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14462 (G > T)

MT-ND4L_5xtc_m_k_TA71K_AB71T

General info

Chr
chrM
Start
14462
End
14462
Ref
G
Alt
T
Mitimpact ID
MI.23744
Gene symbol
MT-ND6
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot name
NU6M_HUMAN
Uniprot ID
P03923
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Gene position
212
AA pos
71
AA ref
T
AA alt
K
Codon substitution
aCa/aAa
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
1.66663 Conservation Score
PhastCons 100v
0.0787402 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
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
.
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

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus+ Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
.
Meta SNP
Disease Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Deleterious Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar July2022 CLNSIG
.
ClinVar July2022 CLNDN
.
ClinVar July2022 Variation ID
.
ClinVar July2022 CLNDISDB
.
MITOMAP Allele
.
MITOMAP Disease Het/Hom
.
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease GenBank Freq
.
MITOMAP Disease GenBank Seqs
.
MITOMAP Disease GenBank Curated refs
.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
Gnomad31 filter
.
Gnomad31 AC hom
.
Gnomad31 AC het
.
Gnomad31 AF hom
.
Gnomad31 AF het
.
Gnomad31 AN
.
HelixMTdb AC hom
.
HelixMTdb AF hom
.
HelixMTdb AC het
.
HelixMTdb AF het
.
HelixMTdb mean ARF
.
HelixMTdb max ARF
.
COSMIC 90
.
dbSNP 155
.

Residue interaction

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

Compensated Pathogenic Deviations

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

14462 (G > A)

MT-ND4L_5xtc_m_k_TA71M_AB71T

General info

Chr
chrM
Start
14462
End
14462
Ref
G
Alt
A
Mitimpact ID
MI.23745
Gene symbol
MT-ND6
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot name
NU6M_HUMAN
Uniprot ID
P03923
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Gene position
212
AA pos
71
AA ref
T
AA alt
M
Codon substitution
aCa/aTa
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
1.66663 Conservation Score
PhastCons 100v
0.0787402 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
.
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

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
Meta SNP
Disease Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Deleterious 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
2
Gnomad31 AC het
4
Gnomad31 AF hom
0.000035445282
Gnomad31 AF het
0.000070890565
Gnomad31 AN
56425
HelixMTdb AC hom
3.0
HelixMTdb AF hom
1.530745e-05
HelixMTdb AC het
7.0
HelixMTdb AF het
3.5717385e-05
HelixMTdb mean ARF
0.31758
HelixMTdb max ARF
0.86145
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
.

14463 (T > G)

MT-ND4L_5xtc_m_k_TA71P_AB71T

General info

Chr
chrM
Start
14463
End
14463
Ref
T
Alt
G
Mitimpact ID
MI.23746
Gene symbol
MT-ND6
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot name
NU6M_HUMAN
Uniprot ID
P03923
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Gene position
211
AA pos
71
AA ref
T
AA alt
P
Codon substitution
Aca/Cca
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.51415 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
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
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor
MutationTaster
.
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

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Vus+ Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
.
Meta SNP
Disease Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Deleterious Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar July2022 CLNSIG
.
ClinVar July2022 CLNDN
.
ClinVar July2022 Variation ID
.
ClinVar July2022 CLNDISDB
.
MITOMAP Allele
.
MITOMAP Disease Het/Hom
.
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease GenBank Freq
.
MITOMAP Disease GenBank Seqs
.
MITOMAP Disease GenBank Curated refs
.
MITOMAP General GenBank Freq
0.00002
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
1
Gnomad31 filter
.
Gnomad31 AC hom
.
Gnomad31 AC het
.
Gnomad31 AF hom
.
Gnomad31 AF het
.
Gnomad31 AN
.
HelixMTdb AC hom
.
HelixMTdb AF hom
.
HelixMTdb AC het
.
HelixMTdb AF het
.
HelixMTdb mean ARF
.
HelixMTdb max ARF
.
COSMIC 90
.
dbSNP 155
.

