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8540 (T > C)

General info

Mitimpact ID
MI.1815
Chr
chrM
Start
8540
Ref
T
Alt
C
Gene symbol
MT-ATP8 Extended gene annotation
Gene position
175
Gene start
8366
Gene end
8572
Gene strand
+
Codon substitution
TGT/CGT
AA pos
59
AA ref
C
AA alt
R
Functional effect
missense
OMIM ID
516070
HGVS
NC_012920.1:g.8540T>C
HGNC ID
7415
RC complex
V
Ensembl gene ID
ENSG00000228253
Ensembl protein ID
ENSP00000355265
Ensembl transcript ID
ENST00000361851
Uniprot ID
P03928
Uniprot name
ATP8_HUMAN
Ncbi gene ID
4509
Ncbi protein ID
YP_003024030.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.698 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.641 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
Disease Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Ambiguous 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
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
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
High 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
235227
Clinvar ALLELEID
236915
Clinvar CLNDISDB
Medgen:cn517202;

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

leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
8540T>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0115%
MITOMAP General GenBank Seqs
7
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56430
Gnomad AC hom
7
Gnomad AF hom
0.000124
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
35
HelixMTdb AF hom
0.0001785
HelixMTdb AC het
3
HelixMTdb AF het
1.53e-05
HelixMTdb mean ARF
0.30696
HelixMTdb max ARF
0.65942
ToMMo JPN54K AC
1
ToMMo JPN54K AF
1.8e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs878852987

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
.

8540 (T > A)

General info

Mitimpact ID
MI.1813
Chr
chrM
Start
8540
Ref
T
Alt
A
Gene symbol
MT-ATP8 Extended gene annotation
Gene position
175
Gene start
8366
Gene end
8572
Gene strand
+
Codon substitution
TGT/AGT
AA pos
59
AA ref
C
AA alt
S
Functional effect
missense
OMIM ID
516070
HGVS
NC_012920.1:g.8540T>A
HGNC ID
7415
RC complex
V
Ensembl gene ID
ENSG00000228253
Ensembl protein ID
ENSP00000355265
Ensembl transcript ID
ENST00000361851
Uniprot ID
P03928
Uniprot name
ATP8_HUMAN
Ncbi gene ID
4509
Ncbi protein ID
YP_003024030.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.698 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.641 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
Ambiguous 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
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
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
High 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
8540T>A
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
.

8540 (T > G)

General info

Mitimpact ID
MI.1814
Chr
chrM
Start
8540
Ref
T
Alt
G
Gene symbol
MT-ATP8 Extended gene annotation
Gene position
175
Gene start
8366
Gene end
8572
Gene strand
+
Codon substitution
TGT/GGT
AA pos
59
AA ref
C
AA alt
G
Functional effect
missense
OMIM ID
516070
HGVS
NC_012920.1:g.8540T>G
HGNC ID
7415
RC complex
V
Ensembl gene ID
ENSG00000228253
Ensembl protein ID
ENSP00000355265
Ensembl transcript ID
ENST00000361851
Uniprot ID
P03928
Uniprot name
ATP8_HUMAN
Ncbi gene ID
4509
Ncbi protein ID
YP_003024030.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.698 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.641 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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 benign Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Tolerated 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
Neutral Score and details of the meta-predictor
Condel
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
High 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
8540T>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
.

8540 (T > A)

General info

Mitimpact ID
MI.33
Chr
chrM
Start
8540
Ref
T
Alt
A
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
14
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CTG/CAG
AA pos
5
AA ref
L
AA alt
Q
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8540T>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.698 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.641 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
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
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
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
Low 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
8540T>A
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
.

8540 (T > C)

General info

Mitimpact ID
MI.32
Chr
chrM
Start
8540
Ref
T
Alt
C
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
14
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CTG/CCG
AA pos
5
AA ref
L
AA alt
P
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8540T>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
7.698 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.641 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
Neutral Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
Disease 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
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
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
Low 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
235227
Clinvar ALLELEID
236915
Clinvar CLNDISDB
Medgen:cn517202;

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

leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
8540T>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0115%
MITOMAP General GenBank Seqs
7
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
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
1
ToMMo JPN54K AF
1.8e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs878852987

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
.

