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10158 (T > C)

General info

Chr
chrM
Start
10158
End
10158
Ref
T
Alt
C
Mitimpact ID
MI.15172
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot name
NU3M_HUMAN
Uniprot ID
P03897
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Gene position
100
AA pos
34
AA ref
S
AA alt
P
Codon substitution
Tcc/Ccc
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Powered by MitoWheel

Conservation

PhyloP 100v
-2.73469 Conservation Score
PhastCons 100v
0 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
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
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
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
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-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
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
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
10158T>C
MITOMAP Disease Het/Hom
+/+
MITOMAP Disease Clinical info
Leigh disease / melas
MITOMAP Disease Status
Cfrm [p]
MITOMAP Disease GenBank Freq
0.000%(0.000%)
MITOMAP Disease GenBank Seqs
0 (0)
MITOMAP Disease GenBank Curated refs
35
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
rs199476117

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
.

10158 (T > A)

General info

Chr
chrM
Start
10158
End
10158
Ref
T
Alt
A
Mitimpact ID
MI.15173
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot name
NU3M_HUMAN
Uniprot ID
P03897
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Gene position
100
AA pos
34
AA ref
S
AA alt
T
Codon substitution
Tcc/Acc
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Powered by MitoWheel

Conservation

PhyloP 100v
-2.73469 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
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
0.00002
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
1
Gnomad31 filter
Pass
Gnomad31 AC hom
3
Gnomad31 AC het
0
Gnomad31 AF hom
0.00005315944
Gnomad31 AF het
0
Gnomad31 AN
56434
HelixMTdb AC hom
3.0
HelixMTdb AF hom
1.530745e-05
HelixMTdb AC het
0.0
HelixMTdb AF het
0.0
HelixMTdb mean ARF
.
HelixMTdb max ARF
.
COSMIC 90
.
dbSNP 155
rs199476117

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
.

10158 (T > G)