Residue interaction

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

Compensated Pathogenic Deviations

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

14463 (T > A)

General info

Chr
chrM
Start
14463
End
14463
Ref
T
Alt
A
Mitimpact ID
MI.23748
Gene symbol
MT-ND6
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot name
NU6M_HUMAN
Uniprot ID
P03923
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Gene position
211
AA pos
71
AA ref
T
AA alt
S
Codon substitution
Aca/Tca
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.51415 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
Damaging 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
.
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
Neutral Score and details of the meta-predictor
APOGEE2
Likely-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
Deleterious Score and details of the meta-predictor
DEOGEN2
Deleterious Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
Medium impact Score and details of the cancer-specific predictor
MutationAssessor transf
Medium impact Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar July2022 CLNSIG
.
ClinVar July2022 CLNDN
.
ClinVar July2022 Variation ID
.
ClinVar July2022 CLNDISDB
.
MITOMAP Allele
.
MITOMAP Disease Het/Hom
.
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease GenBank Freq
.
MITOMAP Disease GenBank Seqs
.
MITOMAP Disease GenBank Curated refs
.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
Gnomad31 filter
.
Gnomad31 AC hom
.
Gnomad31 AC het
.
Gnomad31 AF hom
.
Gnomad31 AF het
.
Gnomad31 AN
.
HelixMTdb AC hom
.
HelixMTdb AF hom
.
HelixMTdb AC het
.
HelixMTdb AF het
.
HelixMTdb mean ARF
.
HelixMTdb max ARF
.
COSMIC 90
.
dbSNP 155
.

Residue interaction

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

Compensated Pathogenic Deviations

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

14463 (T > C)

