;ND3_90;ND3_21;ND3_88;ND3_45;ND3_46;ND3_93;ND3_18;ND3_92;ND3_89;ND4_4;ND4_363;ND4_357;ND4_248;ND4L_19;ND5_420;ND6_86;ND6_150;ND6_165;ND6_142;ND6_139;ND6_102;ND6_140
Covariation Score InterP mfDCA_38.19;mfDCA_26.94;mfDCA_22.33;cMI_64.44566;cMI_62.52018;cMI_60.4021;cMI_56.45133;cMI_54.95405;cMI_53.87512;cMI_51.6195;cMI_51.002;cMI_47.62558;cMI_40.80143;cMI_40.31699;cMI_37.82036;cMI_36.19952;cMI_36.09641;cMI_32.72981;cMI_32.51378;cMI_32.15059;cMI_31.94808;cMI_31.65707;cMI_31.37539;cMI_26.4492;cMI_25.59954;cMI_25.42153;cMI_24.47381;cMI_46.40883;cMI_32.71994;cMI_56.91476;cMI_56.31747;cMI_56.27557;cMI_50.7122;cMI_50.43972;cMI_48.25338;cMI_47.30772 mfDCA_38.19;mfDCA_26.94;mfDCA_22.33;cMI_64.44566;cMI_62.52018;cMI_60.4021;cMI_56.45133;cMI_54.95405;cMI_53.87512;cMI_51.6195;cMI_51.002;cMI_47.62558;cMI_40.80143;cMI_40.31699;cMI_37.82036;cMI_36.19952;cMI_36.09641;cMI_32.72981;cMI_32.51378;cMI_32.15059;cMI_31.94808;cMI_31.65707;cMI_31.37539;cMI_26.4492;cMI_25.59954;cMI_25.42153;cMI_24.47381;cMI_46.40883;cMI_32.71994;cMI_56.91476;cMI_56.31747;cMI_56.27557;cMI_50.7122;cMI_50.43972;cMI_48.25338;cMI_47.30772 mfDCA_38.19;mfDCA_26.94;mfDCA_22.33;cMI_64.44566;cMI_62.52018;cMI_60.4021;cMI_56.45133;cMI_54.95405;cMI_53.87512;cMI_51.6195;cMI_51.002;cMI_47.62558;cMI_40.80143;cMI_40.31699;cMI_37.82036;cMI_36.19952;cMI_36.09641;cMI_32.72981;cMI_32.51378;cMI_32.15059;cMI_31.94808;cMI_31.65707;cMI_31.37539;cMI_26.4492;cMI_25.59954;cMI_25.42153;cMI_24.47381;cMI_46.40883;cMI_32.71994;cMI_56.91476;cMI_56.31747;cMI_56.27557;cMI_50.7122;cMI_50.43972;cMI_48.25338;cMI_47.30772
Site A IntraP ND1_64 ND1_64 ND1_64
Site B IntraP ND1_245;ND1_229;ND1_309;ND1_178;ND1_305;ND1_225;ND1_250;ND1_248;ND1_260;ND1_246;ND1_276 ND1_245;ND1_229;ND1_309;ND1_178;ND1_305;ND1_225;ND1_250;ND1_248;ND1_260;ND1_246;ND1_276 ND1_245;ND1_229;ND1_309;ND1_178;ND1_305;ND1_225;ND1_250;ND1_248;ND1_260;ND1_246;ND1_276
Covariation Score IntraP cMI_14.342117;mfDCA_22.8811;mfDCA_22.5193;mfDCA_22.0516;mfDCA_21.8998;mfDCA_21.564;mfDCA_19.5808;mfDCA_19.0999;mfDCA_18.3416;mfDCA_16.1252;mfDCA_14.823 cMI_14.342117;mfDCA_22.8811;mfDCA_22.5193;mfDCA_22.0516;mfDCA_21.8998;mfDCA_21.564;mfDCA_19.5808;mfDCA_19.0999;mfDCA_18.3416;mfDCA_16.1252;mfDCA_14.823 cMI_14.342117;mfDCA_22.8811;mfDCA_22.5193;mfDCA_22.0516;mfDCA_21.8998;mfDCA_21.564;mfDCA_19.5808;mfDCA_19.0999;mfDCA_18.3416;mfDCA_16.1252;mfDCA_14.823
CPD AA ref . . .
CPD AA alt . . .
CPD Aln pos . . .
CPD Frequency . . .
CPD Species name . . .
CPD RefSeq Protein ID . . .
CPD Ncbi Taxon id . . .