General info

Chr
chrM
Start
10158
End
10158
Ref
T
Alt
G
Mitimpact ID
MI.15174
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot name
NU3M_HUMAN
Uniprot ID
P03897
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Gene position
100
AA pos
34
AA ref
S
AA alt
A
Codon substitution
Tcc/Gcc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-2.73469 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
Medium 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
0.00002
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
1
Gnomad31 filter
Pass
Gnomad31 AC hom
1
Gnomad31 AC het
1
Gnomad31 AF hom
0.00001772013
Gnomad31 AF het
0.00001772013
Gnomad31 AN
56433
HelixMTdb AC hom
4.0
HelixMTdb AF hom
2.0409934e-05
HelixMTdb AC het
0.0
HelixMTdb AF het
0.0
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
.
~ 10158 (T/C) 10158 (T/A) 10158 (T/G)
~ 10158 (Tcc/Ccc) 10158 (Tcc/Acc) 10158 (Tcc/Gcc)
Chr chrM chrM chrM
Start 10158 10158 10158
End 10158 10158 10158
Ref T T T
Alt C A G
MitImpact id MI.15172 MI.15173 MI.15174
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 100 100 100
AA position 34 34 34
AA ref S S S
AA alt P T A
Codon substitution Tcc/Ccc Tcc/Acc Tcc/Gcc
PhyloP 100V -2.73469 -2.73469 -2.73469
PhastCons 100V 0 0 0
PolyPhen2 possibly_damaging benign benign
PolyPhen2 score 0.47 0.0 0.0
SIFT neutral neutral neutral
SIFT score 0.34 0.45 0.57
SIFT4G Damaging Tolerated Tolerated
SIFT4G score 0.015 0.179 0.395
FatHmm neutral neutral neutral
FatHmm score -2.39 -1.1 -0.57
FatHmmW neutral neutral neutral
FatHmmW score 0.88 0.92 0.95
PROVEAN neutral neutral neutral
PROVEAN score -2.09 0.1 0.51
MutationAssessor low impact neutral impact neutral impact
MutationAssessor score 1.78 0.71 0.01
EFIN SP damaging neutral neutral
EFIN SP score 0.2 0.85 0.86
EFIN HD neutral neutral neutral
EFIN HD score 0.42 0.99 0.98
CADD deleterious neutral neutral
CADD score 2.25 0.59 -0.2
CADD phred 17.84 8.09 1.1
VEST pvalue 0.1 0.3 0.31
VEST FDR 0.4 0.45 0.45
PANTHER neutral neutral neutral
PANTHER score 0.5 0.16 0.16
PhD-SNP disease neutral neutral
PhD-SNP score 0.72 0.28 0.18
SNAP neutral neutral neutral
SNAP score 0.48 0.24 0.22
Meta-SNP neutral neutral neutral
Meta-SNP score 0.42 0.44 0.29
Meta-SNP RI 2 1 4
CAROL neutral neutral neutral
CAROL score 0.62 0.54 0.42
Condel neutral deleterious deleterious
Condel score 0.44 0.73 0.79
COVEC WMV neutral neutral neutral
COVEC WMV score -3 -6 -6
MtoolBox neutral neutral neutral
MtoolBox DS 0.4 0.1 0.1
