3736 (G > C)

General info

Chr
chrM
Start
3736
End
3736
Ref
G
Alt
C
Mitimpact ID
MI.11644
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
430
AA pos
144
AA ref
V
AA alt
L
Codon substitution
Gtc/Ctc
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Powered by MitoWheel

Conservation

PhyloP 100v
4.58 Conservation Score
PhastCons 100v
1 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
Disease 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

APOGEE
Pathogenic 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 March2020 ClinSig
.
ClinVar March2020 ClnDBN
.
ClinVar March2020 ClnAllele ID
.
ClinVar March2020 ClnDSDB
.
MITOMAP Allele
.
MITOMAP Phenotype
.
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
.
MITOMAP NRef
.
COSMIC 90
.
dbSNP 153

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
.

General info

Chr
chrM
Start
3736
End
3736
Ref
G
Alt
A
Mitimpact ID
MI.11645
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
430
AA pos
144
AA ref
V
AA alt
I
Codon substitution
Gtc/Atc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
4.58 Conservation Score
PhastCons 100v
1 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
Damaging Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor

Pathogenicity meta-predictors

APOGEE
Pathogenic 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 March2020 ClinSig
Benign
ClinVar March2020 ClnDBN
Leigh syndrome
ClinVar March2020 ClnAllele ID
680929
ClinVar March2020 ClnDSDB
Medgen:c0023264, omim:256000, orphanet:orpha506, snomed ct:29570005
MITOMAP Allele
MITOMAP Phenotype
Lhon
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
Reported
MITOMAP NRef
2
COSMIC 90
COSM6716702
dbSNP 153

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
0.89 CPD variant frequency
AA ref
V
CPD AA alt
I
Aln pos
145
Species name
Lepilemur hubbardorum, Lepilemur ruficaudatus, Pongo pygmaeus, Macaca sylvanus, Pongo abelii, Nomascus gabriellae
Ncbi taxon ID

3736 (G > T)

General info

Chr
chrM
Start
3736
End
3736
Ref
G
Alt
T
Mitimpact ID
MI.11646
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
430
AA pos
144
AA ref
V
AA alt
F
Codon substitution
Gtc/Ttc
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Powered by MitoWheel

Conservation

PhyloP 100v
4.58 Conservation Score
PhastCons 100v
1 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
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
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
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
High impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar March2020 ClinSig
.
ClinVar March2020 ClnDBN
.
ClinVar March2020 ClnAllele ID
.
ClinVar March2020 ClnDSDB
.
MITOMAP Allele
.
MITOMAP Phenotype
.
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
.
MITOMAP NRef
.
COSMIC 90
.
dbSNP 153

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
.

3737 (T > C)

General info

Chr
chrM
Start
3737
End
3737
Ref
T
Alt
C
Mitimpact ID
MI.11647
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
431
AA pos
144
AA ref
V
AA alt
A
Codon substitution
gTc/gCc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.11 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
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
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
Disease 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

APOGEE
Pathogenic 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
. 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
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 March2020 ClinSig
.
ClinVar March2020 ClnDBN
.
ClinVar March2020 ClnAllele ID
.
ClinVar March2020 ClnDSDB
.
MITOMAP Allele
.
MITOMAP Phenotype
.
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
.
MITOMAP NRef
.
COSMIC 90
.
dbSNP 153

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
.

3737 (T > G)

General info

Chr
chrM
Start
3737
End
3737
Ref
T
Alt
G
Mitimpact ID
MI.11648
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
431
AA pos
144
AA ref
V
AA alt
G
Codon substitution
gTc/gGc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.11 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
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
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
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 March2020 ClinSig
.
ClinVar March2020 ClnDBN
.
ClinVar March2020 ClnAllele ID
.
ClinVar March2020 ClnDSDB
.
MITOMAP Allele
.
MITOMAP Phenotype
.
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
.
MITOMAP NRef
.
COSMIC 90
.
dbSNP 153

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
.

