Logo MitImpact
Home Description Output legend Molecular Dynamics How to cite License

8851 (T > C)

General info

Chr
chrM
Start
8851
End
8851
Ref
T
Alt
C
Mitimpact ID
MI.689
Gene symbol
MT-ATP6
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot name
ATP6_HUMAN
Uniprot ID
P00846
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
Gene position
325
AA pos
109
AA ref
W
AA alt
R
Codon substitution
Tga/Cga
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
5.87961 Conservation Score
PhastCons 100v
1 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
High impact Score and details of the predictor
EFIN SP
Damaging 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

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-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 July2022 CLNSIG
Uncertain significance
ClinVar July2022 CLNDN
Leber optic atrophy;

leigh syndrome;

striatonigral degeneration, infantile, mitochondrial;

mitochondrial disease;

not provided
ClinVar July2022 Variation ID
9645
ClinVar July2022 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:0044970, medgen:c0751651, orphanet:orpha68380;

medgen:cn517202
MITOMAP Allele
8851T>C
MITOMAP Disease Het/Hom
+/+
MITOMAP Disease Clinical info
Bsn / leigh syndrome
MITOMAP Disease Status
Cfrm [vus*]
MITOMAP Disease GenBank Freq
0.007%(0.000%)
MITOMAP Disease GenBank Seqs
4 (0)
MITOMAP Disease GenBank Curated refs
9
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
Gnomad31 filter
Pass
Gnomad31 AC hom
2
Gnomad31 AC het
0
Gnomad31 AF hom
0.000035443398
Gnomad31 AF het
0
Gnomad31 AN
56428
HelixMTdb AC hom
10.0
HelixMTdb AF hom
5.1024836e-05
HelixMTdb AC het
4.0
HelixMTdb AF het
2.0409934e-05
HelixMTdb mean ARF
0.29899
HelixMTdb max ARF
0.59701
COSMIC 90
.
dbSNP 155
rs199476136

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
.

8851 (T > G)

General info

Chr
chrM
Start
8851
End
8851
Ref
T
Alt
G
Mitimpact ID
MI.690
Gene symbol
MT-ATP6
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot name
ATP6_HUMAN
Uniprot ID
P00846
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
Gene position
325
AA pos
109
AA ref
W
AA alt
G
Codon substitution
Tga/Gga
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
5.87961 Conservation Score
PhastCons 100v
1 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
High impact Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
VEST
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