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score -0.67 1.99 1.99
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.03 0.14 0.26
MutationAssessor transf medium impact medium impact low impact
MutationAssessor transf score 0.52 -0.46 -1.1
CHASM pvalue 0.13 0.34 0.28
CHASM FDR 0.8 0.8 0.8
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.95 0.37 0.31
APOGEE2 Likely-pathogenic Benign Benign
APOGEE2 score 0.84413850510661 0.0271625478344544 0.0470810836355675
SNPDryad score 0.59 0.02 0.06
MutationTaster disease_causing_automatic polymorphism polymorphism
MutationTaster score 0 1 1
DEOGEN2 score 0.44 0.19 0.17
Mitoclass.1 neutral neutral neutral
dbSNP 155 id rs199476117 rs199476117 .
ClinVar July2022 Variation id . . .
ClinVar July2022 CLNSIG . . .
ClinVar July2022 CLNDN . . .
ClinVar July2022 CLNDISDB . . .
COSMIC 90 . . .
MITOMAP Allele T10158C . .
MITOMAP Disease Het/Hom +/+ . .
MITOMAP Disease Clinical info Leigh Disease / MELAS . .
MITOMAP Disease Status Cfrm [P] . .
MITOMAP Disease GenBank Freq 0.000%(0.000%) . .
MITOMAP Disease GenBank Seqs 0 (0) . .
MITOMAP Disease GenBank Curated refs 35 . .
MITOMAP General GenBank Freq . 0.00002 0.00002
MITOMAP General GenBank Seqs . 1 1
MITOMAP General Curated refs . 1 1
gnomAD 3.1 filter . PASS PASS
gnomAD 3.1 AC Homo . 3 1
gnomAD 3.1 AC Het . 0 1
gnomAD 3.1 AF Hom . 0.00005315944 0.00001772013
gnomAD 3.1 AF Het . 0 0.00001772013
gnomAD 3.1 AN . 56434 56433
HelixMTdb AC Hom . 3.0 4.0
HelixMTdb AF Hom . 1.530745e-05 2.0409934e-05
HelixMTdb AC Het . 0.0 0.0
HelixMTdb AF Het . 0.0 0.0
HelixMTdb mean ARF . . .
HelixMTdb max ARF . . .
EVmutation MT-ND3_34S|36P:0.238298;35T:0.159564;96I:0.154365;43P:0.141245;112D:0.138103;37Y:0.117681;83N:0.09767;94L:0.097578;95I:0.095793;48R:0.085602;67L:0.079523;93L:0.072904;42D:0.063535 MT-ND3_34S|36P:0.238298;35T:0.159564;96I:0.154365;43P:0.141245;112D:0.138103;37Y:0.117681;83N:0.09767;94L:0.097578;95I:0.095793;48R:0.085602;67L:0.079523;93L:0.072904;42D:0.063535 MT-ND3_34S|36P:0.238298;35T:0.159564;96I:0.154365;43P:0.141245;112D:0.138103;37Y:0.117681;83N:0.09767;94L:0.097578;95I:0.095793;48R:0.085602;67L:0.079523;93L:0.072904;42D:0.063535
Site A InterP ND3_34 ND3_34 ND3_34
Site B InterP ND1_280;ND2_84;ND2_118;ND4L_57;ND4L_22;ND4L_26;ND6_122;ND6_44;ND2_90;ND2_318;ND2_151;ND4L_59;ND4L_3;ND4L_44;ND4L_6;ND4L_51;ND4L_5;ND4L_14;ND4L_55;ND4L_9;ND4L_46;ND6_104 ND1_280;ND2_84;ND2_118;ND4L_57;ND4L_22;ND4L_26;ND6_122;ND6_44;ND2_90;ND2_318;ND2_151;ND4L_59;ND4L_3;ND4L_44;ND4L_6;ND4L_51;ND4L_5;ND4L_14;ND4L_55;ND4L_9;ND4L_46;ND6_104 ND1_280;ND2_84;ND2_118;ND4L_57;ND4L_22;ND4L_26;ND6_122;ND6_44;ND2_90;ND2_318;ND2_151;ND4L_59;ND4L_3;ND4L_44;ND4L_6;ND4L_51;ND4L_5;ND4L_14;ND4L_55;ND4L_9;ND4L_46;ND6_104
