10086 (A > T)

General info

Chr
chrM
Start
10086
End
10086
Ref
A
Alt
T
Mitimpact ID
MI.15019
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
28
AA pos
10
AA ref
N
AA alt
Y
Codon substitution
Aac/Tac
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Conservation

PhyloP 100v
-10.98
PhastCons 100v
0

Pathogenicity predictors

PolyPhen2
Probably damaging
PolyPhen2 score
0.98
SIFT
Neutral
SIFT score
0.15
FatHmm
Neutral
FatHmm score
-0.47
FatHMMW
Neutral
FatHMMW score
1.97
PROVEAN
Deleterious
PROVEAN score
-6.14
Mutation Assessor
Medium impact
Mutation Assessor score
2.34
EFIN SP
Neutral
EFIN SP score
0.84
EFIN HD
Neutral
EFIN HD score
0.39
VEST p-value
0.14
VEST FDR
0.4
PANTHER
Neutral
PANTHER score
0.45
PhD-SNP
Disease
PhD-SNP score
0.75
MutationTaster
Polymorphism
MutationTaster score
1
CADD
Deleterious
CADD score
3.44
CADD phred
23
SNAP
Neutral
SNAP score
0.5
MitoClass 1
Damaging
SNPDryad score
0.99

Pathogenicity meta-predictors

CAROL
Deleterious
CAROL score
0.99
Condel
Neutral
Condel score
0.09
COVEC WMV
Deleterious
COVEC WMV score
1
Meta SNP
Disease
Meta SNP score
0.62
Meta SNP RI
2
MtoolBox
Deleterious
MtoolBox DS
0.68
APOGEE
N
APOGEE score
0.34
DEOGEN2 score
0.11

Cancer-specific predictors

PolyPhen2 transf
Low impact
PolyPhen2 transf score
-2.24
SIFT transf
Medium impact
SIFT transf score
-0.23
MutationAssessor transf
Medium impact
MutationAssessor transf score
1.04
CHASM p-value
0.33
CHASM FDR
0.8

Residue interaction

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

Databases of Allelic frequency & Phenotype

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
Rs28358274

Pathogenic variants, CPD

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

General info

Chr
chrM
Start
10086
End
10086
Ref
A
Alt
G
Mitimpact ID
MI.15020
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
28
AA pos
10
AA ref
N
AA alt
D
Codon substitution
Aac/Gac
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Conservation

PhyloP 100v
-10.98
PhastCons 100v
0

Pathogenicity predictors

PolyPhen2
Possibly damaging
PolyPhen2 score
0.9
SIFT
Deleterious
SIFT score
0.02
FatHmm
Neutral
FatHmm score
-0.42
FatHMMW
Neutral
FatHMMW score
1.97
PROVEAN
Deleterious
PROVEAN score
-3.52
Mutation Assessor
Medium impact
Mutation Assessor score
2.34
EFIN SP
Neutral
EFIN SP score
0.96
EFIN HD
Neutral
EFIN HD score
0.57
VEST p-value
0.44
VEST FDR
0.55
PANTHER
Neutral
PANTHER score
0.23
PhD-SNP
Disease
PhD-SNP score
0.68
MutationTaster
Polymorphism
MutationTaster score
1
CADD
Deleterious
CADD score
2.47
CADD phred
19.3
SNAP
Disease
SNAP score
0.57
MitoClass 1
Damaging
SNPDryad score
0.94

Pathogenicity meta-predictors

CAROL
Deleterious
CAROL score
0.99
Condel
Neutral
Condel score
0.06
COVEC WMV
Deleterious
COVEC WMV score
4
Meta SNP
Disease
Meta SNP score
0.69
Meta SNP RI
4
MtoolBox
Deleterious
MtoolBox DS
0.59
APOGEE
P
APOGEE score
0.56
DEOGEN2 score
0.1

Cancer-specific predictors

PolyPhen2 transf
Low impact
PolyPhen2 transf score
-1.58
SIFT transf
Medium impact
SIFT transf score
-0.75
MutationAssessor transf
Medium impact
MutationAssessor transf score
1.04
CHASM p-value
0.28
CHASM FDR
0.8

Residue interaction

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

Databases of Allelic frequency & Phenotype

ClinVar March2020 ClinSig
Benign
ClinVar March2020 ClnDBN
Leigh syndrome
ClinVar March2020 ClnAllele ID
680150
ClinVar March2020 ClnDSDB
Medgen:c0023264, omim:256000, orphanet:orpha506, snomed ct:29570005
MITOMAP Allele
A10086g
MITOMAP Phenotype
Hypertensive end-stage renal disease
MITOMAP Homoplasmy
+
MITOMAP Heteroplasmy
-
MITOMAP Status
Reported
MITOMAP NRef
4
COSMIC 90
.
dbSNP 153
Rs28358274

Pathogenic variants, CPD

Frequency
0.15
AA ref
N
CPD AA alt
D
Aln pos
12
RefSeq protein ID
Yp 002004588
Species name
Propithecus coquereli
Ncbi taxon ID
379532

10086 (A > C)