MT-ND4L_5xtc_m_k_TA71A_AB71T

General info

Chr
chrM
Start
14463
End
14463
Ref
T
Alt
C
Mitimpact ID
MI.23747
Gene symbol
MT-ND6
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot name
NU6M_HUMAN
Uniprot ID
P03923
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Gene position
211
AA pos
71
AA ref
T
AA alt
A
Codon substitution
Aca/Gca
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.51415 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
Deleterious 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
.
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
Deleterious Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
High 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
2
Gnomad31 AC het
1
Gnomad31 AF hom
0.000035441513
Gnomad31 AF het
0.000017720757
Gnomad31 AN
56431
HelixMTdb AC hom
15.0
HelixMTdb AF hom
7.653725e-05
HelixMTdb AC het
5.0
HelixMTdb AF het
2.5512418e-05
HelixMTdb mean ARF
0.36579
HelixMTdb max ARF
0.79137
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
.
~ 14462 (G/T) 14462 (G/A) 14463 (T/G) 14463 (T/A) 14463 (T/C)
~ 14462 (aCa/aAa) 14462 (aCa/aTa) 14463 (Aca/Cca) 14463 (Aca/Tca) 14463 (Aca/Gca)
Chr chrM chrM chrM chrM chrM
Start 14462 14462 14463 14463 14463
End 14462 14462 14463 14463 14463
Ref G G T T T
Alt T A G A C
MitImpact id MI.23744 MI.23745 MI.23746 MI.23748 MI.23747
Gene symbol MT-ND6 MT-ND6 MT-ND6 MT-ND6 MT-ND6
Respiratory Chain complex I I I I I
Ensembl gene id ENSG00000198695 ENSG00000198695 ENSG00000198695 ENSG00000198695 ENSG00000198695
Ensembl protein id ENSP00000354665 ENSP00000354665 ENSP00000354665 ENSP00000354665 ENSP00000354665
Ensembl transcript id ENST00000361681 ENST00000361681 ENST00000361681 ENST00000361681 ENST00000361681
Uniprot name NU6M_HUMAN NU6M_HUMAN NU6M_HUMAN NU6M_HUMAN NU6M_HUMAN
Uniprot id P03923 P03923 P03923 P03923 P03923
Ncbi gene id 4541 4541 4541 4541 4541
Ncbi protein id YP_003024037.1 YP_003024037.1 YP_003024037.1 YP_003024037.1 YP_003024037.1
Gene position 212 212 211 211 211
AA position 71 71 71 71 71
AA ref T T T T T
AA alt K M P S A
Codon substitution aCa/aAa aCa/aTa Aca/Cca Aca/Tca Aca/Gca
PhyloP 100V 1.66663 1.66663 0.51415 0.51415 0.51415
PhastCons 100V 0.0787402 0.0787402 0 0 0
PolyPhen2 possibly_damaging benign possibly_damaging benign benign
PolyPhen2 score 0.58 0.26 0.82 0.37 0.02
SIFT neutral neutral neutral neutral neutral
SIFT score 0.27 0.21 0.16 0.77 1.0
SIFT4G Damaging Damaging Damaging Damaging Tolerated
SIFT4G score 0.002 0.001 0.003 0.024 0.688
FatHmm deleterious neutral deleterious neutral neutral
FatHmm score -3.01 -1.45 -3.05 0.28 -0.24
FatHmmW neutral neutral neutral neutral neutral
FatHmmW score 2.21 2.24 2.21 2.35 2.3
PROVEAN deleterious deleterious deleterious deleterious deleterious
PROVEAN score -5.29 -5.17 -5.29 -3.32 -3.79
MutationAssessor medium impact medium impact medium impact medium impact neutral impact
MutationAssessor score 3.33 3.33 3.33 2.23 0.23
EFIN SP neutral neutral neutral neutral neutral
EFIN SP score 0.69 0.66 0.7 0.81 0.91
EFIN HD neutral neutral neutral neutral neutral
EFIN HD score 0.33 0.38 0.28 0.72 0.93
CADD deleterious deleterious deleterious deleterious neutral