Covariation Score InterP mfDCA_25.87;mfDCA_22.63;mfDCA_22.18;mfDCA_24.22;mfDCA_22.26;mfDCA_21.04;mfDCA_28.76;mfDCA_25.59;cMI_30.82558;cMI_24.13162;cMI_18.54565;cMI_19.9907;cMI_18.27721;cMI_15.89881;cMI_15.33126;cMI_15.26561;cMI_14.38634;cMI_14.2018;cMI_13.19658;cMI_13.00923;cMI_12.39609;cMI_14.91167 mfDCA_25.87;mfDCA_22.63;mfDCA_22.18;mfDCA_24.22;mfDCA_22.26;mfDCA_21.04;mfDCA_28.76;mfDCA_25.59;cMI_30.82558;cMI_24.13162;cMI_18.54565;cMI_19.9907;cMI_18.27721;cMI_15.89881;cMI_15.33126;cMI_15.26561;cMI_14.38634;cMI_14.2018;cMI_13.19658;cMI_13.00923;cMI_12.39609;cMI_14.91167 mfDCA_25.87;mfDCA_22.63;mfDCA_22.18;mfDCA_24.22;mfDCA_22.26;mfDCA_21.04;mfDCA_28.76;mfDCA_25.59;cMI_30.82558;cMI_24.13162;cMI_18.54565;cMI_19.9907;cMI_18.27721;cMI_15.89881;cMI_15.33126;cMI_15.26561;cMI_14.38634;cMI_14.2018;cMI_13.19658;cMI_13.00923;cMI_12.39609;cMI_14.91167
Site A IntraP ND3_34 ND3_34 ND3_34
Site B IntraP ND3_95;ND3_107;ND3_9;ND3_11;ND3_91;ND3_7;ND3_16;ND3_49;ND3_44;ND3_9;ND3_82;ND3_35;ND3_99;ND3_95;ND3_4;ND3_79;ND3_107;ND3_85;ND3_89 ND3_95;ND3_107;ND3_9;ND3_11;ND3_91;ND3_7;ND3_16;ND3_49;ND3_44;ND3_9;ND3_82;ND3_35;ND3_99;ND3_95;ND3_4;ND3_79;ND3_107;ND3_85;ND3_89 ND3_95;ND3_107;ND3_9;ND3_11;ND3_91;ND3_7;ND3_16;ND3_49;ND3_44;ND3_9;ND3_82;ND3_35;ND3_99;ND3_95;ND3_4;ND3_79;ND3_107;ND3_85;ND3_89
Covariation Score IntraP mfDCA_18.6489;mfDCA_16.7056;mfDCA_29.6342;cMI_12.833122;cMI_11.372559;cMI_9.969296;cMI_9.772694;mfDCA_35.5132;mfDCA_31.0358;mfDCA_29.6342;mfDCA_29.3799;mfDCA_29.1947;mfDCA_28.7812;mfDCA_18.6489;mfDCA_18.0247;mfDCA_17.2191;mfDCA_16.7056;mfDCA_16.6283;mfDCA_16.2406 mfDCA_18.6489;mfDCA_16.7056;mfDCA_29.6342;cMI_12.833122;cMI_11.372559;cMI_9.969296;cMI_9.772694;mfDCA_35.5132;mfDCA_31.0358;mfDCA_29.6342;mfDCA_29.3799;mfDCA_29.1947;mfDCA_28.7812;mfDCA_18.6489;mfDCA_18.0247;mfDCA_17.2191;mfDCA_16.7056;mfDCA_16.6283;mfDCA_16.2406 mfDCA_18.6489;mfDCA_16.7056;mfDCA_29.6342;cMI_12.833122;cMI_11.372559;cMI_9.969296;cMI_9.772694;mfDCA_35.5132;mfDCA_31.0358;mfDCA_29.6342;mfDCA_29.3799;mfDCA_29.1947;mfDCA_28.7812;mfDCA_18.6489;mfDCA_18.0247;mfDCA_17.2191;mfDCA_16.7056;mfDCA_16.6283;mfDCA_16.2406