General info

Chr
chrM
Start
10086
End
10086
Ref
A
Alt
C
Mitimpact ID
MI.15021
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
28
AA pos
10
AA ref
N
AA alt
H
Codon substitution
Aac/Cac
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Conservation

PhyloP 100v
-10.98
PhastCons 100v
0

Pathogenicity predictors

PolyPhen2
Probably damaging
PolyPhen2 score
0.98
SIFT
Neutral
SIFT score
0.07
FatHmm
Neutral
FatHmm score
-0.86
FatHMMW
Neutral
FatHMMW score
1.96
PROVEAN
Deleterious
PROVEAN score
-3.9
Mutation Assessor
Medium impact
Mutation Assessor score
3.04
EFIN SP
Neutral
EFIN SP score
0.83
EFIN HD
Neutral
EFIN HD score
0.34
VEST p-value
0.34
VEST FDR
0.5
PANTHER
Neutral
PANTHER score
0.38
PhD-SNP
Disease
PhD-SNP score
0.69
MutationTaster
Polymorphism
MutationTaster score
1
CADD
Deleterious
CADD score
2.84
CADD phred
21.6
SNAP
Disease
SNAP score
0.58
MitoClass 1
Damaging
SNPDryad score
0.98

Pathogenicity meta-predictors

CAROL
Deleterious
CAROL score
0.99
Condel
Neutral
Condel score
0.05
COVEC WMV
Deleterious
COVEC WMV score
1
Meta SNP
Disease
Meta SNP score
0.73
Meta SNP RI
5
MtoolBox
Deleterious
MtoolBox DS
0.65
APOGEE
N
APOGEE score
0.38
DEOGEN2 score
0.1

Cancer-specific predictors

PolyPhen2 transf
Low impact
PolyPhen2 transf score
-2.24
SIFT transf
Medium impact
SIFT transf score
-0.43
MutationAssessor transf
Medium impact
MutationAssessor transf score
1.68
CHASM p-value
0.26
CHASM FDR
0.8

Residue interaction

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

Databases of Allelic frequency & Phenotype

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
Rs28358274

Pathogenic variants, CPD

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

10087 (A > C)

General info

Chr
chrM
Start
10087
End
10087
Ref
A
Alt
C
Mitimpact ID
MI.15022
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
29
AA pos
10
AA ref
N
AA alt
T
Codon substitution
aAc/aCc
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Conservation

PhyloP 100v
1.05
PhastCons 100v
0.07

Pathogenicity predictors

PolyPhen2
Probably damaging
PolyPhen2 score
0.94
SIFT
Neutral
SIFT score
0.23
FatHmm
Neutral
FatHmm score
0.75
FatHMMW
Neutral
FatHMMW score
2.04
PROVEAN
Deleterious
PROVEAN score
-4.13
Mutation Assessor
Low impact
Mutation Assessor score
0.88
EFIN SP
Neutral
EFIN SP score
0.77
EFIN HD
Neutral
EFIN HD score
0.68
VEST p-value
0.29
VEST FDR
0.45
PANTHER
Neutral
PANTHER score
0.19
PhD-SNP
Neutral
PhD-SNP score
0.28
MutationTaster
Polymorphism
MutationTaster score
1
CADD
Neutral
CADD score
1.31
CADD phred
12.34
SNAP
Neutral
SNAP score
0.23
MitoClass 1
Neutral
SNPDryad score
0.96

Pathogenicity meta-predictors

CAROL
Neutral
CAROL score
0.95
Condel
Neutral
Condel score
0.15
COVEC WMV
Neutral
COVEC WMV score
-2
Meta SNP
Neutral
Meta SNP score
0.45
Meta SNP RI
1
MtoolBox
Deleterious
MtoolBox DS
0.6
APOGEE
N
APOGEE score
0.4
DEOGEN2 score
0.1

Cancer-specific predictors

PolyPhen2 transf
Low impact
PolyPhen2 transf score
-1.8
SIFT transf
Medium impact
SIFT transf score
-0.1
MutationAssessor transf
Medium impact
MutationAssessor transf score
-0.3
CHASM p-value
0.3
CHASM FDR
0.8

Residue interaction

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

Databases of Allelic frequency & Phenotype

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
.

Pathogenic variants, CPD

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

10087 (A > G)

General info

Chr
chrM
Start
10087
End
10087
Ref
A
Alt
G
Mitimpact ID
MI.15023
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
29
AA pos
10
AA ref
N
AA alt
S
Codon substitution
aAc/aGc
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Powered by MitoWheel

Conservation

PhyloP 100v
1.05
PhastCons 100v
0.07

Pathogenicity predictors

PolyPhen2
Possibly damaging
PolyPhen2 score
0.9
SIFT
Neutral
SIFT score
0.37
FatHmm
Neutral
FatHmm score
1.01
FatHMMW
Neutral
FatHMMW score
2.1
PROVEAN
Deleterious
PROVEAN score
-3.38
Mutation Assessor
Low impact
Mutation Assessor score
0.86
EFIN SP
Neutral
EFIN SP score
0.78
EFIN HD
Neutral
EFIN HD score
0.64
VEST p-value
0.42
VEST FDR
0.55
PANTHER
Neutral
PANTHER score
0.16
PhD-SNP
Neutral
PhD-SNP score
0.22
MutationTaster
Polymorphism
MutationTaster score
1
CADD
Neutral
CADD score
1.37
CADD phred
12.66
SNAP
Neutral
SNAP score
0.29
MitoClass 1
Neutral
SNPDryad score
0.81