3737 (T > A)

General info

Chr
chrM
Start
3737
End
3737
Ref
T
Alt
A
Mitimpact ID
MI.11649
Gene symbol
MT-ND1
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
431
AA pos
144
AA ref
V
AA alt
D
Codon substitution
gTc/gAc
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.11 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
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
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
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 March2020 ClinSig
.
ClinVar March2020 ClnDBN
.
ClinVar March2020 ClnAllele ID
.
ClinVar March2020 ClnDSDB
.
MITOMAP Allele
.
MITOMAP Phenotype
.
MITOMAP Homoplasmy
.
MITOMAP Heteroplasmy
.
MITOMAP Status
.
MITOMAP NRef
.
COSMIC 90
.
dbSNP 153

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
.
~ 3736 (G/C) 3736 (G/A) 3736 (G/T) 3737 (T/C) 3737 (T/G) 3737 (T/A)
~ 3736 (Gtc/Ctc) 3736 (Gtc/Atc) 3736 (Gtc/Ttc) 3737 (gTc/gCc) 3737 (gTc/gGc) 3737 (gTc/gAc)
Chr chrM chrM chrM chrM chrM chrM
Start 3736 3736 3736 3737 3737 3737
End 3736 3736 3736 3737 3737 3737
Ref G G G T T T
Alt C A T C G A
MitImpact id MI.11644 MI.11645 MI.11646 MI.11647 MI.11648 MI.11649
Gene symbol MT-ND1 MT-ND1 MT-ND1 MT-ND1 MT-ND1 MT-ND1
Respiratory Chain complex I I I I I I
Ensembl gene id ENSG00000198888 ENSG00000198888 ENSG00000198888 ENSG00000198888 ENSG00000198888 ENSG00000198888
Ensembl protein id ENSP00000354687 ENSP00000354687 ENSP00000354687 ENSP00000354687 ENSP00000354687 ENSP00000354687
Ensembl transcript id ENST00000361390 ENST00000361390 ENST00000361390 ENST00000361390 ENST00000361390 ENST00000361390
Uniprot name NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN
Uniprot id P03886 P03886 P03886 P03886 P03886 P03886
Ncbi gene id 4535 4535 4535 4535 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1 YP_003024026.1 YP_003024026.1 YP_003024026.1 YP_003024026.1
Gene position 430 430 430 431 431 431
AA position 144 144 144 144 144 144
AA ref V V V V V V
AA alt L I F A G D
Codon substitution Gtc/Ctc Gtc/Atc Gtc/Ttc gTc/gCc gTc/gGc gTc/gAc
PhyloP 100V 4.58 4.58 4.58 7.11 7.11 7.11
PhastCons 100V 1 1 1 1 1 1
PolyPhen2 benign benign benign possibly_damaging probably_damaging probably_damaging
PolyPhen2 score 0.39 0.05 0.11 0.64 0.93 0.95
SIFT neutral neutral neutral neutral neutral neutral
SIFT score 0.61 0.47 0.54 0.65 0.28 0.16
FatHmm neutral neutral deleterious deleterious deleterious deleterious
FatHmm score -1.51 -0.5 -4.24 -3.66 -5.79 -6.38
FatHmmW neutral neutral neutral neutral neutral neutral
FatHmmW score 2.45 2.66 2.25 2.27 2.23 2.22
PROVEAN deleterious neutral deleterious deleterious deleterious deleterious
PROVEAN score -2.71 -0.89 -4.54 -3.63 -6.36 -6.36
MutationAssessor medium impact low impact high impact medium impact high impact high impact
MutationAssessor score 2.62 1.92 4.74 3.1 4.18 4.74
EFIN SP neutral neutral neutral neutral neutral neutral
EFIN SP score 0.72 0.68 0.71 0.7 0.79 0.73
EFIN HD neutral neutral neutral neutral neutral neutral
EFIN HD score 0.49 0.6 0.5 0.57 0.57 0.49
CADD neutral neutral deleterious neutral deleterious deleterious
CADD score 1.62 1.68 1.99 1.73 2.22 4.21
CADD phred 13.94 14.29 16.13 14.6 17.61 23.9
VEST pvalue 0.26 0.41 0.03 0.08 0.01 0.01
VEST FDR 0.45 0.5 0.35 0.35 0.35 0.35
PANTHER neutral neutral neutral neutral disease disease
PANTHER score 0.18 0.18 0.48 0.37 0.62 0.73
PhD-SNP disease disease disease disease disease disease
PhD-SNP score 0.82 0.58 0.93 0.65 0.87 0.92