8540 (T > G)

General info

Mitimpact ID
MI.34
Chr
chrM
Start
8540
Ref
T
Alt
G
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
14
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CTG/CGG
AA pos
5
AA ref
L
AA alt
R
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8540T>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
7.698 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.641 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
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
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
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
Low 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
8540T>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
.
~ 8540 (T/C) 8540 (T/A) 8540 (T/G) 8540 (T/A) 8540 (T/C) 8540 (T/G)
~ 8540 (TGT/CGT) 8540 (TGT/AGT) 8540 (TGT/GGT) 8540 (CTG/CAG) 8540 (CTG/CCG) 8540 (CTG/CGG)
MitImpact id MI.1815 MI.1813 MI.1814 MI.33 MI.32 MI.34
Chr chrM chrM chrM chrM chrM chrM
Start 8540 8540 8540 8540 8540 8540
Ref T T T T T T
Alt C A G A C G
Gene symbol MT-ATP8 MT-ATP8 MT-ATP8 MT-ATP6 MT-ATP6 MT-ATP6
Extended annotation mitochondrially encoded ATP synthase membrane subunit 8 mitochondrially encoded ATP synthase membrane subunit 8 mitochondrially encoded ATP synthase membrane subunit 8 mitochondrially encoded ATP synthase membrane subunit 6 mitochondrially encoded ATP synthase membrane subunit 6 mitochondrially encoded ATP synthase membrane subunit 6
Gene position 175 175 175 14 14 14
Gene start 8366 8366 8366 8527 8527 8527
Gene end 8572 8572 8572 9207 9207 9207
Gene strand + + + + + +
Codon substitution TGT/CGT TGT/AGT TGT/GGT CTG/CAG CTG/CCG CTG/CGG
AA position 59 59 59 5 5 5
AA ref C C C L L L
AA alt R S G Q P R
Functional effect general missense missense missense missense missense missense
Functional effect detailed missense missense missense missense missense missense
OMIM id 516070 516070 516070 516060 516060 516060
HGVS NC_012920.1:g.8540T>C NC_012920.1:g.8540T>A NC_012920.1:g.8540T>G NC_012920.1:g.8540T>A NC_012920.1:g.8540T>C NC_012920.1:g.8540T>G
HGNC id 7415 7415 7415 7414 7414 7414
Respiratory Chain complex V V V V V V
Ensembl gene id ENSG00000228253 ENSG00000228253 ENSG00000228253 ENSG00000198899 ENSG00000198899 ENSG00000198899
Ensembl transcript id ENST00000361851 ENST00000361851 ENST00000361851 ENST00000361899 ENST00000361899 ENST00000361899
Ensembl protein id ENSP00000355265 ENSP00000355265 ENSP00000355265 ENSP00000354632 ENSP00000354632 ENSP00000354632
Uniprot id P03928 P03928 P03928 P00846 P00846 P00846
Uniprot name ATP8_HUMAN ATP8_HUMAN ATP8_HUMAN ATP6_HUMAN ATP6_HUMAN ATP6_HUMAN
Ncbi gene id 4509 4509 4509 4508 4508 4508
Ncbi protein id YP_003024030.1 YP_003024030.1 YP_003024030.1 YP_003024031.1 YP_003024031.1 YP_003024031.1
PhyloP 100V 7.698 7.698 7.698 7.698 7.698 7.698
PhyloP 470Way 0.742 0.742 0.742 0.742 0.742 0.742
PhastCons 100V 0.994 0.994 0.994 0.994 0.994 0.994
PhastCons 470Way 0.641 0.641 0.641 0.641 0.641 0.641
PolyPhen2 benign benign benign probably_damaging probably_damaging probably_damaging
PolyPhen2 score 0.0 0.0 0.0 0.99 0.99 0.99
SIFT neutral neutral neutral deleterious deleterious deleterious
SIFT score 0.39 0.77 0.59 0 0 0
SIFT4G Damaging Damaging Damaging Damaging Damaging Damaging
SIFT4G score 0.0 0.001 0.0 0.001 0.001 0.0
VEST Neutral Neutral Neutral Neutral Neutral Neutral
VEST pvalue 0.5577664 0.60038707 0.50207441 0.25 0.23 0.23
VEST FDR 0.85 0.85 0.85 0.65 0.65 0.65
Mitoclass.1 neutral damaging damaging damaging neutral damaging
SNPDryad Neutral Neutral Neutral Pathogenic Pathogenic Pathogenic
SNPDryad score 0.33 0.29 0.36 0.98 1 0.99
MutationTaster Disease Polymorphism Polymorphism Polymorphism Disease Polymorphism
MutationTaster score 0.995847 0.99169 0.984143 0.569203 0.999974 0.515194
MutationTaster converted rankscore 0.53665 0.31193 0.31614 0.31193 0.53665 0.31614
MutationTaster model simple_aae simple_aae simple_aae simple_aae simple_aae simple_aae
