9176 (T > C)

General info

Chr
chrM
Start
9176
End
9176
Ref
T
Alt
C
Mitimpact ID
MI.1384
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
650
AA pos
217
AA ref
L
AA alt
P
Codon substitution
cTa/cCa
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Conservation

PhyloP 100v
-0.1 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
.
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
Low 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 October2021 CLNSIG
Pathogenic
ClinVar October2021 CLNDN
Leber hereditary optic neuropathy;

leigh syndrome;

striatonigral degeneration, infantile, mitochondrial;

mitochondrial complex v (atp synthase) deficiency, mitochondrial type 1;

not provided
ClinVar October2021 Variation ID
ClinVar October2021 CLNDISDB
Human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:orpha104, snomed ct:58610003;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:orpha506, snomed ct:29570005;

mondo:mondo:0010774, medgen:c1839022, omim:500003;

mondo:mondo:0027069, medgen:c3275684, omim:500015;

medgen:cn517202
MITOMAP Allele
MITOMAP Disease Het/Hom
+/+
MITOMAP Disease Clinical info
Fbsn / leigh disease / spinocerebellar ataxia
MITOMAP Disease Status
Cfrm
MITOMAP Disease GenBank Freq
0.000%
MITOMAP Disease GenBank Seqs
3 (0)
MITOMAP Disease GenBank Curated refs
34
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
Gnomad31 filter
Pass
Gnomad31 AC hom
0
Gnomad31 AC het
3
Gnomad31 AF hom
0
Gnomad31 AF het
5.3160384e-05
Gnomad31 AN
56433
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
.

9176 (T > A)

General info

Chr
chrM
Start
9176
End
9176
Ref
T
Alt
A
Mitimpact ID
MI.1383
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
650
AA pos
217
AA ref
L
AA alt
Q
Codon substitution
cTa/cAa
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Powered by MitoWheel

Conservation

PhyloP 100v
-0.1 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
.
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
Low 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 October2021 CLNSIG
.
ClinVar October2021 CLNDN
.
ClinVar October2021 Variation ID
ClinVar October2021 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
.
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
.

9176 (T > G)

General info

Chr
chrM
Start
9176
End
9176
Ref
T
Alt
G
Mitimpact ID
MI.1385
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
650
AA pos
217
AA ref
L
AA alt
R
Codon substitution
cTa/cGa
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.1 Conservation Score
PhastCons 100v
0 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
Neutral Score and details of the predictor
PANTHER
.
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
Low 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 October2021 CLNSIG
Pathogenic
ClinVar October2021 CLNDN
Leber hereditary optic neuropathy;

leigh syndrome;

mitochondrial complex v (atp synthase) deficiency, mitochondrial type 1;

not provided
ClinVar October2021 Variation ID
ClinVar October2021 CLNDISDB
Human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:orpha104, snomed ct:58610003;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:orpha506, snomed ct:29570005;

mondo:mondo:0027069, medgen:c3275684, omim:500015;