CADD score 3.66 1.85 3.63 1.9 -0.05
CADD phred 23.2 15.3 23.2 15.57 2.09
VEST pvalue 0.16 0.26 0.15 0.37 0.32
VEST FDR 0.45 0.45 0.4 0.5 0.5
PANTHER neutral disease disease neutral neutral
PANTHER score 0.46 0.61 0.58 0.2 0.15
PhD-SNP disease disease disease disease neutral
PhD-SNP score 0.87 0.73 0.91 0.64 0.18
SNAP disease disease disease neutral neutral
SNAP score 0.73 0.67 0.73 0.33 0.25
Meta-SNP disease disease disease neutral neutral
Meta-SNP score 0.82 0.75 0.84 0.48 0.28
Meta-SNP RI 6 5 7 0 4
CAROL neutral neutral neutral neutral neutral
CAROL score 0.73 0.75 0.91 0.26 0.01
Condel neutral deleterious neutral deleterious deleterious
Condel score 0.35 0.48 0.17 0.7 0.99
COVEC WMV . neutral . neutral neutral
COVEC WMV score 0 -3 0 -3 -6
MtoolBox deleterious neutral deleterious deleterious neutral
MtoolBox DS 0.68 0.42 0.82 0.45 0.13
PolyPhen2 transf medium impact medium impact low impact medium impact medium impact
PolyPhen2 transf score -0.92 -0.38 -1.4 -0.58 0.75
SIFT_transf medium impact medium impact medium impact medium impact high impact
SIFT transf score -0.03 -0.11 -0.19 0.5 1.87
MutationAssessor transf medium impact medium impact medium impact medium impact medium impact
MutationAssessor transf score 1.65 1.65 1.65 0.73 -0.95
CHASM pvalue 0.87 0.86 0.77 0.79 0.62
CHASM FDR 0.9 0.9 0.85 0.85 0.8
APOGEE1 Neutral Neutral Neutral Neutral Neutral
APOGEE1 score 0.37 0.38 0.45 0.31 0.43
APOGEE2 VUS+ VUS VUS+ Likely-benign Benign
APOGEE2 score 0.547302725893702 0.497278736913731 0.686120006597442 0.159702750750223 0.0348437504216969
SNPDryad score 0.94 0.9 0.94 0.68 0.65
MutationTaster . . . . .
MutationTaster score . . . . .
DEOGEN2 score 0.73 0.6 0.73 0.52 0.52
Mitoclass.1 damaging damaging damaging neutral neutral
dbSNP 155 id . . . . .
ClinVar July2022 Variation id . . . . .
ClinVar July2022 CLNSIG . . . . .
ClinVar July2022 CLNDN . . . . .
ClinVar July2022 CLNDISDB . . . . .
COSMIC 90 . . . . .
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 0.00002 . 0.00002
MITOMAP General GenBank Seqs . 1 1 . 1
MITOMAP General Curated refs . 1 1 . 1
gnomAD 3.1 filter . PASS . . PASS
gnomAD 3.1 AC Homo . 2 . . 2
gnomAD 3.1 AC Het . 4 . . 1
gnomAD 3.1 AF Hom . 0.000035445282 . . 0.000035441513
gnomAD 3.1 AF Het . 0.000070890565 . . 0.000017720757
gnomAD 3.1 AN . 56425 . . 56431
HelixMTdb AC Hom . 3.0 . . 15.0
HelixMTdb AF Hom . 1.530745e-05 . . 7.653725e-05
HelixMTdb AC Het . 7.0 . . 5.0
HelixMTdb AF Het . 3.5717385e-05 . . 2.5512418e-05
HelixMTdb mean ARF . 0.31758 . . 0.36579
HelixMTdb max ARF . 0.86145 . . 0.79137
EVmutation MT-ND6_71T|77E:0.191034;76E:0.185333;75I:0.115309;79P:0.072124;72A:0.066189 MT-ND6_71T|77E:0.191034;76E:0.185333;75I:0.115309;79P:0.072124;72A:0.066189 MT-ND6_71T|77E:0.191034;76E:0.185333;75I:0.115309;79P:0.072124;72A:0.066189 MT-ND6_71T|77E:0.191034;76E:0.185333;75I:0.115309;79P:0.072124;72A:0.066189 MT-ND6_71T|77E:0.191034;76E:0.185333;75I:0.115309;79P:0.072124;72A:0.066189
Site A InterP ND6_71 ND6_71 ND6_71 ND6_71 ND6_71
Site B InterP ND1_150;ND4L_58 ND1_150;ND4L_58 ND1_150;ND4L_58 ND1_150;ND4L_58 ND1_150;ND4L_58
Covariation Score InterP mfDCA_22.42;mfDCA_18.95 mfDCA_22.42;mfDCA_18.95 mfDCA_22.42;mfDCA_18.95 mfDCA_22.42;mfDCA_18.95 mfDCA_22.42;mfDCA_18.95