SNAP disease neutral disease disease disease disease
SNAP score 0.57 0.31 0.65 0.61 0.65 0.74
Meta-SNP disease neutral disease disease disease disease
Meta-SNP score 0.66 0.2 0.75 0.65 0.71 0.73
Meta-SNP RI 3 6 5 3 4 5
CAROL neutral neutral neutral neutral neutral neutral
CAROL score 0.35 0.48 0.37 0.57 0.94 0.97
Condel deleterious deleterious deleterious deleterious neutral neutral
Condel score 0.61 0.71 0.72 0.51 0.18 0.11
COVEC WMV neutral neutral neutral . deleterious deleterious
COVEC WMV score -3 -6 -2 0 2 2
MtoolBox neutral neutral neutral deleterious deleterious deleterious
MtoolBox DS 0.34 0.19 0.33 0.54 0.76 0.85
PolyPhen2 transf medium impact medium impact medium impact medium impact low impact low impact
PolyPhen2 transf score -0.57 0.45 0.1 -0.99 -1.81 -1.95
SIFT_transf medium impact medium impact medium impact medium impact medium impact medium impact
SIFT transf score 0.38 0.25 0.31 0.43 0.05 -0.13
MutationAssessor transf medium impact medium impact high impact medium impact high impact high impact
MutationAssessor transf score 1.1 0.49 2.95 1.52 2.46 2.95
CHASM pvalue 0.32 0.72 0.28 0.11 0.31 0.14
CHASM FDR 0.8 0.85 0.8 0.8 0.8 0.8
APOGEE Pathogenic Pathogenic Pathogenic Pathogenic Pathogenic Pathogenic
APOGEE score 0.52 0.7 0.66 0.59 0.63 0.71
SNPDryad score 0.69 0.08 0.98 0.87 0.96 0.99
MutationTaster polymorphism polymorphism polymorphism polymorphism polymorphism polymorphism
MutationTaster score 1 1 1 1 1 1
DEOGEN2 score 0.12 0.03 0.15 0.13 0.2 0.37
Mitoclass.1 damaging damaging damaging damaging damaging damaging
dbSNP 153 id . rs201513497 . . . .
ClinVar March2020 ClinSig . Benign . . . .
ClinVar March2020 ClnDBN . Leigh_syndrome . . . .
ClinVar March2020 ClnAllele id . 680929 . . . .
ClinVar March2020 ClnDSDB . MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005 . . . .
COSMIC 90 . COSM6716702 . . . .
CPD Frequency . 0.89 . . . .
MITOMAP Allele . G3736A . . . .
MITOMAP Phenotype . LHON . . . .
MITOMAP Homoplasmy . . . . . .
MITOMAP Heteroplasmy . . . . . .
MITOMAP Status . Reported . . . .
MITOMAP NRef . 2 . . . .
EVmutation MT-ND1_144V|145T:0.199006;294L:0.154717;301L:0.09302;148I:0.084539;278P:0.069915;191A:0.065596 MT-ND1_144V|145T:0.199006;294L:0.154717;301L:0.09302;148I:0.084539;278P:0.069915;191A:0.065596 MT-ND1_144V|145T:0.199006;294L:0.154717;301L:0.09302;148I:0.084539;278P:0.069915;191A:0.065596 MT-ND1_144V|145T:0.199006;294L:0.154717;301L:0.09302;148I:0.084539;278P:0.069915;191A:0.065596 MT-ND1_144V|145T:0.199006;294L:0.154717;301L:0.09302;148I:0.084539;278P:0.069915;191A:0.065596 MT-ND1_144V|145T:0.199006;294L:0.154717;301L:0.09302;148I:0.084539;278P:0.069915;191A:0.065596
Site A InterP ND1_144 ND1_144 ND1_144 ND1_144 ND1_144 ND1_144
Site B InterP ND3_10;ND6_116;ND6_109 ND3_10;ND6_116;ND6_109 ND3_10;ND6_116;ND6_109 ND3_10;ND6_116;ND6_109 ND3_10;ND6_116;ND6_109 ND3_10;ND6_116;ND6_109
Covariation Score InterP mfDCA_23.8;mfDCA_24.26;mfDCA_22.08 mfDCA_23.8;mfDCA_24.26;mfDCA_22.08 mfDCA_23.8;mfDCA_24.26;mfDCA_22.08 mfDCA_23.8;mfDCA_24.26;mfDCA_22.08 mfDCA_23.8;mfDCA_24.26;mfDCA_22.08 mfDCA_23.8;mfDCA_24.26;mfDCA_22.08
Site A IntraP . . . . . .
Site B IntraP . . . . . .
Covariation Score IntraP . . . . . .
CPD AA ref . V . . . .
CPD AA alt . I . . . .
CPD Aln pos . 145 . . . .
CPD Species name . Lepilemur hubbardorum,Lepilemur ruficaudatus,Pongo pygmaeus,Macaca sylvanus,Pongo abelii,Nomascus gabriellae . . . .
