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8616 (G > T)

General info

Mitimpact ID
MI.190
Chr
chrM
Start
8616
Ref
G
Alt
T
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
90
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
TTG/TTT
AA pos
30
AA ref
L
AA alt
F
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8616G>T
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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Conservation

PhyloP 100v
-2.253 Conservation Score
PhyloP 470way
-0.326 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.001 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Neutral 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 benign Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Low Score and details of the predictor
EFIN SP
Neutral 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
Neutral Score and details of the meta-predictor
APOGEE2
Likely-benign 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
Neutral 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
Medium 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
235626
Clinvar ALLELEID
237307
Clinvar CLNDISDB
Medgen:cn517202;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Not provided;

leigh syndrome
Clinvar CLNSIG
Benign/likely benign
MITOMAP Allele
8616G>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.3484%
MITOMAP General GenBank Seqs
213
MITOMAP General GenBank Curated refs
19050702 16120352 16773565 20211276 11938495 11349229 28187756 14581685 9443868
MITOMAP Variant Class
polymorphism
Gnomad AN
56432
Gnomad AC hom
324
Gnomad AF hom
0.0057414
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
1091
HelixMTdb AF hom
0.0055668
HelixMTdb AC het
2
HelixMTdb AF het
1.02e-05
HelixMTdb mean ARF
0.91198
HelixMTdb max ARF
0.91667
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs41427749

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
.

8616 (G > C)

General info

Mitimpact ID
MI.191
Chr
chrM
Start
8616
Ref
G
Alt
C
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
90
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
TTG/TTC
AA pos
30
AA ref
L
AA alt
F
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8616G>C
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
-2.253 Conservation Score
PhyloP 470way
-0.326 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.001 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Neutral Score and details of the predictor
MitoClass 1
Neutral 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 benign Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Low Score and details of the predictor
EFIN SP
Neutral 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
Likely-benign 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
Neutral 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
Medium 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
8616G>C
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
.
~ 8616 (G/T) 8616 (G/C)
~ 8616 (TTG/TTT) 8616 (TTG/TTC)
MitImpact id MI.190 MI.191
Chr chrM chrM
Start 8616 8616
Ref G G
Alt T C
Gene symbol MT-ATP6 MT-ATP6
Extended annotation mitochondrially encoded ATP synthase membrane subunit 6 mitochondrially encoded ATP synthase membrane subunit 6
Gene position 90 90
Gene start 8527 8527
Gene end 9207 9207
Gene strand + +
Codon substitution TTG/TTT TTG/TTC
AA position 30 30
AA ref L L
AA alt F F
Functional effect general missense missense
Functional effect detailed missense missense
OMIM id 516060 516060
HGVS NC_012920.1:g.8616G>T NC_012920.1:g.8616G>C
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 -2.253 -2.253
PhyloP 470Way -0.326 -0.326
PhastCons 100V 0 0
PhastCons 470Way 0.001 0.001
PolyPhen2 probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0
SIFT neutral neutral
SIFT score 0.39 0.39
SIFT4G Damaging Damaging
SIFT4G score 0.043 0.043
VEST Neutral Neutral
VEST pvalue 0.41 0.41
VEST FDR 0.65 0.65
Mitoclass.1 neutral neutral
SNPDryad Neutral Neutral
SNPDryad score 0.87 0.87
MutationTaster Polymorphism Polymorphism
MutationTaster score 0.999566 0.999566
MutationTaster converted rankscore 0.20970 0.20970
MutationTaster model simple_aae simple_aae
MutationTaster AAE L30F L30F
fathmm Tolerated Tolerated
fathmm score 4.38 4.38
fathmm converted rankscore 0.02255 0.02255
AlphaMissense likely_benign likely_benign
AlphaMissense score 0.1403 0.1403
CADD Neutral Neutral
CADD score 2.327286 2.212057
CADD phred 18.35 17.59
PROVEAN Damaging Damaging
PROVEAN score -3.18 -3.18
MutationAssessor low low
MutationAssessor score 1.58 1.58
EFIN SP Neutral Neutral
EFIN SP score 0.914 0.914
EFIN HD Neutral Neutral
EFIN HD score 0.866 0.866
MLC Neutral Neutral
MLC score 0.009898 0.009898
PANTHER score . .
PhD-SNP score . .
APOGEE1 Neutral Pathogenic
APOGEE1 score 0.5 0.54
APOGEE2 Likely-benign Likely-benign
APOGEE2 score 0.153801814903584 0.153801814903584
CAROL deleterious deleterious
CAROL score 1 1
Condel neutral neutral
Condel score 0.2 0.2
COVEC WMV neutral neutral
COVEC WMV score -2 -2
MtoolBox deleterious deleterious
MtoolBox DS 0.76 0.76
DEOGEN2 Tolerated Tolerated
DEOGEN2 score 0.054682 0.054682
DEOGEN2 converted rankscore 0.29794 0.29794
Meta-SNP . .
Meta-SNP score . .
PolyPhen2 transf low impact low impact
PolyPhen2 transf score -3.6 -3.6
SIFT_transf medium impact medium impact
SIFT transf score 0.18 0.18
MutationAssessor transf medium impact medium impact
MutationAssessor transf score 0.3 0.3
CHASM Neutral Neutral
CHASM pvalue 0.59 0.59
CHASM FDR 0.9 0.9
ClinVar id 235626.0 .
ClinVar Allele id 237307.0 .
ClinVar CLNDISDB MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN not_provided|Leigh_syndrome .
ClinVar CLNSIG Benign/Likely_benign .
MITOMAP Disease Clinical info . .
MITOMAP Disease Status . .
MITOMAP Disease Hom/Het ./. ./.
MITOMAP General GenBank Freq 0.3484% .
MITOMAP General GenBank Seqs 213 .
MITOMAP General Curated refs 19050702;16120352;16773565;20211276;11938495;11349229;28187756;14581685;9443868 .
MITOMAP Variant Class polymorphism .
gnomAD 3.1 AN 56432.0 .
gnomAD 3.1 AC Homo 324.0 .
gnomAD 3.1 AF Hom 0.00574142 .
gnomAD 3.1 AC Het 0.0 .
gnomAD 3.1 AF Het 0.0 .
gnomAD 3.1 filter PASS .
HelixMTdb AC Hom 1091.0 .
HelixMTdb AF Hom 0.0055668093 .
HelixMTdb AC Het 2.0 .
HelixMTdb AF Het 1.0204967e-05 .
HelixMTdb mean ARF 0.91198 .
HelixMTdb max ARF 0.91667 .
ToMMo 54KJPN AC . .
ToMMo 54KJPN AF . .
ToMMo 54KJPN AN . .
COSMIC 90 . .
dbSNP 156 id rs41427749 .
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