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9175 (C > A)

General info

Mitimpact ID
MI.1382
Chr
chrM
Start
9175
Ref
C
Alt
A
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
649
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CTA/ATA
AA pos
217
AA ref
L
AA alt
M
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.9175C>A
HGNC ID
7414
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot ID
P00846
Uniprot name
ATP6_HUMAN
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
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Powered by MitoWheel

Conservation

PhyloP 100v
-0.192 Conservation Score
PhyloP 470way
0.724 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.795 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
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
.
fathmm
.
AlphaMissense
Likely pathogenic Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Tolerated Score and details of the predictor
Mutation Assessor
.
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Vus- 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
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
.

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 Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
9175C>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0049%
MITOMAP General GenBank Seqs
3
MITOMAP General GenBank Curated refs
17072496
MITOMAP Variant Class
polymorphism
Gnomad AN
56434
Gnomad AC hom
1
Gnomad AF hom
1.77e-05
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
12
HelixMTdb AF hom
6.12e-05
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.67665
HelixMTdb max ARF
0.67665
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

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
.

9175 (C > G)

General info

Mitimpact ID
MI.1381
Chr
chrM
Start
9175
Ref
C
Alt
G
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
649
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CTA/GTA
AA pos
217
AA ref
L
AA alt
V
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.9175C>G
HGNC ID
7414
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot ID
P00846
Uniprot name
ATP6_HUMAN
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.192 Conservation Score
PhyloP 470way
0.724 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.795 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
VEST
Neutral Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor
MutationTaster
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely pathogenic Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
High Score and details of the predictor
EFIN SP
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Vus+ 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
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

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 Frequencies and Phenotypes

Clinvar ID
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
9175C>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
.
MITOMAP General GenBank Seqs
.
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
.
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
.

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
.
~ 9175 (C/A) 9175 (C/G)
~ 9175 (CTA/ATA) 9175 (CTA/GTA)
MitImpact id MI.1382 MI.1381
Chr chrM chrM
Start 9175 9175
Ref C C
Alt A G
Gene symbol MT-ATP6 MT-ATP6
Extended annotation mitochondrially encoded ATP synthase membrane subunit 6 mitochondrially encoded ATP synthase membrane subunit 6
Gene position 649 649
Gene start 8527 8527
Gene end 9207 9207
Gene strand + +
Codon substitution CTA/ATA CTA/GTA
AA position 217 217
AA ref L L
AA alt M V
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516060 516060
HGVS NC_012920.1:g.9175C>A NC_012920.1:g.9175C>G
HGNC id 7414 7414
Respiratory Chain complex V V
Ensembl gene id ENSG00000198899 ENSG00000198899
Ensembl transcript id ENST00000361899 ENST00000361899
Ensembl protein id ENSP00000354632 ENSP00000354632
Uniprot id P00846 P00846
Uniprot name ATP6_HUMAN ATP6_HUMAN
Ncbi gene id 4508 4508
Ncbi protein id YP_003024031.1 YP_003024031.1
PhyloP 100V -0.192 -0.192
PhyloP 470Way 0.724 0.724
PhastCons 100V 0 0
PhastCons 470Way 0.795 0.795
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 1.0 0.99
SIFT deleterious deleterious
SIFT score 0 0.01
SIFT4G Damaging Damaging
SIFT4G score 0.0 0.0
VEST Neutral Neutral
VEST pvalue 0.16 0.2
VEST FDR 0.65 0.65
Mitoclass.1 damaging damaging
SNPDryad Pathogenic Neutral
SNPDryad score 0.96 0.87
MutationTaster . Polymorphism
MutationTaster score . 0.818404
MutationTaster converted rankscore . 0.28913
MutationTaster model . simple_aae
MutationTaster AAE . L217V
fathmm . Tolerated
fathmm score . 2.32
fathmm converted rankscore . 0.16640
AlphaMissense likely_pathogenic likely_pathogenic
AlphaMissense score 0.7785 0.8663
CADD Deleterious Deleterious
CADD score 3.856233 3.52406
CADD phred 23.5 23.1
PROVEAN Tolerated Damaging
PROVEAN score -1.78 -2.67
MutationAssessor . high
MutationAssessor score . 4.985
EFIN SP Damaging Damaging
EFIN SP score 0.432 0.356
EFIN HD Neutral Neutral
EFIN HD score 0.596 0.514
MLC Neutral Neutral
MLC score 0.08775424 0.08775424
PANTHER score . .
PhD-SNP score . .
APOGEE1 Pathogenic Pathogenic
APOGEE1 score 0.62 0.61
APOGEE2 VUS- VUS+
APOGEE2 score 0.366250668285401 0.551760265175148
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 0.82 0.85
DEOGEN2 . Tolerated
DEOGEN2 score . 0.417708
DEOGEN2 converted rankscore . 0.77027
Meta-SNP . .
Meta-SNP score . .
PolyPhen2 transf low impact low impact
PolyPhen2 transf score -3.6 -2.65
SIFT_transf low impact medium impact
SIFT transf score -1.4 -0.84
MutationAssessor transf high impact high impact
MutationAssessor transf score 2.82 2.34
CHASM Neutral Neutral
CHASM pvalue 0.58 0.68
CHASM FDR 0.9 0.9
ClinVar id . .
ClinVar Allele id . .
ClinVar CLNDISDB . .
ClinVar CLNDN . .
ClinVar CLNSIG . .
MITOMAP Disease Clinical info . .
MITOMAP Disease Status . .
MITOMAP Disease Hom/Het ./. ./.
MITOMAP General GenBank Freq 0.0049% .
MITOMAP General GenBank Seqs 3 .
MITOMAP General Curated refs 17072496 .
MITOMAP Variant Class polymorphism .
gnomAD 3.1 AN 56434.0 .
gnomAD 3.1 AC Homo 1.0 .
gnomAD 3.1 AF Hom 1.77198e-05 .
gnomAD 3.1 AC Het 0.0 .
gnomAD 3.1 AF Het 0.0 .
gnomAD 3.1 filter PASS .
HelixMTdb AC Hom 12.0 .
HelixMTdb AF Hom 6.12298e-05 .
HelixMTdb AC Het 1.0 .
HelixMTdb AF Het 5.1024836e-06 .
HelixMTdb mean ARF 0.67665 .
HelixMTdb max ARF 0.67665 .
ToMMo 54KJPN AC . .
ToMMo 54KJPN AF . .
ToMMo 54KJPN AN . .
COSMIC 90 . .
dbSNP 156 id . .
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.
0
Details:
0
Score:  
0
  [min -20, max 10]
  • Predicted accelerated evolution:  score <= 0
  • Conserved:  score > 0
Score:  
0
  [min -20, max 12]
  • 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]
  • 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 -16.13, max 10.64]
  • Neutral:  score > 1.5
  • Deleterious:  score <= 1.5
Score:  
0
  [min 0.0, max 1.0]
  • Likely benign:  score <= 0.34
  • Ambiguous:  0.34 < score < 0.56
  • Likely pathogenic:  score >= 0.56
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 Unlimited]
  • Neutral:  score < 20 (soft threshold)
  • Deleterious:  score >= 20
Score:  
0
  [min 0, max 1]
  • Neutral:  score < 0.5 (soft threshold)
  • Deleterious:  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