Pathogenicity meta-predictors

CAROL
Neutral
CAROL score
0.9
Condel
Neutral
Condel score
0.24
COVEC WMV
Neutral
COVEC WMV score
-3
Meta SNP
Neutral
Meta SNP score
0.35
Meta SNP RI
3
MtoolBox
Deleterious
MtoolBox DS
0.58
APOGEE
N
APOGEE score
0.37
DEOGEN2 score
0.09

Cancer-specific predictors

PolyPhen2 transf
Low impact
PolyPhen2 transf score
-1.58
SIFT transf
Medium impact
SIFT transf score
0.06
MutationAssessor transf
Medium impact
MutationAssessor transf score
-0.32
CHASM p-value
0.27
CHASM FDR
0.8

Residue interaction

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

Databases of Allelic frequency & Phenotype

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
.

Pathogenic variants, CPD

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

10087 (A > T)

General info

Chr
chrM
Start
10087
End
10087
Ref
A
Alt
T
Mitimpact ID
MI.15024
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
29
AA pos
10
AA ref
N
AA alt
I
Codon substitution
aAc/aTc
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Powered by MitoWheel

Conservation

PhyloP 100v
1.05
PhastCons 100v
0.07

Pathogenicity predictors

PolyPhen2
Probably damaging
PolyPhen2 score
0.98
SIFT
Neutral
SIFT score
1
FatHmm
Neutral
FatHmm score
0.95
FatHMMW
Neutral
FatHMMW score
2.02
PROVEAN
Deleterious
PROVEAN score
-6.66
Mutation Assessor
Low impact
Mutation Assessor score
1.14
EFIN SP
Neutral
EFIN SP score
0.82
EFIN HD
Neutral
EFIN HD score
0.54
VEST p-value
0.16
VEST FDR
0.45
PANTHER
Neutral
PANTHER score
0.34
PhD-SNP
Disease
PhD-SNP score
0.84
MutationTaster
Polymorphism
MutationTaster score
1
CADD
Deleterious
CADD score
3.73
CADD phred
23.3
SNAP
Neutral
SNAP score
0.3
MitoClass 1
Neutral
SNPDryad score
0.99

Pathogenicity meta-predictors

CAROL
Deleterious
CAROL score
0.98
Condel
Deleterious
Condel score
0.51
COVEC WMV
Neutral
COVEC WMV score
-2
Meta SNP
Disease
Meta SNP score
0.6
Meta SNP RI
2
MtoolBox
Deleterious
MtoolBox DS
0.67
APOGEE
N
APOGEE score
0.22
DEOGEN2 score
0.11

Cancer-specific predictors

PolyPhen2 transf
Low impact
PolyPhen2 transf score
-2.24
SIFT transf
High impact
SIFT transf score
1.85
MutationAssessor transf
Medium impact
MutationAssessor transf score
-0.06
CHASM p-value
0.24
CHASM FDR
0.8

Residue interaction

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

Databases of Allelic frequency & Phenotype

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
.

Pathogenic variants, CPD

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

General info

Chr
chrM
Start
10088
End
10088
Ref
C
Alt
A
Mitimpact ID
MI.15025
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
30
AA pos
10
AA ref
N
AA alt
K
Codon substitution
aaC/aaA
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Powered by MitoWheel

Conservation

PhyloP 100v
2.67
PhastCons 100v
0.15

Pathogenicity predictors

PolyPhen2
Probably damaging
PolyPhen2 score
0.94
SIFT
Deleterious
SIFT score
0.03
FatHmm
Neutral
FatHmm score
0.52
FatHMMW
Neutral
FatHMMW score
2.01
PROVEAN
Deleterious
PROVEAN score
-4.5
Mutation Assessor
Medium impact
Mutation Assessor score
3.04
EFIN SP
Neutral
EFIN SP score
0.83
EFIN HD
Neutral
EFIN HD score
0.31
VEST p-value
0.37
VEST FDR
0.5
PANTHER
Neutral
PANTHER score
0.17
PhD-SNP
Disease
PhD-SNP score
0.82
MutationTaster
Polymorphism
MutationTaster score
1
CADD
Deleterious
CADD score
4.09
CADD phred
23.7
SNAP
Disease
SNAP score
0.58
MitoClass 1
Damaging
SNPDryad score
1

Pathogenicity meta-predictors

CAROL
Deleterious
CAROL score
0.99
Condel
Neutral
Condel score
0.05
COVEC WMV
Deleterious
COVEC WMV score
5
Meta SNP
Disease
Meta SNP score
0.78
Meta SNP RI
6
MtoolBox
Deleterious
MtoolBox DS
0.63
APOGEE
N
APOGEE score
0.42
DEOGEN2 score
0.1

Cancer-specific predictors

PolyPhen2 transf
Low impact
PolyPhen2 transf score
-1.8
SIFT transf
Medium impact
SIFT transf score
-0.65
MutationAssessor transf
Medium impact
MutationAssessor transf score
1.68
CHASM p-value
0.41
CHASM FDR
0.8

Residue interaction

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

Databases of Allelic frequency & Phenotype

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
.