DDG intra MT-ND1:A64S:T245A:0.190663:0.249641:-0.0212179;MT-ND1:A64S:T245P:-1.74279:0.249641:-2.15484;MT-ND1:A64S:T245S:0.824595:0.249641:0.59531;MT-ND1:A64S:T245M:-0.13552:0.249641:-0.233521;MT-ND1:A64S:T245K:2.92241:0.249641:2.88431;MT-ND1:A64S:T246M:0.355215:0.249641:0.113932;MT-ND1:A64S:T246S:0.1281:0.249641:-0.121189;MT-ND1:A64S:T246A:0.642818:0.249641:0.393197;MT-ND1:A64S:T246K:0.817687:0.249641:0.53622;MT-ND1:A64S:T246P:-0.709822:0.249641:-0.949064;MT-ND1:A64S:D248E:0.213008:0.249641:-0.0363487;MT-ND1:A64S:D248G:1.27018:0.249641:1.01568;MT-ND1:A64S:D248V:0.692142:0.249641:0.460803;MT-ND1:A64S:D248A:0.771225:0.249641:0.469864;MT-ND1:A64S:D248H:0.980396:0.249641:0.709978;MT-ND1:A64S:D248Y:0.223799:0.249641:-0.0124181;MT-ND1:A64S:D248N:0.513177:0.249641:0.27503;MT-ND1:A64S:L250F:0.285672:0.249641:0.0290031;MT-ND1:A64S:L250R:-0.27005:0.249641:-0.508427;MT-ND1:A64S:L250V:0.739592:0.249641:0.518854;MT-ND1:A64S:L250I:0.678127:0.249641:0.412886;MT-ND1:A64S:L250P:1.24729:0.249641:1.11168;MT-ND1:A64S:L250H:0.34658:0.249641:0.108448;MT-ND1:A64S:A276G:0.623825:0.249641:0.386782;MT-ND1:A64S:A276E:0.303716:0.249641:0.0557187;MT-ND1:A64S:A276P:1.48856:0.249641:1.16054;MT-ND1:A64S:A276V:0.879093:0.249641:0.62968;MT-ND1:A64S:A276T:0.921644:0.249641:0.683193;MT-ND1:A64S:A276S:0.0497663:0.249641:-0.200186 MT-ND1:A64T:T245A:0.276091:0.187811:-0.0212179;MT-ND1:A64T:T245K:2.8503:0.187811:2.88431;MT-ND1:A64T:T245P:-1.77736:0.187811:-2.15484;MT-ND1:A64T:T245M:0.0980715:0.187811:-0.233521;MT-ND1:A64T:T245S:0.801626:0.187811:0.59531;MT-ND1:A64T:T246A:0.579593:0.187811:0.393197;MT-ND1:A64T:T246P:-0.775521:0.187811:-0.949064;MT-ND1:A64T:T246S:0.0648742:0.187811:-0.121189;MT-ND1:A64T:T246M:0.326569:0.187811:0.113932;MT-ND1:A64T:T246K:0.75316:0.187811:0.53622;MT-ND1:A64T:D248H:0.999094:0.187811:0.709978;MT-ND1:A64T:D248Y:0.325915:0.187811:-0.0124181;MT-ND1:A64T:D248G:1.25568:0.187811:1.01568;MT-ND1:A64T:D248A:0.729766:0.187811:0.469864;MT-ND1:A64T:D248E:0.211487:0.187811:-0.0363487;MT-ND1:A64T:D248N:0.480687:0.187811:0.27503;MT-ND1:A64T:D248V:0.786552:0.187811:0.460803;MT-ND1:A64T:L250I:0.606484:0.187811:0.412886;MT-ND1:A64T:L250F:0.218952:0.187811:0.0290031;MT-ND1:A64T:L250V:0.701436:0.187811:0.518854;MT-ND1:A64T:L250P:1.2973:0.187811:1.11168;MT-ND1:A64T:L250H:0.352982:0.187811:0.108448;MT-ND1:A64T:L250R:-0.354091:0.187811:-0.508427;MT-ND1:A64T:A276G:0.571749:0.187811:0.386782;MT-ND1:A64T:A276V:0.816931:0.187811:0.62968;MT-ND1:A64T:A276T:0.897024:0.187811:0.683193;MT-ND1:A64T:A276E:0.241989:0.187811:0.0557187;MT-ND1:A64T:A276P:1.44294:0.187811:1.16054;MT-ND1:A64T:A276S:-0.0237564:0.187811:-0.200186 