8528 (T > C)

General info

Chr
chrM
Start
8528
End
8528
Ref
T
Alt
C
Mitimpact ID
MI.1789
Gene symbol
MT-ATP8
RC complex
V
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
163
AA pos
55
AA ref
W
AA alt
R
Codon substitution
Tga/Cga
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Conservation

PhyloP 100v
5.68 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
Damaging 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
Disease causing automatic 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
Deleterious 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
Pathogenic
ClinVar March2020 ClnDBN
Infantile histiocytoid cardiomyopathy;

cardiomyopathy, infantile hypertrophic
ClinVar March2020 ClnAllele ID
24679
ClinVar March2020 ClnDSDB
Human phenotype ontology:hp:0005152, medgen:c1708371, omim:500000, orphanet:orpha137675;

medgen:c2748884, omim:500006
MITOMAP Allele
MITOMAP Phenotype
Infantile cardiomyopathy
MITOMAP Homoplasmy
+
MITOMAP Heteroplasmy
+
MITOMAP Status
Cfrm
MITOMAP NRef
3
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
.

8528 (T > G)

General info

Chr
chrM
Start
8528
End
8528
Ref
T
Alt
G
Mitimpact ID
MI.1788
Gene symbol
MT-ATP8
RC complex
V
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
163
AA pos
55
AA ref
W
AA alt
G
Codon substitution
Tga/Gga
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Powered by MitoWheel

Conservation

PhyloP 100v
5.68 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
Damaging 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
Disease causing 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
Deleterious 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
.

8528 (T > A)

General info

Chr
chrM
Start
8528
End
8528
Ref
T
Alt
A
Mitimpact ID
MI.3
Gene symbol
MT-ATP6
RC complex
V
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
2
AA pos
1
AA ref
M
AA alt
K
Codon substitution
aTg/aAg
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Powered by MitoWheel

Conservation

PhyloP 100v
5.68 Conservation Score
PhastCons 100v
1 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Deleterious 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
.
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Damaging 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

APOGEE
Pathogenic Score and details of the meta-predictor
CAROL
Deleterious 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
. Score and details of the cancer-specific predictor
SIFT transf
. Score and details of the cancer-specific predictor
MutationAssessor transf
. 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
.

8528 (T > C)

General info

Chr
chrM
Start
8528
End
8528
Ref
T
Alt
C
Mitimpact ID
MI.4
Gene symbol
MT-ATP6
RC complex
V
Ensembl gene ID
Ensembl protein ID
Ensembl transcript ID
Uniprot name
Uniprot ID
Ncbi gene ID
Ncbi protein ID
Gene position
2
AA pos
1
AA ref
M
AA alt
T
Codon substitution
aTg/aCg
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
5.68 Conservation Score
PhastCons 100v
1 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Deleterious 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
.
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
Disease Score and details of the predictor
PhD-SNP
Neutral 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

APOGEE
Pathogenic Score and details of the meta-predictor
CAROL
Deleterious 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
. Score and details of the cancer-specific predictor
SIFT transf
. Score and details of the cancer-specific predictor
MutationAssessor transf
. Score and details of the cancer-specific predictor
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Phenotypes

ClinVar March2020 ClinSig
Pathogenic
ClinVar March2020 ClnDBN
Infantile histiocytoid cardiomyopathy;

cardiomyopathy, infantile hypertrophic
ClinVar March2020 ClnAllele ID
24679
ClinVar March2020 ClnDSDB
Human phenotype ontology:hp:0005152, medgen:c1708371, omim:500000, orphanet:orpha137675;