Pathogenic variants, CPD

Frequency
.
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

General info

Chr
chrM
Start
10088
End
10088
Ref
C
Alt
G
Mitimpact ID
MI.15026
Gene symbol
MT-ND3
RC complex
I
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
30
AA pos
10
AA ref
N
AA alt
K
Codon substitution
aaC/aaG
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Powered by MitoWheel

Conservation

PhyloP 100v
2.67
PhastCons 100v
0.15

Pathogenicity predictors

PolyPhen2
Probably damaging
PolyPhen2 score
0.94
SIFT
Deleterious
SIFT score
0.03
FatHmm
Neutral
FatHmm score
0.52
FatHMMW
Neutral
FatHMMW score
2.01
PROVEAN
Deleterious
PROVEAN score
-4.5
Mutation Assessor
Medium impact
Mutation Assessor score
3.04
EFIN SP
Neutral
EFIN SP score
0.83
EFIN HD
Neutral
EFIN HD score
0.31
VEST p-value
0.37
VEST FDR
0.5
PANTHER
Neutral
PANTHER score
0.17
PhD-SNP
Disease
PhD-SNP score
0.82
MutationTaster
Polymorphism
MutationTaster score
1
CADD
Deleterious
CADD score
3.64
CADD phred
23.2
SNAP
Disease
SNAP score
0.58
MitoClass 1
Damaging
SNPDryad score
1

Pathogenicity meta-predictors

CAROL
Deleterious
CAROL score
0.99
Condel
Neutral
Condel score
0.05
COVEC WMV
Deleterious
COVEC WMV score
5
Meta SNP
Disease
Meta SNP score
0.78
Meta SNP RI
6
MtoolBox
Deleterious
MtoolBox DS
0.63
APOGEE
N
APOGEE score
0.42
DEOGEN2 score
0.1

Cancer-specific predictors

PolyPhen2 transf
Low impact
PolyPhen2 transf score
-1.8
SIFT transf
Medium impact
SIFT transf score
-0.65
MutationAssessor transf
Medium impact
MutationAssessor transf score
1.68
CHASM p-value
0.41
CHASM FDR
0.8