Site A IntraP . . . . .
Site B IntraP . . . . .
Covariation Score IntraP . . . . .
CPD AA ref . . . . .
CPD AA alt . . . . .
CPD Aln pos . . . . .
CPD Frequency . . . . .
CPD Species name . . . . .
CPD RefSeq Protein ID . . . . .
CPD Ncbi Taxon id . . . . .
DDG intra . . . . .
DDG intra interface . . . . .
DDG inter MT-ND6:MT-ND4L:5lc5:J:K:T71K:A71E:1.20206:0.349819183:1.10695875;MT-ND6:MT-ND4L:5lc5:J:K:T71K:A71T:0.0875:0.349819183:-0.234632105;MT-ND6:MT-ND4L:5lc5:J:K:T71K:A71V:-0.51587:0.349819183:-0.85572207;MT-ND6:MT-ND4L:5lc5:J:K:T71K:A71S:0.05905:0.349819183:0.0984386429;MT-ND6:MT-ND4L:5lc5:J:K:T71K:A71G:0.72669:0.349819183:0.47907868;MT-ND6:MT-ND4L:5lc5:J:K:T71K:A71P:0.53301:0.349819183:0.18503876;MT-ND6:MT-ND4L:5ldw:J:K:T71K:A71E:0.92579:0.330052197:0.799778759;MT-ND6:MT-ND4L:5ldw:J:K:T71K:A71T:0.06819:0.330052197:-0.196310431;MT-ND6:MT-ND4L:5ldw:J:K:T71K:A71V:-0.3223:0.330052197:-0.60515976;MT-ND6:MT-ND4L:5ldw:J:K:T71K:A71S:0.41987:0.330052197:0.0573913567;MT-ND6:MT-ND4L:5ldw:J:K:T71K:A71G:0.58838:0.330052197:0.278140247;MT-ND6:MT-ND4L:5ldw:J:K:T71K:A71P:0.44585:0.330052197:0.117359921;MT-ND6:MT-ND4L:5ldx:J:K:T71K:A71E:1.89528:0.38250047:1.14978099;MT-ND6:MT-ND4L:5ldx:J:K:T71K:A71T:-0.18584:0.38250047:-0.633990109;MT-ND6:MT-ND4L:5ldx:J:K:T71K:A71V:-0.76177:0.38250047:-1.18210983;MT-ND6:MT-ND4L:5ldx:J:K:T71K:A71S:-0.23114:0.38250047:-0.592829108;MT-ND6:MT-ND4L:5ldx:J:K:T71K:A71G:1.02073:0.38250047:0.612800598;MT-ND6:MT-ND4L:5ldx:J:K:T71K:A71P:0.64698:0.38250047:0.28040123 MT-ND6:MT-ND4L:5lc5:J:K:T71M:A71G:0.57344:0.272438824:0.47907868;MT-ND6:MT-ND4L:5lc5:J:K:T71M:A71T:0.03951:0.272438824:-0.234632105;MT-ND6:MT-ND4L:5lc5:J:K:T71M:A71P:0.44657:0.272438824:0.18503876;MT-ND6:MT-ND4L:5lc5:J:K:T71M:A71S:0.33742:0.272438824:0.0984386429;MT-ND6:MT-ND4L:5lc5:J:K:T71M:A71V:-0.5836:0.272438824:-0.85572207;MT-ND6:MT-ND4L:5lc5:J:K:T71M:A71E:1.21359:0.272438824:1.10695875;MT-ND6:MT-ND4L:5ldw:J:K:T71M:A71G:0.5724:0.330003351:0.278140247;MT-ND6:MT-ND4L:5ldw:J:K:T71M:A71T:0.03124:0.330003351:-0.196310431;MT-ND6:MT-ND4L:5ldw:J:K:T71M:A71P:0.41534:0.330003351:0.117359921;MT-ND6:MT-ND4L:5ldw:J:K:T71M:A71S:0.44635:0.330003351:0.0573913567;MT-ND6:MT-ND4L:5ldw:J:K:T71M:A71V:-0.33601:0.330003351:-0.60515976;MT-ND6:MT-ND4L:5ldw:J:K:T71M:A71E:1.13745:0.330003351:0.799778759;MT-ND6:MT-ND4L:5ldx:J:K:T71M:A71G:0.99472:0.38127023:0.612800598;MT-ND6:MT-ND4L:5ldx:J:K:T71M:A71T:-0.11459:0.38127023:-0.633990109;MT-ND6:MT-ND4L:5ldx:J:K:T71M:A71P:0.63739:0.38127023:0.28040123;MT-ND6:MT-ND4L:5ldx:J:K:T71M:A71S:-0.24956:0.38127023:-0.592829108;MT-ND6:MT-ND4L:5ldx:J:K:T71M:A71V:-0.81334:0.38127023:-1.18210983;MT-ND6:MT-ND4L:5ldx:J:K:T71M:A71E:1.85701:0.38127023:1.14978099 