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-ND3:S34P:L107M:0.548673:0.727451:-0.186263;MT-ND3:S34P:L107P:5.50837:0.727451:4.56316;MT-ND3:S34P:L107V:2.31255:0.727451:1.58272;MT-ND3:S34P:L107Q:1.70736:0.727451:0.964638;MT-ND3:S34P:L107R:1.38663:0.727451:0.654602;MT-ND3:S34P:T35A:0.826253:0.727451:0.0855016;MT-ND3:S34P:T35S:1.04628:0.727451:0.233842;MT-ND3:S34P:T35N:1.1268:0.727451:0.309927;MT-ND3:S34P:T35I:0.282204:0.727451:-0.515883;MT-ND3:S34P:T35P:1.16727:0.727451:0.442305;MT-ND3:S34P:M44T:1.13607:0.727451:0.4131;MT-ND3:S34P:M44V:1.21785:0.727451:0.489564;MT-ND3:S34P:M44K:1.06238:0.727451:0.331748;MT-ND3:S34P:M44I:1.04539:0.727451:0.322536;MT-ND3:S34P:M44L:1.09157:0.727451:0.360285;MT-ND3:S34P:V49G:1.70031:0.727451:0.888794;MT-ND3:S34P:V49D:0.149364:0.727451:-0.607087;MT-ND3:S34P:V49I:0.242226:0.727451:-0.482548;MT-ND3:S34P:V49A:0.937724:0.727451:0.193963;MT-ND3:S34P:V49F:0.123732:0.727451:-0.639481;MT-ND3:S34P:V49L:0.454091:0.727451:-0.289594;MT-ND3:S34P:L79R:1.71445:0.727451:1.00907;MT-ND3:S34P:L79P:4.3724:0.727451:3.64483;MT-ND3:S34P:L79M:0.556009:0.727451:-0.174798;MT-ND3:S34P:L79V:2.42671:0.727451:1.69291;MT-ND3:S34P:L79Q:1.40825:0.727451:0.615227;MT-ND3:S34P:T82A:0.536349:0.727451:-0.191936;MT-ND3:S34P:T82I:0.697307:0.727451:-0.0304783;MT-ND3:S34P:T82N:0.505022:0.727451:-0.22203;MT-ND3:S34P:T82P:0.0779146:0.727451:-0.650578;MT-ND3:S34P:T82S:0.487112:0.727451:-0.242397;MT-ND3:S34P:A4G:1.81671:0.727451:1.08914;MT-ND3:S34P:A4S:1.63003:0.727451:0.901348;MT-ND3:S34P:A4P:-0.754722:0.727451:-1.526;MT-ND3:S34P:A4V:0.86379:0.727451:0.176529;MT-ND3:S34P:A4T:2.33205:0.727451:1.29799;MT-ND3:S34P:A4D:0.929645:0.727451:0.190562 MT-ND3:S34T:L107M:-0.112921:0.0669337:-0.186263;MT-ND3:S34T:L107P:4.82899:0.0669337:4.56316;MT-ND3:S34T:L107V:1.65112:0.0669337:1.58272;MT-ND3:S34T:L107Q:1.06368:0.0669337:0.964638;MT-ND3:S34T:T35I:-0.409125:0.0669337:-0.515883;MT-ND3:S34T:T35P:0.380437:0.0669337:0.442305;MT-ND3:S34T:T35N:0.434286:0.0669337:0.309927;MT-ND3:S34T:T35S:0.311889:0.0669337:0.233842;MT-ND3:S34T:M44L:0.421102:0.0669337:0.360285;MT-ND3:S34T:M44T:0.476336:0.0669337:0.4131;MT-ND3:S34T:M44K:0.395013:0.0669337:0.331748;MT-ND3:S34T:M44V:0.556805:0.0669337:0.489564;MT-ND3:S34T:V49I:-0.418962:0.0669337:-0.482548;MT-ND3:S34T:V49F:-0.568474:0.0669337:-0.639481;MT-ND3:S34T:V49G:0.99295:0.0669337:0.888794;MT-ND3:S34T:V49D:-0.547124:0.0669337:-0.607087;MT-ND3:S34T:V49L:-0.223925:0.0669337:-0.289594;MT-ND3:S34T:L79M:-0.103305:0.0669337:-0.174798;MT-ND3:S34T:L79R:1.05801:0.0669337:1.00907;MT-ND3:S34T:L79V:1.75901:0.0669337:1.69291;MT-ND3:S34T:L79P:3.71119:0.0669337:3.64483;MT-ND3:S34T:T82N:-0.15137:0.0669337:-0.22203;MT-ND3:S34T:T82S:-0.175