Residue interaction

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

Databases of Allelic frequency & Phenotype

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

Pathogenic variants, CPD

Frequency
.
AA ref
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CPD AA alt
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Aln pos
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RefSeq protein ID
.
Species name
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Ncbi taxon ID
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~ 10086 (A/T) 10086 (A/G) 10086 (A/C) 10087 (A/C) 10087 (A/G) 10087 (A/T) 10088 (C/A) 10088 (C/G)
~ 10086 (Aac/Tac) 10086 (Aac/Gac) 10086 (Aac/Cac) 10087 (aAc/aCc) 10087 (aAc/aGc) 10087 (aAc/aTc) 10088 (aaC/aaA) 10088 (aaC/aaG)
Chr chrM chrM chrM chrM chrM chrM chrM chrM
Start 10086 10086 10086 10087 10087 10087 10088 10088
End 10086 10086 10086 10087 10087 10087 10088 10088
Ref A A A A A A C C
Alt T G C C G T A G
MitImpact id MI.15019 MI.15020 MI.15021 MI.15022 MI.15023 MI.15024 MI.15025 MI.15026
Gene symbol MT-ND3 MT-ND3 MT-ND3 MT-ND3 MT-ND3 MT-ND3 MT-ND3 MT-ND3
Respiratory Chain complex I I I I I I I I
Ensembl gene id ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840 ENSG00000198840
Ensembl protein id ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206 ENSP00000355206
Ensembl transcript id ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227 ENST00000361227
Uniprot name NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN
Uniprot id P03897 P03897 P03897 P03897 P03897 P03897 P03897 P03897
Ncbi gene id 4537 4537 4537 4537 4537 4537 4537 4537
Ncbi protein id YP_003024033.1 YP_003024033.1 YP_003024033.1 YP_003024033.1 YP_003024033.1 YP_003024033.1 YP_003024033.1 YP_003024033.1
Gene position 28 28 28 29 29 29 30 30
AA position 10 10 10 10 10 10 10 10
AA ref N N N N N N N N
AA alt Y D H T S I K K
Codon substitution Aac/Tac Aac/Gac Aac/Cac aAc/aCc aAc/aGc aAc/aTc aaC/aaA aaC/aaG
PhyloP 100V -10.98 -10.98 -10.98 1.05 1.05 1.05 2.67 2.67
PhastCons 100V 0 0 0 0.07 0.07 0.07 0.15 0.15
PolyPhen2 probably_damaging possibly_damaging probably_damaging probably_damaging possibly_damaging probably_damaging probably_damaging probably_damaging
PolyPhen2 score 0.98 0.9 0.98 0.94 0.9 0.98 0.94 0.94
SIFT neutral deleterious neutral neutral neutral neutral deleterious deleterious
SIFT score 0.15 0.02 0.07 0.23 0.37 1 0.03 0.03
FatHmm neutral neutral neutral neutral neutral neutral neutral neutral
FatHmm score -0.47 -0.42 -0.86 0.75 1.01 0.95 0.52 0.52
FatHmmW neutral neutral neutral neutral neutral neutral neutral neutral
FatHmmW score 1.97 1.97 1.96 2.04 2.1 2.02 2.01 2.01
PROVEAN deleterious deleterious deleterious deleterious deleterious deleterious deleterious deleterious
PROVEAN score -6.14 -3.52 -3.9 -4.13 -3.38 -6.66 -4.5 -4.5
MutationAssessor medium impact medium impact medium impact low impact low impact low impact medium impact medium impact
MutationAssessor score 2.34 2.34 3.04 0.88 0.86 1.14 3.04 3.04
EFIN SP neutral neutral neutral neutral neutral neutral neutral neutral
EFIN SP score 0.84 0.96 0.83 0.77 0.78 0.82 0.83 0.83
EFIN HD neutral neutral neutral neutral neutral neutral neutral neutral
EFIN HD score 0.39 0.57 0.34 0.68 0.64 0.54 0.31 0.31
CADD deleterious deleterious deleterious neutral neutral deleterious deleterious deleterious
CADD score 3.44 2.47 2.84 1.31 1.37 3.73 4.09 3.64
CADD phred 23 19.3 21.6 12.34 12.66 23.3 23.7 23.2
VEST pvalue 0.14 0.44 0.34 0.29 0.42 0.16 0.37 0.37
VEST FDR 0.4 0.55 0.5 0.45 0.55 0.45 0.5 0.5
PANTHER neutral neutral neutral neutral neutral neutral neutral neutral
PANTHER score 0.45 0.23 0.38 0.19 0.16 0.34 0.17 0.17