CPD RefSeq Protein ID . YP_003856721,YP_008379047,NP_008225,NP_114334,NP_007835,YP_006883018 . . . .
CPD Ncbi Taxon id . 756882,78866,9600,9546,9601,61852 . . . .
DDG intra . . . . . .
DDG intra interface . . . . . .
DDG inter MT-ND1:MT-ND3:5lc5:H:A:V144L:N10D:-0.41196:-2.40359163:1.9348892;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10T:-3.0952:-2.40359163:-0.845690131;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10H:-3.18939:-2.40359163:-0.468639374;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10K:-2.06377:-2.40359163:0.559670269;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10Y:-2.80684:-2.40359163:-1.04049873;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10I:-2.86892:-2.40359163:-0.200120538;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10S:-1.30784:-2.40359163:1.00994909;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10D:0.5791:-0.945389569:1.56138194;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10T:-1.89848:-0.945389569:-0.944197059;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10H:-2.28821:-0.945389569:-1.41110837;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10K:-1.263:-0.945389569:-0.557247937;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10Y:-2.68569:-0.945389569:-1.868029;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10I:-2.92276:-0.945389569:-1.98465884;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10S:-0.19617:-0.945389569:0.722851157;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10D:0.66908:-1.05275989:1.77093887;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10T:-1.6146:-1.05275989:-0.727460086;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10H:-2.23498:-1.05275989:-1.23474002;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10K:-2.04694:-1.05275989:-0.983650565;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10Y:-3.41559:-1.05275989:-1.7146492;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10I:-2.75453:-1.05275989:-1.75487101;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10S:-0.09797:-1.05275989:0.834559619 MT-ND1:MT-ND3:5lc5:H:A:V144I:N10H:-0.84139:-0.425349414:-0.468639374;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10K:-0.16116:-0.425349414:0.559670269;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10S:0.5813:-0.425349414:1.00994909;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10I:-0.54679:-0.425349414:-0.200120538;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10T:-1.33442:-0.425349414:-0.845690131;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10D:1.4578:-0.425349414:1.9348892;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10Y:-0.55928:-0.425349414:-1.04049873;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10H:-2.16077:-0.742519736:-1.41110837;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10K:-1.24705:-0.742519736:-0.557247937;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10S:-0.02027:-0.742519736:0.722851157;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10I:-2.80958:-0.742519736:-1.98465884;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10T:-1.76381:-0.742519736:-0.944197059;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10D:0.76455:-0.742519736:1.56138194;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10Y:-2.80113:-0.742519736:-1.868029;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10H:-1.89614:-0.622790158:-1.23474002;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10K:-1.46186:-0.622790158:-0.983650565;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10S:0.27821:-0.622790158:0.834559619;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10I:-2.35861:-0.622790158:-1.75487101;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10T:-1.25017:-0.622790158:-0.727460086;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10D:1.20721:-0.622790158:1.77093887;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10Y:-2.90714:-0.622790158:-1.7146492 