MT-ND6:MT-ND4L:5lc5:J:K:T71P:A71G:0.85927:0.521499276:0.47907868;MT-ND6:MT-ND4L:5lc5:J:K:T71P:A71V:-0.31524:0.521499276:-0.85572207;MT-ND6:MT-ND4L:5lc5:J:K:T71P:A71E:1.48224:0.521499276:1.10695875;MT-ND6:MT-ND4L:5lc5:J:K:T71P:A71P:0.73229:0.521499276:0.18503876;MT-ND6:MT-ND4L:5lc5:J:K:T71P:A71T:0.23344:0.521499276:-0.234632105;MT-ND6:MT-ND4L:5lc5:J:K:T71P:A71S:0.71729:0.521499276:0.0984386429;MT-ND6:MT-ND4L:5ldw:J:K:T71P:A71G:0.7762:0.499993145:0.278140247;MT-ND6:MT-ND4L:5ldw:J:K:T71P:A71V:-0.07942:0.499993145:-0.60515976;MT-ND6:MT-ND4L:5ldw:J:K:T71P:A71E:1.45455:0.499993145:0.799778759;MT-ND6:MT-ND4L:5ldw:J:K:T71P:A71P:0.6621:0.499993145:0.117359921;MT-ND6:MT-ND4L:5ldw:J:K:T71P:A71T:0.29108:0.499993145:-0.196310431;MT-ND6:MT-ND4L:5ldw:J:K:T71P:A71S:0.57588:0.499993145:0.0573913567;MT-ND6:MT-ND4L:5ldx:J:K:T71P:A71G:0.9902:0.374649823:0.612800598;MT-ND6:MT-ND4L:5ldx:J:K:T71P:A71V:-0.80963:0.374649823:-1.18210983;MT-ND6:MT-ND4L:5ldx:J:K:T71P:A71E:1.84041:0.374649823:1.14978099;MT-ND6:MT-ND4L:5ldx:J:K:T71P:A71P:0.58679:0.374649823:0.28040123;MT-ND6:MT-ND4L:5ldx:J:K:T71P:A71T:-0.24866:0.374649823:-0.633990109;MT-ND6:MT-ND4L:5ldx:J:K:T71P:A71S:-0.23925:0.374649823:-0.592829108 MT-ND6:MT-ND4L:5lc5:J:K:T71S:A71T:0.2707:0.545650125:-0.234632105;MT-ND6:MT-ND4L:5lc5:J:K:T71S:A71E:1.48238:0.545650125:1.10695875;MT-ND6:MT-ND4L:5lc5:J:K:T71S:A71S:0.60418:0.545650125:0.0984386429;MT-ND6:MT-ND4L:5lc5:J:K:T71S:A71P:0.67734:0.545650125:0.18503876;MT-ND6:MT-ND4L:5lc5:J:K:T71S:A71G:0.92094:0.545650125:0.47907868;MT-ND6:MT-ND4L:5lc5:J:K:T71S:A71V:-0.27984:0.545650125:-0.85572207;MT-ND6:MT-ND4L:5ldw:J:K:T71S:A71T:0.19323:0.506391168:-0.196310431;MT-ND6:MT-ND4L:5ldw:J:K:T71S:A71E:1.26368:0.506391168:0.799778759;MT-ND6:MT-ND4L:5ldw:J:K:T71S:A71S:0.6229:0.506391168:0.0573913567;MT-ND6:MT-ND4L:5ldw:J:K:T71S:A71P:0.59015:0.506391168:0.117359921;MT-ND6:MT-ND4L:5ldw:J:K:T71S:A71G:0.74623:0.506391168:0.278140247;MT-ND6:MT-ND4L:5ldw:J:K:T71S:A71V:-0.1642:0.506391168:-0.60515976;MT-ND6:MT-ND4L:5ldx:J:K:T71S:A71T:-0.07485:0.496649563:-0.633990109;MT-ND6:MT-ND4L:5ldx:J:K:T71S:A71E:1.90631:0.496649563:1.14978099;MT-ND6:MT-ND4L:5ldx:J:K:T71S:A71S:-0.13127:0.496649563:-0.592829108;MT-ND6:MT-ND4L:5ldx:J:K:T71S:A71P:0.75052:0.496649563:0.28040123;MT-ND6:MT-ND4L:5ldx:J:K:T71S:A71G:1.10989:0.496649563:0.612800598;MT-ND6:MT-ND4L:5ldx:J:K:T71S:A71V:-0.68776:0.496649563:-1.18210983 MT-ND6:MT-ND4L:5lc5:J:K:T71A:A71V:-0.39334:0.462280273:-0.85572207;MT-ND6:MT-ND4L:5lc5:J:K:T71A:A71P:0.64721:0.462280273:0.18503876;MT-ND6:MT-ND4L:5lc5:J:K:T71A:A71S:0.55369:0.462280273:0.0984386429;MT-ND6:MT-ND4L:5lc5:J:K:T71A:A71T:0.22846:0.462280273:-0.234632105;MT-ND6:MT-ND4L:5lc5:J:K:T71A:A71G:0.80792:0.462280273:0.47907868;MT-ND6:MT-ND4L:5lc5:J:K:T71A:A71E:1.59815:0.462280273:1.10695875;MT-ND6:MT-ND4L:5ldw:J:K:T71A:A71V:-0.20614:0.443702698:-0.60515976;MT-ND6:MT-ND4L:5ldw:J:K:T71A:A71P:0.51735:0.443702698:0.117359921;MT-ND6:MT-ND4L:5ldw:J:K:T71A:A71S:0.52161:0.443702698:0.0573913567;MT-ND6:MT-ND4L:5ldw:J:K:T71A:A71T:0.15385:0.443702698:-0.196310431;MT-ND6:MT-ND4L:5ldw:J:K:T71A:A71G:0.67433:0.443702698:0.278140247;MT-ND6:MT-ND4L:5ldw:J:K:T71A:A71E:1.18736:0.443702698:0.799778759;MT-ND6:MT-ND4L:5ldx:J:K:T71A:A71V:-0.84686:0.337310016:-1.18210983;MT-ND6:MT-ND4L:5ldx:J:K:T71A:A71P:0.62069:0.337310016:0.28040123;MT-ND6:MT-ND4L:5ldx:J:K:T71A:A71S:-0.28049:0.337310016:-0.592829108;MT-ND6:MT-ND4L:5ldx:J:K:T71A:A71T:-0.21315:0.337310016:-0.633990109;MT-ND6:MT-ND4L:5ldx:J:K:T71A:A71G:0.95238:0.337310016:0.612800598;MT-ND6:MT-ND4L:5ldx:J:K:T71A:A71E:1.63535:0.337310016:1.14978099
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