PhD-SNP disease disease disease neutral neutral disease disease disease
PhD-SNP score 0.75 0.68 0.69 0.28 0.22 0.84 0.82 0.82
SNAP neutral disease disease neutral neutral neutral disease disease
SNAP score 0.5 0.57 0.58 0.23 0.29 0.3 0.58 0.58
Meta-SNP disease disease disease neutral neutral disease disease disease
Meta-SNP score 0.62 0.69 0.73 0.45 0.35 0.6 0.78 0.78
Meta-SNP RI 2 4 5 1 3 2 6 6
CAROL deleterious deleterious deleterious neutral neutral deleterious deleterious deleterious
CAROL score 0.99 0.99 0.99 0.95 0.9 0.98 0.99 0.99
Condel neutral neutral neutral neutral neutral deleterious neutral neutral
Condel score 0.09 0.06 0.05 0.15 0.24 0.51 0.05 0.05
COVEC WMV deleterious deleterious deleterious neutral neutral neutral deleterious deleterious
COVEC WMV score 1 4 1 -2 -3 -2 5 5
MtoolBox deleterious deleterious deleterious deleterious deleterious deleterious deleterious deleterious
MtoolBox DS 0.68 0.59 0.65 0.6 0.58 0.67 0.63 0.63
PolyPhen2 transf low impact low impact low impact low impact low impact low impact low impact low impact
PolyPhen2 transf score -2.24 -1.58 -2.24 -1.8 -1.58 -2.24 -1.8 -1.8
SIFT_transf medium impact medium impact medium impact medium impact medium impact high impact medium impact medium impact
SIFT transf score -0.23 -0.75 -0.43 -0.1 0.06 1.85 -0.65 -0.65
MutationAssessor transf medium impact medium impact medium impact medium impact medium impact medium impact medium impact medium impact
MutationAssessor transf score 1.04 1.04 1.68 -0.3 -0.32 -0.06 1.68 1.68
CHASM pvalue 0.33 0.28 0.26 0.3 0.27 0.24 0.41 0.41
CHASM FDR 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8
APOGEE N P N N N N N N
APOGEE score 0.34 0.56 0.38 0.4 0.37 0.22 0.42 0.42
SNPDryad score 0.99 0.94 0.98 0.96 0.81 0.99 1 1
MutationTaster polymorphism polymorphism polymorphism polymorphism polymorphism polymorphism polymorphism polymorphism
MutationTaster score 1 1 1 1 1 1 1 1
DEOGEN2 score 0.11 0.1 0.1 0.1 0.09 0.11 0.1 0.1
Mitoclass.1 damaging damaging damaging neutral neutral neutral damaging damaging
dbSNP 153 id rs28358274 rs28358274 rs28358274 . . . . .
ClinVar March2020 ClinSig . Benign . . . . . .
ClinVar March2020 ClnDBN . Leigh_syndrome . . . . . .
ClinVar March2020 ClnAllele id . 680150 . . . . . .
ClinVar March2020 ClnDSDB . MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005 . . . . . .
COSMIC 90 . . . . . . . .
CPD Frequency . 0.15 . . . . . .
MITOMAP Allele . A10086G . . . . . .
MITOMAP Phenotype . Hypertensive end-stage renal disease . . . . . .
MITOMAP Homoplasmy . + . . . . . .
MITOMAP Heteroplasmy . - . . . . . .
MITOMAP Status . Reported . . . . . .
MITOMAP NRef . 4 . . . . . .
EVmutation MT-ND3_10N|11T:0.279235;14A:0.257447;21T:0.201914;109K:0.156388;81T:0.148862;12L:0.1465;18M:0.143412;27L:0.125761;17L:0.122564;93L:0.106498;78A:0.10349;26Q:0.093994;91S:0.083012;25P:0.079571;103A:0.074663;28N:0.073532;113W:0.072372;86L:0.06848;16L:0.067363 MT-ND3_10N|11T:0.279235;14A:0.257447;21T:0.201914;109K:0.156388;81T:0.148862;12L:0.1465;18M:0.143412;27L:0.125761;17L:0.122564;93L:0.106498;78A:0.10349;26Q:0.093994;91S:0.083012;25P:0.079571;103A:0.074663;28N:0.073532;113W:0.072372;86L:0.06848;16L:0.067363 MT-ND3_10N|11T:0.279235;14A:0.257447;21T:0.201914;109K:0.156388;81T:0.148862;12L:0.1465;18M:0.143412;27L:0.125761;17L:0.122564;93L:0.106498;78A:0.10349;26Q:0.093994;91S:0.083012;25P:0.079571;103A:0.074663;28N:0.073532;113W:0.072372;86L:0.06848;16L:0.067363 MT-ND3_10N|11T:0.279235;14A:0.257447;21T:0.201914;109K:0.156388;81T:0.148862;12L:0.1465;18M:0.143412;27L:0.125761;17L:0.122564;93L:0.106498;78A:0.10349;26Q:0.093994;91S:0.083012;25P:0.079571;103A:0.074663;28N:0.073532;113W:0.072372;86L:0.06848;16L:0.067363 