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Likely-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 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
Npg
Gnomad31 AC hom
0
Gnomad31 AC het
0
Gnomad31 AF hom
0
Gnomad31 AF het
0
Gnomad31 AN
56433
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
.
~ 8851 (T/C) 8851 (T/G)
~ 8851 (Tga/Cga) 8851 (Tga/Gga)
Chr chrM chrM
Start 8851 8851
End 8851 8851
Ref T T
Alt C G
MitImpact id MI.689 MI.690
Gene symbol MT-ATP6 MT-ATP6
Respiratory Chain complex V V
Ensembl gene id ENSG00000198899 ENSG00000198899
Ensembl protein id ENSP00000354632 ENSP00000354632
Ensembl transcript id ENST00000361899 ENST00000361899
Uniprot name ATP6_HUMAN ATP6_HUMAN
Uniprot id P00846 P00846
Ncbi gene id 4508 4508
Ncbi protein id YP_003024031.1 YP_003024031.1
Gene position 325 325
AA position 109 109
AA ref W W
AA alt R G
Codon substitution Tga/Cga Tga/Gga
PhyloP 100V 5.87961 5.87961
PhastCons 100V 1 1
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 1.0 0.99
SIFT deleterious deleterious
SIFT score 0 0
SIFT4G Damaging Damaging
SIFT4G score 0 0
FatHmm deleterious neutral
FatHmm score -3.07 -2.76
FatHmmW neutral neutral
FatHmmW score 4.18 4.15
PROVEAN deleterious deleterious
PROVEAN score -12.91 -11.98
MutationAssessor high impact high impact
MutationAssessor score 4.46 4.46
EFIN SP damaging neutral
EFIN SP score 0.41 0.62
EFIN HD damaging neutral
EFIN HD score 0.25 0.42
CADD deleterious deleterious
CADD score 3.56 3.87
CADD phred 23.1 23.5
VEST pvalue 0.28 0.24
VEST FDR 0.65 0.65
PANTHER disease disease
PANTHER score 0.82 0.83
PhD-SNP disease disease
PhD-SNP score 0.96 0.92
SNAP disease disease
SNAP score 0.79 0.75
Meta-SNP disease disease
Meta-SNP score 0.77 0.71
Meta-SNP RI 5 4
CAROL deleterious deleterious
CAROL score 1 1
Condel neutral neutral
Condel score 0 0.01
COVEC WMV deleterious deleterious
COVEC WMV score 6 6
MtoolBox deleterious deleterious
MtoolBox DS 0.9 0.84
PolyPhen2 transf low impact low impact
PolyPhen2 transf score -3.6 -2.65
SIFT_transf low impact low impact
SIFT transf score -1.4 -1.4
MutationAssessor transf high impact high impact
MutationAssessor transf score 2.72 2.72
CHASM pvalue 0.24 0.28
CHASM FDR 0.9 0.9
APOGEE1 Pathogenic Neutral
APOGEE1 score 0.69 0.5
APOGEE2 Likely-pathogenic Likely-pathogenic
APOGEE2 score 0.867435890954745 0.72895471332079
SNPDryad score 0.97 1
MutationTaster disease_causing_automatic disease_causing
MutationTaster score 0.98 0.99
DEOGEN2 score 0.43 0.41
Mitoclass.1 damaging damaging
dbSNP 155 id rs199476136 .
ClinVar July2022 Variation id 9645 .
ClinVar July2022 CLNSIG Uncertain_significance .
ClinVar July2022 CLNDN Leber_optic_atrophy|Leigh_syndrome|Striatonigral_degeneration,_infantile,_mitochondrial|Mitochondrial_disease|not_provided .
ClinVar July2022 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:0044970,MedGen:C0751651,Orphanet:ORPHA68380|MedGen:CN517202 .
COSMIC 90 . .
MITOMAP Allele T8851C .
MITOMAP Disease Het/Hom +/+ .
MITOMAP Disease Clinical info BSN / Leigh syndrome .
MITOMAP Disease Status Cfrm [VUS*] .
MITOMAP Disease GenBank Freq 0.007%(0.000%) .
MITOMAP Disease GenBank Seqs 4 (0) .
MITOMAP Disease GenBank Curated refs 9 .
MITOMAP General GenBank Freq . .
MITOMAP General GenBank Seqs . .
MITOMAP General Curated refs . .
gnomAD 3.1 filter PASS npg
gnomAD 3.1 AC Homo 2 0
gnomAD 3.1 AC Het 0 0
gnomAD 3.1 AF Hom 0.000035443398 0
gnomAD 3.1 AF Het 0 0
gnomAD 3.1 AN 56428 56433
HelixMTdb AC Hom 10.0 .
HelixMTdb AF Hom 5.1024836e-05 .
HelixMTdb AC Het 4.0 .
HelixMTdb AF Het 2.0409934e-05 .
HelixMTdb mean ARF 0.29899 .
HelixMTdb max ARF 0.59701 .
EVmutation MT-ATP6_109W|153P:0.295096;112T:0.25175;110A:0.229063;156L:0.197917;148S:0.176581;113V:0.162301;149L:0.156156;152Q:0.136676;221Y:0.131585;114I:0.111246;151I:0.094802;129L:0.093224;173L:0.092062;223H:0.089033;165T:0.084286;145E:0.075977;158V:0.07021;150L:0.069853;163N:0.065282;207A:0.063482 MT-ATP6_109W|153P:0.295096;112T:0.25175;110A:0.229063;156L:0.197917;148S:0.176581;113V:0.162301;149L:0.156156;152Q:0.136676;221Y:0.131585;114I:0.111246;151I:0.094802;129L:0.093224;173L:0.092062;223H:0.089033;165T:0.084286;145E:0.075977;158V:0.07021;150L:0.069853;163N:0.065282;207A:0.063482
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 <= 0.7
  • 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