medgen:c2748884, omim:500006
MITOMAP Allele
MITOMAP Phenotype
Infantile cardiomyopathy
MITOMAP Homoplasmy
+
MITOMAP Heteroplasmy
+
MITOMAP Status
Cfrm
MITOMAP NRef
3
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
.
~ 8528 (T/C) 8528 (T/G) 8528 (T/A) 8528 (T/C)
~ 8528 (Tga/Cga) 8528 (Tga/Gga) 8528 (aTg/aAg) 8528 (aTg/aCg)
Chr chrM chrM chrM chrM
Start 8528 8528 8528 8528
End 8528 8528 8528 8528
Ref T T T T
Alt C G A C
MitImpact id MI.1789 MI.1788 MI.3 MI.4
Gene symbol MT-ATP8 MT-ATP8 MT-ATP6 MT-ATP6
Respiratory Chain complex V V V V
Ensembl gene id ENSG00000228253 ENSG00000228253 ENSG00000198899 ENSG00000198899
Ensembl protein id ENSP00000355265 ENSP00000355265 ENSP00000354632 ENSP00000354632
Ensembl transcript id ENST00000361851 ENST00000361851 ENST00000361899 ENST00000361899
Uniprot name ATP8_HUMAN ATP8_HUMAN ATP6_HUMAN ATP6_HUMAN
Uniprot id P03928 P03928 P00846 P00846
Ncbi gene id 4509 4509 4508 4508
Ncbi protein id YP_003024030.1 YP_003024030.1 YP_003024031.1 YP_003024031.1
Gene position 163 163 2 2
AA position 55 55 1 1
AA ref W W M M
AA alt R G K T
Codon substitution Tga/Cga Tga/Gga aTg/aAg aTg/aCg
PhyloP 100V 5.68 5.68 5.68 5.68
PhastCons 100V 1 1 1 1
PolyPhen2 probably_damaging probably_damaging possibly_damaging possibly_damaging
PolyPhen2 score 1 0.98 0.8 0.8
SIFT neutral neutral deleterious deleterious
SIFT score 0.31 0.34 0 0
FatHmm deleterious deleterious neutral neutral
FatHmm score -11.02 -11.1 -0.95 -0.97
FatHmmW neutral neutral neutral neutral
FatHmmW score -0.53 -0.53 4.49 4.49
PROVEAN deleterious deleterious deleterious deleterious
PROVEAN score -12.74 -12.02 -4.89 -4.97
MutationAssessor high impact high impact . .
MutationAssessor score 3.7 3.7 . .
EFIN SP neutral neutral neutral neutral
EFIN SP score 0.85 0.84 0.61 0.7
EFIN HD damaging damaging damaging damaging
EFIN HD score 0.06 0.1 0.09 0.13
CADD deleterious deleterious deleterious deleterious
CADD score 3.65 3.96 6.26 3.65
CADD phred 23.2 23.6 28.9 23.2
VEST pvalue 0.15055088 0.13200123 0.25 0.47
VEST FDR 0.85 0.85 0.65 0.65
PANTHER disease disease neutral disease
PANTHER score 0.89 0.85 0.39 0.58
PhD-SNP disease disease disease neutral
PhD-SNP score 0.74 0.71 0.57 0.5
SNAP disease disease disease disease
SNAP score 0.84 0.81 0.67 0.65
Meta-SNP disease disease disease disease
Meta-SNP score 0.77 0.76 0.67 0.66
Meta-SNP RI 5 5 3 3
CAROL deleterious deleterious deleterious deleterious
CAROL score 1 0.98 1 1
Condel neutral neutral neutral neutral
Condel score 0.16 0.18 0.1 0.1
COVEC WMV deleterious deleterious deleterious deleterious
COVEC WMV score 2 2 3 3
MtoolBox deleterious deleterious deleterious deleterious
MtoolBox DS 0.9 0.87 0.73 0.76
PolyPhen2 transf low impact low impact . .
PolyPhen2 transf score -3.6 -2.36 . .
SIFT_transf medium impact medium impact . .
SIFT transf score 0.1 0.13 . .
MutationAssessor transf high impact high impact . .
MutationAssessor transf score 2.07 2.07 . .
CHASM pvalue 0.08 0.06 0.42 0.24
CHASM FDR 0.85 0.85 0.9 0.9
APOGEE Pathogenic Pathogenic Pathogenic Pathogenic
APOGEE score 0.58 0.64 0.58 0.63
SNPDryad score 0.97 0.93 0.99 0.97
MutationTaster disease_causing_automatic disease_causing . .
MutationTaster score 0.95 0.98 . .
DEOGEN2 score 0.25 0.4 0.24 0.31
Mitoclass.1 damaging damaging damaging damaging
dbSNP 153 id rs387906422 . . rs387906422
ClinVar March2020 ClinSig Pathogenic . . Pathogenic
ClinVar March2020 ClnDBN Infantile_histiocytoid_cardiomyopathy|Cardiomyopathy,_infantile_hypertrophic . . Infantile_histiocytoid_cardiomyopathy|Cardiomyopathy,_infantile_hypertrophic
ClinVar March2020 ClnAllele id 24679 . . 24679
ClinVar March2020 ClnDSDB Human_Phenotype_Ontology:HP:0005152,MedGen:C1708371,OMIM:500000,Orphanet:ORPHA137675|MedGen:C2748884,OMIM:500006 . . Human_Phenotype_Ontology:HP:0005152,MedGen:C1708371,OMIM:500000,Orphanet:ORPHA137675|MedGen:C2748884,OMIM:500006
COSMIC 90 . . . .
CPD Frequency . . . .
MITOMAP Allele T8528C . . T8528C
MITOMAP Phenotype Infantile cardiomyopathy . . Infantile cardiomyopathy
MITOMAP Homoplasmy + . . +
MITOMAP Heteroplasmy + . . +
MITOMAP Status Cfrm . . Cfrm
MITOMAP NRef 3 . . 3
EVmutation . . . .
Site A InterP ATP8_55 ATP8_55 . .
Site B InterP ATP6_2;ATP6_36 ATP6_2;ATP6_36 . .
Covariation Score InterP mfDCA_49.75;mfDCA_32.8 mfDCA_49.75;mfDCA_32.8 . .
Site A IntraP . . . .
Site B IntraP . . . .
Covariation Score IntraP . . . .
CPD AA ref . . . .
CPD AA alt . . . .
CPD Aln pos . . . .
CPD Species name . . . .
CPD RefSeq Protein ID . . . .
CPD Ncbi Taxon id . . . .
DDG intra . . . .
DDG intra interface . . . .
DDG inter . . . .
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
ΔΔG values >±0.61 Kcal/mol are indicative of disrupting variants.
ΔΔG values close to zero (<±0.1 Kcal/mol) are indicative of possibly
compensating double mutants.
For more info, please check the output legend.
For more info, please check the output legend.
Score:  
0
  [min -20, max 10]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min 0, max 1]
  • Non-conserved:  score <= 0.9
  • 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