MT-ND3_10N|11T:0.279235;14A:0.257447;21T:0.201914;109K:0.156388;81T:0.148862;12L:0.1465;18M:0.143412;27L:0.125761;17L:0.122564;93L:0.106498;78A:0.10349;26Q:0.093994;91S:0.083012;25P:0.079571;103A:0.074663;28N:0.073532;113W:0.072372;86L:0.06848;16L:0.067363 MT-ND3_10N|11T:0.279235;14A:0.257447;21T:0.201914;109K:0.156388;81T:0.148862;12L:0.1465;18M:0.143412;27L:0.125761;17L:0.122564;93L:0.106498;78A:0.10349;26Q:0.093994;91S:0.083012;25P:0.079571;103A:0.074663;28N:0.073532;113W:0.072372;86L:0.06848;16L:0.067363 MT-ND3_10N|11T:0.279235;14A:0.257447;21T:0.201914;109K:0.156388;81T:0.148862;12L:0.1465;18M:0.143412;27L:0.125761;17L:0.122564;93L:0.106498;78A:0.10349;26Q:0.093994;91S:0.083012;25P:0.079571;103A:0.074663;28N:0.073532;113W:0.072372;86L:0.06848;16L:0.067363 MT-ND3_10N|11T:0.279235;14A:0.257447;21T:0.201914;109K:0.156388;81T:0.148862;12L:0.1465;18M:0.143412;27L:0.125761;17L:0.122564;93L:0.106498;78A:0.10349;26Q:0.093994;91S:0.083012;25P:0.079571;103A:0.074663;28N:0.073532;113W:0.072372;86L:0.06848;16L:0.067363
Site A InterP ND3_10 ND3_10 ND3_10 ND3_10 ND3_10 ND3_10 ND3_10 ND3_10
Site B InterP ND4_279;ND4_268;ND4_280;ND4L_39;ND4L_73;ND6_51 ND4_279;ND4_268;ND4_280;ND4L_39;ND4L_73;ND6_51 ND4_279;ND4_268;ND4_280;ND4L_39;ND4L_73;ND6_51 ND4_279;ND4_268;ND4_280;ND4L_39;ND4L_73;ND6_51 ND4_279;ND4_268;ND4_280;ND4L_39;ND4L_73;ND6_51 ND4_279;ND4_268;ND4_280;ND4L_39;ND4L_73;ND6_51 ND4_279;ND4_268;ND4_280;ND4L_39;ND4L_73;ND6_51 ND4_279;ND4_268;ND4_280;ND4L_39;ND4L_73;ND6_51
Covariation Score InterP mfDCA:29.0674;mfDCA:29.0671;mfDCA:23.2294;mfDCA:46.3506;mfDCA:42.5017;mfDCA:21.9911 mfDCA:29.0674;mfDCA:29.0671;mfDCA:23.2294;mfDCA:46.3506;mfDCA:42.5017;mfDCA:21.9911 mfDCA:29.0674;mfDCA:29.0671;mfDCA:23.2294;mfDCA:46.3506;mfDCA:42.5017;mfDCA:21.9911 mfDCA:29.0674;mfDCA:29.0671;mfDCA:23.2294;mfDCA:46.3506;mfDCA:42.5017;mfDCA:21.9911 mfDCA:29.0674;mfDCA:29.0671;mfDCA:23.2294;mfDCA:46.3506;mfDCA:42.5017;mfDCA:21.9911 mfDCA:29.0674;mfDCA:29.0671;mfDCA:23.2294;mfDCA:46.3506;mfDCA:42.5017;mfDCA:21.9911 mfDCA:29.0674;mfDCA:29.0671;mfDCA:23.2294;mfDCA:46.3506;mfDCA:42.5017;mfDCA:21.9911 mfDCA:29.0674;mfDCA:29.0671;mfDCA:23.2294;mfDCA:46.3506;mfDCA:42.5017;mfDCA:21.9911
Site A IntraP ND3_10 ND3_10 ND3_10 ND3_10 ND3_10 ND3_10 ND3_10 ND3_10
Site B IntraP ND3_13;ND3_13 ND3_13;ND3_13 ND3_13;ND3_13 ND3_13;ND3_13 ND3_13;ND3_13 ND3_13;ND3_13 ND3_13;ND3_13 ND3_13;ND3_13
Covariation Score IntraP cMI:10.246769;mfDCA:16.2715 cMI:10.246769;mfDCA:16.2715 cMI:10.246769;mfDCA:16.2715 cMI:10.246769;mfDCA:16.2715 cMI:10.246769;mfDCA:16.2715 cMI:10.246769;mfDCA:16.2715 cMI:10.246769;mfDCA:16.2715 cMI:10.246769;mfDCA:16.2715
CPD AA ref . N . . . . . .
CPD AA alt . D . . . . . .
CPD Aln pos . 12 . . . . . .
CPD Species name . Propithecus coquereli . . . . . .
CPD RefSeq Protein ID . YP_002004588 . . . . . .
CPD Ncbi Taxon id . 379532 . . . . . .
DDG intra MT-ND3:N10Y:L13M:-0.731209:-0.754297:-0.0344781;MT-ND3:N10Y:L13R:0.21245:-0.754297:0.952128;MT-ND3:N10Y:L13V:0.686742:-0.754297:1.41472;MT-ND3:N10Y:L13P:3.98045:-0.754297:5.34847;MT-ND3:N10Y:L13Q:0.375097:-0.754297:1.11416 MT-ND3:N10D:L13Q:0.949085:-0.131219:1.11416;MT-ND3:N10D:L13V:1.29727:-0.131219:1.41472;MT-ND3:N10D:L13M:-0.115349:-0.131219:-0.0344781;MT-ND3:N10D:L13R:0.829787:-0.131219:0.952128;MT-ND3:N10D:L13P:4.9478:-0.131219:5.34847 MT-ND3:N10H:L13Q:0.972834:-0.0810654:1.11416;MT-ND3:N10H:L13R:0.87392:-0.0810654:0.952128;MT-ND3:N10H:L13V:1.34779:-0.0810654:1.41472;MT-ND3:N10H:L13M:-0.0484309:-0.0810654:-0.0344781;MT-ND3:N10H:L13P:4.74993:-0.0810654:5.34847 MT-ND3:N10T:L13Q:1.28158:0.201104:1.11416;MT-ND3:N10T:L13R:1.17029:0.201104:0.952128;MT-ND3:N10T:L13P:5.27428:0.201104:5.34847;MT-ND3:N10T:L13V:1.62251:0.201104:1.41472;MT-ND3:N10T:L13M:0.206991:0.201104:-0.0344781 