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14462 (G > A)

MT-ND4L_5xtc_m_k_TA71M_AB71T

General info

Mitimpact ID
MI.23745
Chr
chrM
Start
14462
Ref
G
Alt
A
Gene symbol
MT-ND6 Extended gene annotation
Gene position
212
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
ACA/ATA
AA pos
71
AA ref
T
AA alt
M
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14462G>A
HGNC ID
7462
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot ID
P03923
Uniprot name
NU6M_HUMAN
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
1.744 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
0.086 Conservation Score
PhastCons 470way
0.979 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
Pathogenic Score and details of the predictor
MutationTaster
.
fathmm
.
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
.
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Deleterious 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
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
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium 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
693725
Clinvar ALLELEID
680615
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Likely benign
MITOMAP Allele
14462G>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56425
Gnomad AC hom
2
Gnomad AF hom
3.54e-05
Gnomad AC het
4
Gnomad AF het
7.08e-05
Gnomad filter
Pass
HelixMTdb AC hom
3
HelixMTdb AF hom
1.53e-05
HelixMTdb AC het
7
HelixMTdb AF het
3.57e-05
HelixMTdb mean ARF
0.3175799
HelixMTdb max ARF
0.86145
ToMMo JPN54K AC
1
ToMMo JPN54K AF
1.8e-05
ToMMo JPN54K AN
54302
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
.

14462 (G > T)

MT-ND4L_5xtc_m_k_TA71K_AB71T

General info

Mitimpact ID
MI.23744
Chr
chrM
Start
14462
Ref
G
Alt
T
Gene symbol
MT-ND6 Extended gene annotation
Gene position
212
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
ACA/AAA
AA pos
71
AA ref
T
AA alt
K
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14462G>T
HGNC ID
7462
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot ID
P03923
Uniprot name
NU6M_HUMAN
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
1.744 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
0.086 Conservation Score
PhastCons 470way
0.979 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly 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
Damaging 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
Medium 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
Deleterious 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
Neutral Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
.
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Damaging Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium 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
14462G>T
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
.

14463 (T > A)

General info

Mitimpact ID
MI.23748
Chr
chrM
Start
14463
Ref
T
Alt
A
Gene symbol
MT-ND6 Extended gene annotation
Gene position
211
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
ACA/TCA
AA pos
71
AA ref
T
AA alt
S
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14463T>A
HGNC ID
7462
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot ID
P03923
Uniprot name
NU6M_HUMAN
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.553 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.001 Conservation Score
PhastCons 470way
0.983 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
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
Deleterious 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
Deleterious Score and details of the meta-predictor
DEOGEN2
Damaging Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium 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
14463T>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
.

14463 (T > C)

MT-ND4L_5xtc_m_k_TA71A_AB71T

General info

Mitimpact ID
MI.23747
Chr
chrM
Start
14463
Ref
T
Alt
C
Gene symbol
MT-ND6 Extended gene annotation
Gene position
211
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
ACA/GCA
AA pos
71
AA ref
T
AA alt
A
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14463T>C
HGNC ID
7462
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot ID
P03923
Uniprot name
NU6M_HUMAN
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.553 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.001 Conservation Score
PhastCons 470way
0.983 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Tolerated 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
Neutral 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
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
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
Damaging Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
High 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
14463T>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56431
Gnomad AC hom
2
Gnomad AF hom
3.54e-05
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
15
HelixMTdb AF hom
7.65e-05
HelixMTdb AC het
5
HelixMTdb AF het
2.55e-05
HelixMTdb mean ARF
0.36579
HelixMTdb max ARF
0.79137
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
.

14463 (T > G)