MT-ND1:A64P:T245S:-0.801278:-1.39502:0.59531;MT-ND1:A64P:T245K:0.807853:-1.39502:2.88431;MT-ND1:A64P:T245A:-1.35626:-1.39502:-0.0212179;MT-ND1:A64P:T245P:-3.55983:-1.39502:-2.15484;MT-ND1:A64P:T245M:-1.6935:-1.39502:-0.233521;MT-ND1:A64P:T246K:-0.851043:-1.39502:0.53622;MT-ND1:A64P:T246A:-1.00295:-1.39502:0.393197;MT-ND1:A64P:T246S:-1.51726:-1.39502:-0.121189;MT-ND1:A64P:T246M:-1.26842:-1.39502:0.113932;MT-ND1:A64P:T246P:-2.35894:-1.39502:-0.949064;MT-ND1:A64P:D248H:-0.652272:-1.39502:0.709978;MT-ND1:A64P:D248Y:-1.31704:-1.39502:-0.0124181;MT-ND1:A64P:D248N:-1.12795:-1.39502:0.27503;MT-ND1:A64P:D248G:-0.343827:-1.39502:1.01568;MT-ND1:A64P:D248A:-0.892202:-1.39502:0.469864;MT-ND1:A64P:D248V:-0.989584:-1.39502:0.460803;MT-ND1:A64P:D248E:-1.43335:-1.39502:-0.0363487;MT-ND1:A64P:L250R:-1.93156:-1.39502:-0.508427;MT-ND1:A64P:L250V:-0.882259:-1.39502:0.518854;MT-ND1:A64P:L250I:-0.969771:-1.39502:0.412886;MT-ND1:A64P:L250P:-0.416392:-1.39502:1.11168;MT-ND1:A64P:L250H:-1.24722:-1.39502:0.108448;MT-ND1:A64P:L250F:-1.32045:-1.39502:0.0290031;MT-ND1:A64P:A276V:-0.765791:-1.39502:0.62968;MT-ND1:A64P:A276T:-0.717143:-1.39502:0.683193;MT-ND1:A64P:A276G:-1.0173:-1.39502:0.386782;MT-ND1:A64P:A276P:-0.384061:-1.39502:1.16054;MT-ND1:A64P:A276E:-1.33989:-1.39502:0.0557187;MT-ND1:A64P:A276S:-1.60267:-1.39502:-0.200186
DDG intra interface . . .
DDG inter MT-ND1:MT-ND3:5lc5:H:A:A64S:S45A:-0.09243:-0.015329361:-0.0903697982;MT-ND1:MT-ND3:5lc5:H:A:A64S:S45F:-0.23046:-0.015329361:-0.184449762;MT-ND1:MT-ND3:5lc5:H:A:A64S:S45T:0.13552:-0.015329361:0.215980917;MT-ND1:MT-ND3:5lc5:H:A:A64S:S45P:-1.0989:-0.015329361:-1.09178007;MT-ND1:MT-ND3:5lc5:H:A:A64S:S45C:-0.40206:-0.015329361:-0.407060623;MT-ND1:MT-ND3:5lc5:H:A:A64S:S45Y:-0.24798:-0.015329361:-0.209069446;MT-ND1:MT-ND3:5ldw:H:A:A64S:P46T:0.44609:-0.00129890442:0.476390839;MT-ND1:MT-ND3:5ldw:H:A:A64S:P46R:-0.46345:-0.00129890442:-0.374820709;MT-ND1:MT-ND3:5ldw:H:A:A64S:P46L:-0.45383:-0.00129890442:-0.427488327;MT-ND1:MT-ND3:5ldw:H:A:A64S:P46H:-0.09613:-0.00129890442:-0.123018265;MT-ND1:MT-ND3:5ldw:H:A:A64S:P46S:0.22519:-0.00129890442:0.256430447;MT-ND1:MT-ND3:5ldw:H:A:A64S:P46A:0.13265:-0.00129890442:0.124702454;MT-ND1:MT-ND3:5ldw:H:A:A64S:S45A:-0.01984:-0.00129890442:-0.0156085966;MT-ND1:MT-ND3:5ldw:H:A:A64S:S45F:0.01067:-0.00129890442:0.122009657;MT-ND1:MT-ND3:5ldw:H:A:A64S:S45T:0.31238:-0.00129