297:0.0669337:-0.242397;MT-ND3:S34T:T82P:-0.583742:0.0669337:-0.650578;MT-ND3:S34T:T82A:-0.125015:0.0669337:-0.191936;MT-ND3:S34T:T35A:0.159488:0.0669337:0.0855016;MT-ND3:S34T:L79Q:0.662474:0.0669337:0.615227;MT-ND3:S34T:L107R:0.73573:0.0669337:0.654602;MT-ND3:S34T:V49A:0.269701:0.0669337:0.193963;MT-ND3:S34T:M44I:0.394216:0.0669337:0.322536;MT-ND3:S34T:T82I:0.0365844:0.0669337:-0.0304783;MT-ND3:S34T:A4G:1.15604:0.0669337:1.08914;MT-ND3:S34T:A4V:0.441354:0.0669337:0.176529;MT-ND3:S34T:A4S:0.967652:0.0669337:0.901348;MT-ND3:S34T:A4P:-1.45058:0.0669337:-1.526;MT-ND3:S34T:A4T:1.46285:0.0669337:1.29799;MT-ND3:S34T:A4D:0.219138:0.0669337:0.190562 MT-ND3:S34A:L107M:-0.0980692:0.0916949:-0.186263;MT-ND3:S34A:L107V:1.66859:0.0916949:1.58272;MT-ND3:S34A:L107P:4.79278:0.0916949:4.56316;MT-ND3:S34A:L107R:0.753058:0.0916949:0.654602;MT-ND3:S34A:L107Q:1.07183:0.0916949:0.964638;MT-ND3:S34A:T35N:0.375578:0.0916949:0.309927;MT-ND3:S34A:T35A:0.159523:0.0916949:0.0855016;MT-ND3:S34A:T35P:0.38896:0.0916949:0.442305;MT-ND3:S34A:T35S:0.311047:0.0916949:0.233842;MT-ND3:S34A:T35I:-0.437969:0.0916949:-0.515883;MT-ND3:S34A:M44V:0.580765:0.0916949:0.489564;MT-ND3:S34A:M44I:0.41097:0.0916949:0.322536;MT-ND3:S34A:M44K:0.423855:0.0916949:0.331748;MT-ND3:S34A:M44L:0.442666:0.0916949:0.360285;MT-ND3:S34A:M44T:0.501284:0.0916949:0.4131;MT-ND3:S34A:V49I:-0.399223:0.0916949:-0.482548;MT-ND3:S34A:V49F:-0.543118:0.0916949:-0.639481;MT-ND3:S34A:V49D:-0.514398:0.0916949:-0.607087;MT-ND3:S34A:V49L:-0.188779:0.0916949:-0.289594;MT-ND3:S34A:V49A:0.286066:0.0916949:0.193963;MT-ND3:S34A:V49G:1.02158:0.0916949:0.888794;MT-ND3:S34A:L79M:-0.0789711:0.0916949:-0.174798;MT-ND3:S34A:L79Q:0.741995:0.0916949:0.615227;MT-ND3:S34A:L79V:1.79764:0.0916949:1.69291;MT-ND3:S34A:L79P:3.73358:0.0916949:3.64483;MT-ND3:S34A:L79R:1.08647:0.0916949:1.00907;MT-ND3:S34A:T82S:-0.150704:0.0916949:-0.242397;MT-ND3:S34A:T82N:-0.127697:0.0916949:-0.22203;MT-ND3:S34A:T82A:-0.100202:0.0916949:-0.191936;MT-ND3:S34A:T82I:0.0612726:0.0916949:-0.0304783;MT-ND3:S34A:T82P:-0.559105:0.0916949:-0.650578;MT-ND3:S34A:A4V:0.205849:0.0916949:0.176529;MT-ND3:S34A:A4P:-1.37703:0.0916949:-1.526;MT-ND3:S34A:A4S:0.992959:0.0916949:0.901348;MT-ND3:S34A:A4G:1.18061:0.0916949:1.08914;MT-ND3:S34A:A4T:1.54145:0.0916949:1.29799;MT-ND3:S34A:A4D:0.287236:0.0916949:0.190562