MT-ND4L_5xtc_m_k_TA71P_AB71T

General info

Mitimpact ID
MI.23746
Chr
chrM
Start
14463
Ref
T
Alt
G
Gene symbol
MT-ND6 Extended gene annotation
Gene position
211
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
ACA/CCA
AA pos
71
AA ref
T
AA alt
P
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14463T>G
HGNC ID
7462
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot ID
P03923
Uniprot name
NU6M_HUMAN
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.553 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.001 Conservation Score
PhastCons 470way
0.983 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly 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
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
Medium 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
Deleterious 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
Neutral Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
.
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
Damaging 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
14463T>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
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
.
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
.
~ 14462 (G/A) 14462 (G/T) 14463 (T/A) 14463 (T/C) 14463 (T/G)
~ 14462 (ACA/ATA) 14462 (ACA/AAA) 14463 (ACA/TCA) 14463 (ACA/GCA) 14463 (ACA/CCA)
MitImpact id MI.23745 MI.23744 MI.23748 MI.23747 MI.23746
Chr chrM chrM chrM chrM chrM
Start 14462 14462 14463 14463 14463
Ref G G T T T
Alt A T A C G
Gene symbol MT-ND6 MT-ND6 MT-ND6 MT-ND6 MT-ND6
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6
Gene position 212 212 211 211 211
Gene start 14149 14149 14149 14149 14149
Gene end 14673 14673 14673 14673 14673
Gene strand - - - - -
Codon substitution ACA/ATA ACA/AAA ACA/TCA ACA/GCA ACA/CCA
AA position 71 71 71 71 71
AA ref T T T T T
AA alt M K S A P
Functional effect general missense missense missense missense missense
Functional effect detailed missense missense missense missense missense
OMIM id 516006 516006 516006 516006 516006
HGVS NC_012920.1:g.14462G>A NC_012920.1:g.14462G>T NC_012920.1:g.14463T>A NC_012920.1:g.14463T>C NC_012920.1:g.14463T>G
HGNC id 7462 7462 7462 7462 7462
Respiratory Chain complex I I I I I
Ensembl gene id ENSG00000198695 ENSG00000198695 ENSG00000198695 ENSG00000198695 ENSG00000198695
Ensembl transcript id ENST00000361681 ENST00000361681 ENST00000361681 ENST00000361681 ENST00000361681
Ensembl protein id ENSP00000354665 ENSP00000354665 ENSP00000354665 ENSP00000354665 ENSP00000354665
Uniprot id P03923 P03923 P03923 P03923 P03923
Uniprot name NU6M_HUMAN NU6M_HUMAN NU6M_HUMAN NU6M_HUMAN NU6M_HUMAN
Ncbi gene id 4541 4541 4541 4541 4541
Ncbi protein id YP_003024037.1 YP_003024037.1 YP_003024037.1 YP_003024037.1 YP_003024037.1
PhyloP 100V 1.744 1.744 0.553 0.553 0.553
PhyloP 470Way 0.848 0.848 0.666 0.666 0.666
PhastCons 100V 0.086 0.086 0.001 0.001 0.001
PhastCons 470Way 0.979 0.979 0.983 0.983 0.983
PolyPhen2 benign possibly_damaging benign benign possibly_damaging
PolyPhen2 score 0.26 0.58 0.37 0.02 0.82
SIFT neutral neutral neutral neutral neutral
SIFT score 0.21 0.27 0.77 1.0 0.16
SIFT4G Damaging Damaging Damaging Tolerated Damaging
SIFT4G score 0.001 0.002 0.024 0.688 0.003
VEST Neutral Neutral Neutral Neutral Neutral
VEST pvalue 0.26 0.16 0.37 0.32 0.15
VEST FDR 0.45 0.45 0.5 0.5 0.4
Mitoclass.1 damaging damaging neutral neutral damaging
SNPDryad Pathogenic Pathogenic Neutral Neutral Pathogenic
SNPDryad score 0.9 0.94 0.68 0.65 0.94
MutationTaster . Disease Polymorphism Polymorphism Polymorphism
MutationTaster score . 1 1 1 1