MT-ND1:MT-ND3:5lc5:H:A:V144F:N10K:1.56466:0.667149723:0.559670269;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10T:0.04708:0.667149723:-0.845690131;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10H:-0.04231:0.667149723:-0.468639374;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10Y:-0.30979:0.667149723:-1.04049873;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10S:1.74823:0.667149723:1.00994909;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10I:0.1666:0.667149723:-0.200120538;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10D:2.6989:0.667149723:1.9348892;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10K:0.30533:1.16558003:-0.557247937;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10T:0.12131:1.16558003:-0.944197059;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10H:-0.32227:1.16558003:-1.41110837;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10Y:-0.82489:1.16558003:-1.868029;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10S:1.81696:1.16558003:0.722851157;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10I:-1.08114:1.16558003:-1.98465884;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10D:2.45502:1.16558003:1.56138194;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10K:0.0192:0.767220318:-0.983650565;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10T:0.0218:0.767220318:-0.727460086;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10H:-0.54073:0.767220318:-1.23474002;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10Y:-1.89816:0.767220318:-1.7146492;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10S:1.68158:0.767220318:0.834559619;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10I:-0.86444:0.767220318:-1.75487101;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10D:2.41322:0.767220318:1.77093887 MT-ND1:MT-ND3:5lc5:H:A:V144A:N10S:1.5254:0.477989584:1.00994909;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10K:0.95416:0.477989584:0.559670269;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10D:2.40856:0.477989584:1.9348892;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10Y:-0.01481:0.477989584:-1.04049873;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10T:-0.32927:0.477989584:-0.845690131;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10H:-0.34081:0.477989584:-0.468639374;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10I:0.26565:0.477989584:-0.200120538;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10S:2.08637:1.37451053:0.722851157;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10K:0.80985:1.37451053:-0.557247937;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10D:2.94017:1.37451053:1.56138194;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10Y:-0.45072:1.37451053:-1.868029;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10T:0.39451:1.37451053:-0.944197059;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10H:-0.04321:1.37451053:-1.41110837;