MutationTaster AAE C59R C59S C59G L5Q L5P L5R
fathmm Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated
fathmm score 1.92 1.95 1.92 4.33 4.31 4.33
fathmm converted rankscore 0.23082 0.22474 0.23082 0.02363 0.02412 0.02363
AlphaMissense ambiguous ambiguous likely_benign likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.4767 0.3537 0.2436 0.7274 0.6238 0.6975
CADD Deleterious Deleterious Deleterious Deleterious Deleterious Deleterious
CADD score 3.7208 3.935551 4.028121 3.935551 3.7208 4.028121
CADD phred 23.3 23.5 23.6 23.5 23.3 23.6
PROVEAN Tolerated Tolerated Tolerated Damaging Damaging Damaging
PROVEAN score -1.56 -1.28 -2.28 -4.7 -5.58 -4.69
MutationAssessor . . low high high high
MutationAssessor score . . 0.895 4.025 4.025 4.025
EFIN SP Neutral Neutral Neutral Neutral Neutral Neutral
EFIN SP score 0.992 0.998 1.0 0.79 0.724 0.762
EFIN HD Neutral Neutral Neutral Neutral Neutral Neutral
EFIN HD score 0.542 0.612 0.542 0.438 0.316 0.36
MLC Neutral Neutral Neutral Neutral Neutral Neutral
MLC score 0.05902589 0.05902589 0.05902589 0.05902589 0.05902589 0.05902589
PANTHER score . . . . . .
PhD-SNP score . . . . . .
APOGEE1 Neutral Neutral Neutral Neutral Neutral Neutral
APOGEE1 score 0.39 0.28 0.3 0.31 0.28 0.31
APOGEE2 Likely-benign Likely-benign Likely-benign VUS VUS VUS
APOGEE2 score 0.100643722049738 0.164040877125515 0.111036373796718 0.463394309312935 0.419498594453134 0.476557804816833
CAROL neutral neutral neutral deleterious deleterious deleterious
CAROL score 0.6 0.22 0.4 1 1 1
Condel deleterious deleterious deleterious neutral neutral neutral
Condel score 0.7 0.89 0.8 0.01 0.01 0.01
COVEC WMV neutral neutral neutral deleterious deleterious deleterious
COVEC WMV score -6 -6 -6 5 5 5
MtoolBox neutral neutral neutral deleterious deleterious deleterious
MtoolBox DS 0.26 0.2 0.24 0.83 0.88 0.88
DEOGEN2 Tolerated Tolerated Tolerated Tolerated Tolerated Tolerated
DEOGEN2 score 0.081537 0.084426 0.103814 0.340208 0.348164 0.340208
DEOGEN2 converted rankscore 0.36620 0.37275 0.41282 0.70925 0.71619 0.70925
Meta-SNP . . . . . .
Meta-SNP score . . . . . .
PolyPhen2 transf high impact high impact high impact low impact low impact low impact
PolyPhen2 transf score 2.09 2.09 2.09 -2.65 -2.65 -2.65
SIFT_transf medium impact medium impact medium impact low impact low impact low impact
SIFT transf score 0.18 0.59 0.38 -1.4 -1.4 -1.4
MutationAssessor transf medium impact medium impact medium impact medium impact medium impact medium impact
MutationAssessor transf score 0.09 0.09 0.09 1.41 1.41 1.41
CHASM Neutral Neutral Neutral Neutral Neutral Neutral
CHASM pvalue 0.26 0.54 0.35 0.66 0.55 0.66
CHASM FDR 0.85 0.85 0.85 0.9 0.9 0.9
ClinVar id 235227.0 . . . 235227.0 .
ClinVar Allele id 236915.0 . . . 236915.0 .
ClinVar CLNDISDB MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . . . MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN not_provided|Leigh_syndrome . . . not_provided|Leigh_syndrome .
ClinVar CLNSIG Uncertain_significance . . . Uncertain_significance .
MITOMAP Disease Clinical info . . . . . .
MITOMAP Disease Status . . . . . .
MITOMAP Disease Hom/Het ./. ./. ./. ./. ./. ./.
MITOMAP General GenBank Freq 0.0115% . . . 0.0115% .
MITOMAP General GenBank Seqs 7 . . . 7 .
MITOMAP General Curated refs . . . . . .
MITOMAP Variant Class polymorphism . . . polymorphism .
gnomAD 3.1 AN 56430.0 . . . . .
gnomAD 3.1 AC Homo 7.0 . . . . .
gnomAD 3.1 AF Hom 0.000124047 . . . . .
gnomAD 3.1 AC Het 0.0 . . . . .
gnomAD 3.1 AF Het 0.0 . . . . .
gnomAD 3.1 filter PASS . . . . .
HelixMTdb AC Hom 35.0 . . . . .
HelixMTdb AF Hom 0.00017858692 . . . . .
HelixMTdb AC Het 3.0 . . . . .
HelixMTdb AF Het 1.530745e-05 . . . . .
HelixMTdb mean ARF 0.30696 . . . . .
HelixMTdb max ARF 0.65942 . . . . .
ToMMo 54KJPN AC 1 . . . 1 .
ToMMo 54KJPN AF 1.8e-05 . . . 1.8e-05 .
ToMMo 54KJPN AN 54302 . . . 54302 .
COSMIC 90 . . . . . .
dbSNP 156 id rs878852987 . . . rs878852987 .
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