DDG intra interface MT-ND3:MT-ND1:5lc5:A:H:S34P:T11A:0.12608:-0.03459:0.17384;MT-ND3:MT-ND1:5lc5:A:H:S34P:T11I:-0.28838:-0.03459:-0.23954;MT-ND3:MT-ND1:5lc5:A:H:S34P:T11N:0.07564:-0.03459:0.10255;MT-ND3:MT-ND1:5lc5:A:H:S34P:T11P:1.06271:-0.03459:1.12302;MT-ND3:MT-ND1:5lc5:A:H:S34P:T11S:0.22462:-0.03459:0.26884;MT-ND3:MT-ND1:5ldw:A:H:S34P:T11A:-0.20089:-0.32915:0.19987;MT-ND3:MT-ND1:5ldw:A:H:S34P:T11I:-0.48939:-0.32915:-0.1174;MT-ND3:MT-ND1:5ldw:A:H:S34P:T11N:-0.22604:-0.32915:0.13924;MT-ND3:MT-ND1:5ldw:A:H:S34P:T11P:0.02548:-0.32915:0.40528;MT-ND3:MT-ND1:5ldw:A:H:S34P:T11S:-0.15002:-0.32915:0.25325;MT-ND3:MT-ND1:5ldx:A:H:S34P:T11A:-0.57218:-0.69431:0.13556;MT-ND3:MT-ND1:5ldx:A:H:S34P:T11I:-0.87464:-0.69431:-0.1541;MT-ND3:MT-ND1:5ldx:A:H:S34P:T11N:-0.51338:-0.69431:0.20002;MT-ND3:MT-ND1:5ldx:A:H:S34P:T11P:-0.0022:-0.69431:0.62655;MT-ND3:MT-ND1:5ldx:A:H:S34P:T11S:-0.55533:-0.69431:0.16256 MT-ND3:MT-ND1:5lc5:A:H:S34T:T11A:0.48173:0.29717:0.17384;MT-ND3:MT-ND1:5lc5:A:H:S34T:T11I:0.05827:0.29717:-0.23954;MT-ND3:MT-ND1:5lc5:A:H:S34T:T11N:0.36504:0.29717:0.10255;MT-ND3:MT-ND1:5lc5:A:H:S34T:T11P:1.33486:0.29717:1.12302;MT-ND3:MT-ND1:5lc5:A:H:S34T:T11S:0.57192:0.29717:0.26884;MT-ND3:MT-ND1:5ldw:A:H:S34T:T11A:1.70052:1.50149:0.19987;MT-ND3:MT-ND1:5ldw:A:H:S34T:T11I:1.41391:1.50149:-0.1174;MT-ND3:MT-ND1:5ldw:A:H:S34T:T11N:1.65315:1.50149:0.13924;MT-ND3:MT-ND1:5ldw:A:H:S34T:T11P:1.90656:1.50149:0.40528;MT-ND3:MT-ND1:5ldw:A:H:S34T:T11S:1.76809:1.50149:0.25325;MT-ND3:MT-ND1:5ldx:A:H:S34T:T11A:1.57915:1.38492:0.13556;MT-ND3:MT-ND1:5ldx:A:H:S34T:T11I:1.25354:1.38492:-0.1541;MT-ND3:MT-ND1:5ldx:A:H:S34T:T11N:1.57705:1.38492:0.20002;MT-ND3:MT-ND1:5ldx:A:H:S34T:T11P:2.06519:1.38492:0.62655;MT-ND3:MT-ND1:5ldx:A:H:S34T:T11S:1.61754:1.38492:0.16256 MT-ND3:MT-ND1:5lc5:A:H:S34A:T11A:-0.20905:-0.36992:0.17384;MT-ND3:MT-ND1:5lc5:A:H:S34A:T11I:-0.60968:-0.36992:-0.23954;MT-ND3:MT-ND1:5lc5:A:H:S34A:T11N:-0.31016:-0.36992:0.10255;MT-ND3:MT-ND1:5lc5:A:H:S34A:T11P:0.7082:-0.36992:1.12302;MT-ND3:MT-ND1:5lc5:A:H:S34A:T11S:-0.09481:-0.36992:0.26884;MT-ND3:MT-ND1:5ldw:A:H:S34A:T11A:0.45762:0.2565:0.19987;MT-ND3:MT-ND1:5ldw:A:H:S34A:T11I:0.14962:0.2565:-0.1174;MT-ND3:MT-ND1:5ldw:A:H:S34A:T11N:0.41055:0.2565:0.13924;MT-ND3:MT-ND1:5ldw:A:H:S34A:T11P:0.67586:0.2565:0.40528;MT-ND3:MT-ND1:5ldw:A:H:S34A:T11S:0.51267:0.2565:0.25325;MT-ND3:MT-ND1:5ldx:A:H:S34A:T11A:0.1276:-0.01016:0.13556;MT-ND3:MT-ND1:5ldx:A:H:S34A:T11I:-0.15844:-0.01016:-0.1541;MT-ND3:MT-ND1:5ldx:A:H:S34A:T11N:0.18813:-0.01016:0.20002;MT-ND3:MT-ND1:5ldx:A:H:S34A:T11P:0.57922:-0.01016:0.62655;MT-ND3:MT-ND1:5ldx:A:H:S34A:T11S:0.1956:-0.01016:0.16256
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