MutationTaster converted rankscore . 0.81001 0.08975 0.08975 0.08975
MutationTaster model . complex_aae simple_aae simple_aae simple_aae
MutationTaster AAE . Y36* Y36F Y36C Y36S
fathmm . Tolerated Tolerated Tolerated Tolerated
fathmm score . 2.21 2.35 2.3 2.21
fathmm converted rankscore . 0.18414 0.16217 0.16953 0.18414
AlphaMissense likely_benign likely_pathogenic likely_benign likely_benign likely_pathogenic
AlphaMissense score 0.2362 0.9232 0.2594 0.074 0.8941
CADD Neutral Deleterious Neutral Neutral Deleterious
CADD score 1.852799 3.655132 1.897424 -0.054642 3.629161
CADD phred 15.3 23.2 15.57 2.091 23.2
PROVEAN Damaging Damaging Damaging Damaging Damaging
PROVEAN score -5.17 -5.29 -3.32 -3.79 -5.29
MutationAssessor . medium low neutral medium
MutationAssessor score . 2.755 1.055 -0.485 2.405
EFIN SP Neutral Neutral Neutral Neutral Neutral
EFIN SP score 0.658 0.69 0.814 0.91 0.696
EFIN HD Neutral Neutral Neutral Neutral Neutral
EFIN HD score 0.382 0.326 0.716 0.926 0.284
MLC Deleterious Deleterious Deleterious Deleterious Deleterious
MLC score 0.79600459 0.79600459 0.78948639 0.78948639 0.78948639
PANTHER score . . . . .
PhD-SNP score . . . . .
APOGEE1 Neutral Neutral Neutral Neutral Neutral
APOGEE1 score 0.38 0.37 0.31 0.43 0.45
APOGEE2 VUS VUS+ Likely-benign Benign VUS+
APOGEE2 score 0.497278736913731 0.547302725893702 0.159702750750223 0.0348437504216969 0.686120006597442
CAROL neutral neutral neutral neutral neutral
CAROL score 0.75 0.73 0.26 0.01 0.91
Condel deleterious neutral deleterious deleterious neutral
Condel score 0.48 0.35 0.7 0.99 0.17
COVEC WMV neutral . neutral neutral .
COVEC WMV score -3 0 -3 -6 0
MtoolBox neutral deleterious deleterious neutral deleterious
MtoolBox DS 0.42 0.68 0.45 0.13 0.82
DEOGEN2 . Damaging Damaging Damaging Damaging
DEOGEN2 score . 0.729353 0.517068 0.522818 0.729353
DEOGEN2 converted rankscore . 0.92412 0.83039 0.83344 0.92412
Meta-SNP . . . . .
Meta-SNP score . . . . .
PolyPhen2 transf medium impact medium impact medium impact medium impact low impact
PolyPhen2 transf score -0.38 -0.92 -0.58 0.75 -1.4
SIFT_transf medium impact medium impact medium impact high impact medium impact
SIFT transf score -0.11 -0.03 0.5 1.87 -0.19
MutationAssessor transf medium impact medium impact medium impact medium impact medium impact
MutationAssessor transf score 1.65 1.65 0.73 -0.95 1.65
CHASM Neutral Neutral Neutral Neutral Neutral
CHASM pvalue 0.86 0.87 0.79 0.62 0.77
CHASM FDR 0.9 0.9 0.85 0.8 0.85
ClinVar id 693725.0 . . . .
ClinVar Allele id 680615.0 . . . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . . . .
ClinVar CLNDN Leigh_syndrome . . . .
ClinVar CLNSIG Likely_benign . . . .
MITOMAP Disease Clinical info . . . . .
MITOMAP Disease Status . . . . .
MITOMAP Disease Hom/Het ./. ./. ./. ./. ./.
MITOMAP General GenBank Freq 0.0016% . . 0.0016% 0.0016%
MITOMAP General GenBank Seqs 1 . . 1 1
MITOMAP General Curated refs . . . . .
MITOMAP Variant Class polymorphism . . polymorphism polymorphism
gnomAD 3.1 AN 56425.0 . . 56431.0 .
gnomAD 3.1 AC Homo 2.0 . . 2.0 .
gnomAD 3.1 AF Hom 3.54453e-05 . . 3.54415e-05 .
gnomAD 3.1 AC Het 4.0 . . 1.0 .
gnomAD 3.1 AF Het 7.089060000000001e-05 . . 1.77208e-05 .
gnomAD 3.1 filter PASS . . PASS .
HelixMTdb AC Hom 3.0 . . 15.0 .
HelixMTdb AF Hom 1.530745e-05 . . 7.653725e-05 .
HelixMTdb AC Het 7.0 . . 5.0 .
HelixMTdb AF Het 3.5717385e-05 . . 2.5512418e-05 .
HelixMTdb mean ARF 0.31758 . . 0.36579 .
HelixMTdb max ARF 0.86145 . . 0.79137 .
ToMMo 54KJPN AC 1 . . . .
ToMMo 54KJPN AF 1.8e-05 . . . .
ToMMo 54KJPN AN 54302 . . . .
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