890442:0.170780182;MT-ND1:MT-ND3:5ldw:H:A:A64S:S45P:-0.31463:-0.00129890442:-0.288380057;MT-ND1:MT-ND3:5ldw:H:A:A64S:S45C:-0.32393:-0.00129890442:-0.0661293045;MT-ND1:MT-ND3:5ldw:H:A:A64S:S45Y:0.34543:-0.00129890442:0.377010345;MT-ND1:MT-ND3:5ldx:H:A:A64S:P46T:0.19556:-0.00452117901:0.200049967;MT-ND1:MT-ND3:5ldx:H:A:A64S:P46R:-0.44234:-0.00452117901:-0.366769791;MT-ND1:MT-ND3:5ldx:H:A:A64S:P46L:-0.54013:-0.00452117901:-0.57003057;MT-ND1:MT-ND3:5ldx:H:A:A64S:P46H:-0.18595:-0.00452117901:-0.150340647;MT-ND1:MT-ND3:5ldx:H:A:A64S:P46S:0.19682:-0.00452117901:0.202388763;MT-ND1:MT-ND3:5ldx:H:A:A64S:P46A:0.16036:-0.00452117901:0.17194137;MT-ND1:MT-ND3:5ldx:H:A:A64S:S45A:0.54492:-0.00452117901:0.531179786;MT-ND1:MT-ND3:5ldx:H:A:A64S:S45F:0.50879:-0.00452117901:0.507999063;MT-ND1:MT-ND3:5ldx:H:A:A64S:S45T:0.37223:-0.00452117901:0.424250036;MT-ND1:MT-ND3:5ldx:H:A:A64S:S45P:0.74854:-0.00452117901:0.854759216;MT-ND1:MT-ND3:5ldx:H:A:A64S:S45C:0.49515:-0.00452117901:0.429790109;MT-ND1:MT-ND3:5ldx:H:A:A64S:S45Y:0.50502:-0.00452117901:0.507420719 MT-ND1:MT-ND3:5lc5:H:A:A64T:S45F:-0.01885:0.20746994:-0.184449762;MT-ND1:MT-ND3:5lc5:H:A:A64T:S45Y:0.03366:0.20746994:-0.209069446;MT-ND1:MT-ND3:5lc5:H:A:A64T:S45A:0.11013:0.20746994:-0.0903697982;MT-ND1:MT-ND3:5lc5:H:A:A64T:S45T:0.38004:0.20746994:0.215980917;MT-ND1:MT-ND3:5lc5:H:A:A64T:S45C:-0.26711:0.20746994:-0.407060623;MT-ND1:MT-ND3:5lc5:H:A:A64T:S45P:-0.9239:0.20746994:-1.09178007;MT-ND1:MT-ND3:5ldw:H:A:A64T:P46A:0.24139:0.10172081:0.124702454;MT-ND1:MT-ND3:5ldw:H:A:A64T:P46S:0.33821:0.10172081:0.256430447;MT-ND1:MT-ND3:5ldw:H:A:A64T:P46T:0.5889:0.10172081:0.476390839;MT-ND1:MT-ND3:5ldw:H:A:A64T:P46R:-0.35933:0.10172081:-0.374820709;MT-ND1:MT-ND3:5ldw:H:A:A64T:P46L:-0.40207:0.10172081:-0.427488327;MT-ND1:MT-ND3:5ldw:H:A:A64T:P46H:-0.01653:0.10172081:-0.123018265;MT-ND1:MT-ND3:5ldw:H:A:A64T:S45F:0.05697:0.10172081:0.122009657;MT-ND1:MT-ND3:5ldw:H:A:A64T:S45Y:0.80886:0.10172081:0.377010345;MT-ND1:MT-ND3:5ldw:H:A:A64T:S45A:0.08599:0.10172081:-0.0156085966;MT-ND1:MT-ND3:5ldw:H:A:A64T:S45T:0.35343:0.10172081:0.170780182;MT-ND1:MT-ND3:5ldw:H:A:A64T:S45C:0.00913:0.10172081:-0.0661293045;MT-ND1:MT-ND3:5ldw:H:A:A64T:S45P:-0.18431:0.10172081:-0.288380057;MT-ND1:MT-ND3:5ldx:H:A:A64T:P46A:0.27275:0.107588194:0.17194137;MT-ND1:MT-ND3:5ldx:H:A:A64T:P46S:0.32556:0.107588194:0.202388763;MT-ND1:MT-ND3:5ldx:H:A:A64T:P46T:0.30775:0.107588194:0.200049967;MT-ND1:MT-ND3:5ldx:H:A:A64T:P46R:-0.37666:0.107588194:-0.366769791;MT-ND1:MT-ND3:5ldx:H:A:A64T:P46L:-0.42001:0.107588194:-0.57003057;MT-ND1:MT-ND3:5ldx:H:A:A64T:P46H:-0.06405:0.107588194:-0.150340647;MT-ND1:MT-ND3:5ldx:H:A:A64T:S45F:0.62142:0.107588194:0.507999063;MT-ND1:MT-ND3:5ldx:H:A:A64T:S45Y:0.61503:0.107588194:0.507420719;MT-ND1:MT-ND3:5ldx:H:A:A64T:S45A:0.65342:0.107588194:0.531179786;MT-ND1:MT-ND3:5ldx:H:A:A64T:S45T:0.48902:0.107588194:0.424250036;MT-ND1:MT-ND3:5ldx:H:A:A64T:S45C:0.6507:0.107588194:0.429790109;MT-ND1:MT-ND3:5ldx:H:A:A64T:S45P:0.88499:0.107588194:0.854759216 MT-ND1:MT-ND3:5lc5:H:A:A64P:S45Y:3.25654:3.39117956:-0.209069446;MT-ND1:MT-ND3:5lc5:H:A:A64P:S45P:2.34015:3.39117956:-1.09178007;MT-ND1:MT-ND3:5lc5:H:A:A64P:S45T:3.61842:3.39117956:0.215980917;MT-ND1:MT-ND3:5lc5:H:A:A64P:S45A:3.33631:3.39117956:-0.0903697982;MT-ND1:MT-ND3:5lc5:H:A:A64P:S45C:3.08538:3.39117956:-0.407060623;MT-ND1:MT-ND3:5lc5:H:A:A64P:S45F:3.22824:3.39117956:-0.184449762;MT-ND1:MT-ND3:5ldw:H:A:A64P:P46R:1.25886:1.89254951:-0.374820709;MT-ND1:MT-ND3:5ldw:H:A:A64P:P46T:2.20987:1.89254951:0.476390839;MT-ND1:MT-ND3:5ldw:H:A:A64P:P46S:1.98009:1.89254951:0.256430447;MT-ND1:MT-ND3:5ldw:H:A:A64P:P46L:1.26295:1.89254951:-0.427488327;MT-ND1:MT-ND3:5ldw:H:A:A64P:P46A:2.16525:1.89254951:0.124702454;MT-ND1:MT-ND3:5ldw:H:A:A64P:P46H:1.50292:1.89254951:-0.123018265;MT-ND1:MT-ND3:5ldw:H:A:A64P:S45Y:2.15745:1.89254951:0.377010345;MT-ND1:MT-ND3:5ldw:H:A:A64P:S45P:1.51753:1.89254951:-0.288380057;MT-ND1:MT-ND3:5ldw:H:A:A64P:S45T:2.16184:1.89254951:0.170780182;MT-ND1:MT-ND3:5ldw:H:A:A64P:S45A:1.82161:1.89254951:-0.0156085966;MT-ND1:MT-ND3:5ldw:H:A:A64P:S45C:1.58854:1.89254951:-0.0661293045;MT-ND1:MT-ND3:5ldw:H:A:A64P:S45F:2.22822:1.89254951:0.122009657;MT-ND1:MT-ND3:5ldx:H:A:A64P:P46R:3.38708:3.81227994:-0.366769791;MT-ND1:MT-ND3:5ldx:H:A:A64P:P46T:2.83305:3.81227994:0.200049967;MT-ND1:MT-ND3:5ldx:H:A:A64P:P46S:3.24829:3.81227994:0.202388763;MT-ND1:MT-ND3:5ldx:H:A:A64P:P46L:3.03385:3.81227994:-0.57003057;MT-ND1:MT-ND3:5ldx:H:A:A64P:P46A:3.56607:3.81227994:0.17194137;MT-ND1:MT-ND3:5ldx:H:A:A64P:P46H:3.36807:3.81227994:-0.150340647;MT-ND1:MT-ND3:5ldx:H:A:A64P:S45Y:4.3976:3.81227994:0.507420719;MT-ND1:MT-ND3:5ldx:H:A:A64P:S45P:4.03637:3.81227994:0.854759216;MT-ND1:MT-ND3:5ldx:H:A:A64P:S45T:3.51497:3.81227994:0.424250036;MT-ND1:MT-ND3:5ldx:H:A:A64P:S45A:3.25567:3.81227994:0.531179786;MT-ND1:MT-ND3:5ldx:H:A:A64P:S45C:3.28226:3.81227994:0.429790109;MT-ND1:MT-ND3:5ldx:H:A:A64P:S45F:3.71931:3.81227994:0.507999063
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