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10I:-0.57641:1.37451053:-1.98465884;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10S:2.27043:1.45349884:0.834559619;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10K:0.50927:1.45349884:-0.983650565;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10D:3.18168:1.45349884:1.77093887;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10Y:-0.508:1.45349884:-1.7146492;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10T:0.7206:1.45349884:-0.727460086;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10H:0.22963:1.45349884:-1.23474002;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10I:-0.33633:1.45349884:-1.75487101 MT-ND1:MT-ND3:5lc5:H:A:V144G:N10I:0.36105:1.03733063:-0.200120538;MT-ND1:MT-ND3:5lc5:H:A:V144G:N10K:1.661:1.03733063:0.559670269;MT-ND1:MT-ND3:5lc5:H:A:V144G:N10D:3.01504:1.03733063:1.9348892;MT-ND1:MT-ND3:5lc5:H:A:V144G:N10H:0.60091:1.03733063:-0.468639374;MT-ND1:MT-ND3:5lc5:H:A:V144G:N10T:0.29826:1.03733063:-0.845690131;MT-ND1:MT-ND3:5lc5:H:A:V144G:N10S:2.20028:1.03733063:1.00994909;MT-ND1:MT-ND3:5lc5:H:A:V144G:N10Y:0.12207:1.03733063:-1.04049873;MT-ND1:MT-ND3:5ldw:H:A:V144G:N10I:-0.14854:1.9026897:-1.98465884;MT-ND1:MT-ND3:5ldw:H:A:V144G:N10K:1.35738:1.9026897:-0.557247937;MT-ND1:MT-ND3:5ldw:H:A:V144G:N10D:3.46538:1.9026897:1.56138194;MT-ND1:MT-ND3:5ldw:H:A:V144G:N10H:0.55671:1.9026897:-1.41110837;MT-ND1:MT-ND3:5ldw:H:A:V144G:N10T:0.95542:1.9026897:-0.944197059;MT-ND1:MT-ND3:5ldw:H:A:V144G:N10S:2.67871:1.9026897:0.722851157;MT-ND1:MT-ND3:5ldw:H:A:V144G:N10Y:0.10878:1.9026897:-1.868029;MT-ND1:MT-ND3:5ldx:H:A:V144G:N10I:0.03869:1.83056986:-1.75487101;MT-ND1:MT-ND3:5ldx:H:A:V144G:N10K:0.9242:1.83056986:-0.983650565;MT-ND1:MT-ND3:5ldx:H:A:V144G:N10D:3.58236:1.83056986:1.77093887;MT-ND1:MT-ND3:5ldx:H:A:V144G:N10H:0.649:1.83056986:-1.23474002;MT-ND1:MT-ND3:5ldx:H:A:V144G:N10T:1.0825:1.83056986:-0.727460086;MT-ND1:MT-ND3:5ldx:H:A:V144G:N10S:2.69215:1.83056986:0.834559619;MT-ND1:MT-ND3:5ldx:H:A:V144G:N10Y:-0.36689:1.83056986:-1.7146492 MT-ND1:MT-ND3:5lc5:H:A:V144D:N10D:4.02764:2.00195003:1.9348892;MT-ND1:MT-ND3:5lc5:H:A:V144D:N10I:1.10277:2.00195003:-0.200120538;MT-ND1:MT-ND3:5lc5:H:A:V144D:N10K:2.64491:2.00195003:0.559670269;MT-ND1:MT-ND3:5lc5:H:A:V144D:N10T:1.23572:2.00195003:-0.845690131;MT-ND1:MT-ND3:5lc5:H:A:V144D:N10H:1.75997:2.00195003:-0.468639374;MT-ND1:MT-ND3:5lc5:H:A:V144D:N10S:3.15835:2.00195003:1.00994909;MT-ND1:MT-ND3:5lc5:H:A:V144D:N10Y:1.19635:2.00195003:-1.04049873;MT-ND1:MT-ND3:5ldw:H:A:V144D:N10D:4.85764:3.30468059:1.56138194;MT-ND1:MT-ND3:5ldw:H:A:V144D:N10I:1.21247:3.30468059:-1.98465884;MT-ND1:MT-ND3:5ldw:H:A:V144D:N10K:2.53392:3.30468059:-0.557247937;MT-ND1:MT-ND3:5ldw:H:A:V144D:N10T:2.33287:3.30468059:-0.944197059;MT-ND1:MT-ND3:5ldw:H:A:V144D:N10H:1.91989:3.30468059:-1.41110837;MT-ND1:MT-ND3:5ldw:H:A:V144D:N10S:4.00442:3.30468059:0.722851157;MT-ND1:MT-ND3:5ldw:H:A:V144D:N10Y:1.27381:3.30468059:-1.868029;MT-ND1:MT-ND3:5ldx:H:A:V144D:N10D:4.86838:3.1031003:1.77093887;MT-ND1:MT-ND3:5ldx:H:A:V144D:N10I:1.28499:3.1031003:-1.75487101;MT-ND1:MT-ND3:5ldx:H:A:V144D:N10K:2.16171:3.1031003:-0.983650565;MT-ND1:MT-ND3:5ldx:H:A:V144D:N10T:2.38511:3.1031003:-0.727460086;MT-ND1:MT-ND3:5ldx:H:A:V144D:N10H:1.80722:3.1031003:-1.23474002;MT-ND1:MT-ND3:5ldx:H:A:V144D:N10S:4.00514:3.1031003:0.834559619;MT-ND1:MT-ND3:5ldx:H:A:V144D:N10Y:1.66248:3.1031003:-1.7146492
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