medgen:cn517202
MITOMAP Allele
MITOMAP Disease Het/Hom
+/+
MITOMAP Disease Clinical info
Leigh disease / spastic paraplegia / spinocerebellar ataxia
MITOMAP Disease Status
Cfrm
MITOMAP Disease GenBank Freq
0.000%
MITOMAP Disease GenBank Seqs
1 (0)
MITOMAP Disease GenBank Curated refs
11
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
.
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
.
~ 9176 (T/C) 9176 (T/A) 9176 (T/G)
~ 9176 (cTa/cCa) 9176 (cTa/cAa) 9176 (cTa/cGa)
Chr chrM chrM chrM
Start 9176 9176 9176
End 9176 9176 9176
Ref T T T
Alt C A G
MitImpact id MI.1384 MI.1383 MI.1385
Gene symbol MT-ATP6 MT-ATP6 MT-ATP6
Respiratory Chain complex V V V
Ensembl gene id ENSG00000198899 ENSG00000198899 ENSG00000198899
Ensembl protein id ENSP00000354632 ENSP00000354632 ENSP00000354632
Ensembl transcript id ENST00000361899 ENST00000361899 ENST00000361899
Uniprot name ATP6_HUMAN ATP6_HUMAN ATP6_HUMAN
Uniprot id P00846 P00846 P00846
Ncbi gene id 4508 4508 4508
Ncbi protein id YP_003024031.1 YP_003024031.1 YP_003024031.1
Gene position 650 650 650
AA position 217 217 217
AA ref L L L
AA alt P Q R
Codon substitution cTa/cCa cTa/cAa cTa/cGa
PhyloP 100V -0.1 -0.1 -0.1
PhastCons 100V 0 0 0
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1 1 1
SIFT deleterious deleterious deleterious
SIFT score 0 0 0
FatHmm deleterious deleterious deleterious
FatHmm score -9.53 -9.42 -9.28
FatHmmW neutral neutral neutral
FatHmmW score 2.16 2.16 2.16
PROVEAN deleterious deleterious deleterious
PROVEAN score -6.26 -5.35 -5.36
MutationAssessor high impact high impact high impact
MutationAssessor score 4.22 4.57 4.57
EFIN SP damaging damaging damaging
EFIN SP score 0.06 0.41 0.18
EFIN HD neutral neutral neutral
EFIN HD score 0.44 0.45 0.36
CADD deleterious deleterious deleterious
CADD score 4 4.13 4.29
CADD phred 23.6 23.8 24
VEST pvalue 0.12 0.11 0.11
VEST FDR 0.65 0.65 0.65
PANTHER . . .
PANTHER score . . .
PhD-SNP disease disease disease
PhD-SNP score 0.8 0.82 0.88
SNAP disease disease disease
SNAP score 0.84 0.79 0.85
Meta-SNP disease disease disease
Meta-SNP score 0.78 0.76 0.84
Meta-SNP RI 6 5 7
CAROL deleterious deleterious deleterious
CAROL score 1 1 1
Condel neutral neutral neutral
Condel score 0 0 0
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 6 6 6
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.92 0.87 0.92
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.6 -3.6 -3.6
SIFT_transf low impact low impact low impact
SIFT transf score -1.4 -1.4 -1.4
MutationAssessor transf high impact high impact high impact
MutationAssessor transf score 2.52 2.82 2.82
CHASM pvalue 0.54 0.61 0.37
CHASM FDR 0.9 0.9 0.9
APOGEE Pathogenic Pathogenic Pathogenic
APOGEE score 0.92 0.66 0.9
SNPDryad score 1 0.98 0.99
MutationTaster disease_causing_automatic disease_causing disease_causing_automatic
MutationTaster score 1 0.88 0.9
DEOGEN2 score 0.42 0.41 0.41
Mitoclass.1 damaging damaging damaging
dbSNP 155 id rs199476135 . rs199476135
ClinVar October2021 Variation id 9644 . 9650
ClinVar October2021 CLNSIG Pathogenic . Pathogenic
ClinVar October2021 CLNDN Leber_hereditary_optic_neuropathy|Leigh_syndrome|Striatonigral_degeneration,_infantile,_mitochondrial|Mitochondrial_complex_v_(atp_synthase)_deficiency,_mitochondrial_type_1|not_provided . Leber_hereditary_optic_neuropathy|Leigh_syndrome|Mitochondrial_complex_v_(atp_synthase)_deficiency,_mitochondrial_type_1|not_provided
ClinVar October2021 CLNDISDB Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:ORPHA104,SNOMED_CT:58610003|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005|MONDO:MONDO:0010774,MedGen:C1839022,OMIM:500003|MONDO:MONDO:0027069,MedGen:C3275684,OMIM:500015|MedGen:CN517202 . Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:ORPHA104,SNOMED_CT:58610003|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005|MONDO:MONDO:0027069,MedGen:C3275684,OMIM:500015|MedGen:CN517202
COSMIC 90 . . .
MITOMAP Allele T9176C . T9176G
MITOMAP Disease Het/Hom +/+ . +/+
MITOMAP Disease Clinical info FBSN / Leigh Disease / Spinocerebellar Ataxia . Leigh Disease / Spastic Paraplegia / Spinocerebellar Ataxia
MITOMAP Disease Status Cfrm . Cfrm
MITOMAP Disease GenBank Freq 0.000% . 0.000%
MITOMAP Disease GenBank Seqs 3 (0) . 1 (0)
MITOMAP Disease GenBank Curated refs 34 . 11
MITOMAP General GenBank Freq . . .
MITOMAP General GenBank Seqs . . .
MITOMAP General Curated refs . . .
gnomAD 3.1 filter PASS . .
gnomAD 3.1 AC Homo 0 . .
gnomAD 3.1 AC Het 3 . .
gnomAD 3.1 AF Hom 0 . .
gnomAD 3.1 AF Het 5.3160384e-05 . .
gnomAD 3.1 AN 56433 . .
EVmutation MT-ATP6_217L|221Y:0.106331 MT-ATP6_217L|221Y:0.106331 MT-ATP6_217L|221Y:0.106331
Site A InterP . . .
Site B InterP . . .
Covariation Score InterP . . .
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 . . .
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