MT-ND3:N10S:L13M:0.110302:0.0787259:-0.0344781;MT-ND3:N10S:L13V:1.50718:0.0787259:1.41472;MT-ND3:N10S:L13P:5.11937:0.0787259:5.34847;MT-ND3:N10S:L13Q:1.20433:0.0787259:1.11416;MT-ND3:N10S:L13R:1.03445:0.0787259:0.952128 MT-ND3:N10I:L13Q:0.58307:-0.481867:1.11416;MT-ND3:N10I:L13P:4.32645:-0.481867:5.34847;MT-ND3:N10I:L13V:0.918172:-0.481867:1.41472;MT-ND3:N10I:L13R:0.472396:-0.481867:0.952128;MT-ND3:N10I:L13M:-0.48696:-0.481867:-0.0344781 MT-ND3:N10K:L13Q:0.453672:-0.610655:1.11416;MT-ND3:N10K:L13M:-0.52605:-0.610655:-0.0344781;MT-ND3:N10K:L13R:0.395018:-0.610655:0.952128;MT-ND3:N10K:L13V:0.821744:-0.610655:1.41472;MT-ND3:N10K:L13P:4.51002:-0.610655:5.34847 MT-ND3:N10K:L13Q:0.453672:-0.610655:1.11416;MT-ND3:N10K:L13M:-0.52605:-0.610655:-0.0344781;MT-ND3:N10K:L13R:0.395018:-0.610655:0.952128;MT-ND3:N10K:L13V:0.821744:-0.610655:1.41472;MT-ND3:N10K:L13P:4.51002:-0.610655:5.34847
DDG intra interface MT-ND3:MT-ND1:5lc5:A:H:N10Y:N2D:-1.74348:-0.98804:0.02153;MT-ND3:MT-ND1:5lc5:A:H:N10Y:N2H:-1.06429:-0.98804:-0.15939;MT-ND3:MT-ND1:5lc5:A:H:N10Y:N2I:-0.84401:-0.98804:-0.30046;MT-ND3:MT-ND1:5lc5:A:H:N10Y:N2K:-2.04281:-0.98804:-0.39659;MT-ND3:MT-ND1:5lc5:A:H:N10Y:N2S:-1.79848:-0.98804:0.07383;MT-ND3:MT-ND1:5lc5:A:H:N10Y:N2T:-1.73987:-0.98804:0.04246;MT-ND3:MT-ND1:5lc5:A:H:N10Y:N2Y:-1.66542:-0.98804:-1.16395;MT-ND3:MT-ND1:5ldw:A:H:N10Y:N2D:-2.04095:-1.67045:-0.02208;MT-ND3:MT-ND1:5ldw:A:H:N10Y:N2H:-2.12456:-1.67045:-0.16726;MT-ND3:MT-ND1:5ldw:A:H:N10Y:N2I:-2.0948:-1.67045:-0.28811;MT-ND3:MT-ND1:5ldw:A:H:N10Y:N2K:-2.48052:-1.67045:-0.3758;MT-ND3:MT-ND1:5ldw:A:H:N10Y:N2S:-1.96355:-1.67045:0.0765;MT-ND3:MT-ND1:5ldw:A:H:N10Y:N2T:-1.9824:-1.67045:0.03795;MT-ND3:MT-ND1:5ldw:A:H:N10Y:N2Y:-3.35403:-1.67045:-1.30653;MT-ND3:MT-ND1:5ldx:A:H:N10Y:N2D:-1.59301:-1.65144:0.06599;MT-ND3:MT-ND1:5ldx:A:H:N10Y:N2H:-1.87091:-1.65144:-0.22309;MT-ND3:MT-ND1:5ldx:A:H:N10Y:N2I:-2.28846:-1.65144:-0.2603;MT-ND3:MT-ND1:5ldx:A:H:N10Y:N2K:-2.37662:-1.65144:-0.32806;MT-ND3:MT-ND1:5ldx:A:H:N10Y:N2S:-2.0388:-1.65144:0.16465;MT-ND3:MT-ND1:5ldx:A:H:N10Y:N2T:-1.87034:-1.65144:0.11107;MT-ND3:MT-ND1:5ldx:A:H:N10Y:N2Y:-2.70364:-1.65144:-1.1875 MT-ND3:MT-ND1:5lc5:A:H:N10D:N2D:1.92022:1.83785:0.02153;MT-ND3:MT-ND1:5lc5:A:H:N10D:N2H:1.68923:1.83785:-0.15939;MT-ND3:MT-ND1:5lc5:A:H:N10D:N2I:1.5658:1.83785:-0.30046;MT-ND3:MT-ND1:5lc5:A:H:N10D:N2K:1.43709:1.83785:-0.39659;MT-ND3:MT-ND1:5lc5:A:H:N10D:N2S:1.89407:1.83785:0.07383;MT-ND3:MT-ND1:5lc5:A:H:N10D:N2T:1.89719:1.83785:0.04246;MT-ND3:MT-ND1:5lc5:A:H:N10D:N2Y:0.61335:1.83785:-1.16395;MT-ND3:MT-ND1:5ldw:A:H:N10D:N2D:1.43189:1.47863:-0.02208;MT-ND3:MT-ND1:5ldw:A:H:N10D:N2H:1.32428:1.47863:-0.16726;MT-ND3:MT-ND1:5ldw:A:H:N10D:N2I:1.21783:1.47863:-0.28811;MT-ND3:MT-ND1:5ldw:A:H:N10D:N2K:1.00829:1.47863:-0.3758;MT-ND3:MT-ND1:5ldw:A:H:N10D:N2S:1.54713:1.47863:0.0765;MT-ND3:MT-ND1:5ldw:A:H:N10D:N2T:1.4876:1.47863:0.03795;MT-ND3:MT-ND1:5ldw:A:H:N10D:N2Y:0.04057:1.47863:-1.30653;MT-ND3:MT-ND1:5ldx:A:H:N10D:N2D:1.77531:1.75792:0.06599;MT-ND3:MT-ND1:5ldx:A:H:N10D:N2H:1.49392:1.75792:-0.22309;MT-ND3:MT-ND1:5ldx:A:H:N10D:N2I:1.4992:1.75792:-0.2603;MT-ND3:MT-ND1:5ldx:A:H:N10D:N2K:1.29042:1.75792:-0.32806;MT-ND3:MT-ND1:5ldx:A:H:N10D:N2S:1.84521:1.75792:0.16465;MT-ND3:MT-ND1:5ldx:A:H:N10D:N2T:1.79562:1.75792:0.11107;MT-ND3:MT-ND1:5ldx:A:H:N10D:N2Y:0.46121:1.75792:-1.1875 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DDG inter 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For more info, please check the output legend.
For more info, please check the output legend.
For more info, please check the output legend.
For more info, please check the output legend.
For more info, please check the output legend.