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

14477 (A > G)

General info

Mitimpact ID
MI.23775
Chr
chrM
Start
14477
Ref
A
Alt
G
Gene symbol
MT-ND6 Extended gene annotation
Gene position
197
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
GTC/GCC
AA pos
66
AA ref
V
AA alt
A
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14477A>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
5.719 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0.998 Conservation Score
PhastCons 470way
0.979 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
Damaging 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
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
Damaging 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-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
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
523306
Clinvar ALLELEID
514151
Clinvar CLNDISDB
Human phenotype ontology:hp:0002128, human phenotype ontology:hp:0002129, human phenotype ontology:hp:0002302, human phenotype ontology:hp:0002337, human phenotype ontology:hp:0002441, human phenotype ontology:hp:0006972, human phenotype ontology:hp:0006998, human phenotype ontology:hp:0007211, human phenotype ontology:hp:0100543, medgen:c0338656;

human phenotype ontology:hp:0003394, human phenotype ontology:hp:0009018, medgen:c0037763;

human phenotype ontology:hp:0002082, human phenotype ontology:hp:0003401, medgen:c0030554;

human phenotype ontology:hp:0000266, human phenotype ontology:hp:0001354, human phenotype ontology:hp:0002315, medgen:c0018681;

human phenotype ontology:hp:0012443, medgen:c4021085;

human phenotype ontology:hp:0002321, medgen:c0042571;

human phenotype ontology:hp:0001133, human phenotype ontology:hp:0007887, human phenotype ontology:hp:0007981, medgen:c0235095
Clinvar CLNDN
Cognitive impairment;

muscle spasm;

paresthesia;

headache;

abnormal brain morphology;

vertigo;

constriction of peripheral visual field
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
14477A>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0033%
MITOMAP General GenBank Seqs
2
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56434
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
8
HelixMTdb AF hom
4.08e-05
HelixMTdb AC het
3
HelixMTdb AF het
1.53e-05
HelixMTdb mean ARF
0.17234
HelixMTdb max ARF
0.19048
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs1556424448

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
.

14477 (A > C)

General info

Mitimpact ID
MI.23774
Chr
chrM
Start
14477
Ref
A
Alt
C
Gene symbol
MT-ND6 Extended gene annotation
Gene position
197
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
GTC/GGC
AA pos
66
AA ref
V
AA alt
G
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14477A>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
5.719 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0.998 Conservation Score
PhastCons 470way
0.979 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
Damaging 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
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
Damaging 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-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
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
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
14477A>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
.

14477 (A > T)

General info

Mitimpact ID
MI.23776
Chr
chrM
Start
14477
Ref
A
Alt
T
Gene symbol
MT-ND6 Extended gene annotation
Gene position
197
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
GTC/GAC
AA pos
66
AA ref
V
AA alt
D
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14477A>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
5.719 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0.998 Conservation Score
PhastCons 470way
0.979 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
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
Damaging Score and details of the predictor
EFIN HD
Damaging 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-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
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
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
14477A>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
.
~ 14477 (A/G) 14477 (A/C) 14477 (A/T)
~ 14477 (GTC/GCC) 14477 (GTC/GGC) 14477 (GTC/GAC)
MitImpact id MI.23775 MI.23774 MI.23776
Chr chrM chrM chrM
Start 14477 14477 14477
Ref A A A
Alt G C T
Gene symbol 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
Gene position 197 197 197
Gene start 14149 14149 14149
Gene end 14673 14673 14673
Gene strand - - -
Codon substitution GTC/GCC GTC/GGC GTC/GAC
AA position 66 66 66
AA ref V V V
AA alt A G D
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516006 516006 516006
HGVS NC_012920.1:g.14477A>G NC_012920.1:g.14477A>C NC_012920.1:g.14477A>T
HGNC id 7462 7462 7462
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198695 ENSG00000198695 ENSG00000198695
Ensembl transcript id ENST00000361681 ENST00000361681 ENST00000361681
Ensembl protein id ENSP00000354665 ENSP00000354665 ENSP00000354665
Uniprot id P03923 P03923 P03923
Uniprot name NU6M_HUMAN NU6M_HUMAN NU6M_HUMAN
Ncbi gene id 4541 4541 4541
Ncbi protein id YP_003024037.1 YP_003024037.1 YP_003024037.1
PhyloP 100V 5.719 5.719 5.719
PhyloP 470Way 0.819 0.819 0.819
PhastCons 100V 0.998 0.998 0.998
PhastCons 470Way 0.979 0.979 0.979
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1 1 1
SIFT neutral neutral deleterious
SIFT score 0.08 0.05 0.01
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.0 0.0 0.0
VEST Neutral Neutral Neutral
VEST pvalue 0.3 0.14 0.1
VEST FDR 0.45 0.4 0.4
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Neutral Pathogenic
SNPDryad score 0.52 0.83 0.94
MutationTaster Disease Disease Disease
MutationTaster score 1 0.720039 0.720039
MutationTaster converted rankscore 0.81001 0.33608 0.33608
MutationTaster model without_aae simple_aae simple_aae
MutationTaster AAE . C31W C31W
fathmm Tolerated Tolerated Tolerated
fathmm score 2.15 2.13 2.12
fathmm converted rankscore 0.19311 0.19588 0.19726
AlphaMissense likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.9038 0.8341 0.9649
CADD Deleterious Deleterious Deleterious
CADD score 3.497929 3.36291 3.902858
CADD phred 23.1 22.9 23.5
PROVEAN Damaging Damaging Damaging
PROVEAN score -3.99 -6.98 -6.97
MutationAssessor high high high
MutationAssessor score 3.515 3.515 3.865
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.534 0.5 0.57
EFIN HD Damaging Damaging Damaging
EFIN HD score 0.08 0.062 0.038
MLC Deleterious Deleterious Deleterious
MLC score 0.61364597 0.61364597 0.61364597
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.28 0.3 0.33
APOGEE2 Likely-pathogenic Likely-pathogenic Likely-pathogenic
APOGEE2 score 0.75750567921606 0.828898108614759 0.867152374149287
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 1.0
Condel neutral neutral neutral
Condel score 0.04 0.03 0.01
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 2 2 6
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.8 0.86 0.88
DEOGEN2 Damaging Damaging Damaging
DEOGEN2 score 0.848126 0.838241 0.813611
DEOGEN2 converted rankscore 0.96518 0.96203 0.95369
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.55 -3.55 -3.55
SIFT_transf medium impact medium impact medium impact
SIFT transf score -0.38 -0.5 -0.9
MutationAssessor transf medium impact high impact high impact
MutationAssessor transf score 1.93 2.21 2.21
CHASM Neutral Neutral Neutral
CHASM pvalue 0.6 0.64 0.71
CHASM FDR 0.8 0.8 0.85
ClinVar id 523306.0 . .
ClinVar Allele id 514151.0 . .
ClinVar CLNDISDB Human_Phenotype_Ontology:HP:0002128,Human_Phenotype_Ontology:HP:0002129,Human_Phenotype_Ontology:HP:0002302,Human_Phenotype_Ontology:HP:0002337,Human_Phenotype_Ontology:HP:0002441,Human_Phenotype_Ontology:HP:0006972,Human_Phenotype_Ontology:HP:0006998,Human_Phenotype_Ontology:HP:0007211,Human_Phenotype_Ontology:HP:0100543,MedGen:C0338656|Human_Phenotype_Ontology:HP:0003394,Human_Phenotype_Ontology:HP:0009018,MedGen:C0037763|Human_Phenotype_Ontology:HP:0002082,Human_Phenotype_Ontology:HP:0003401,MedGen:C0030554|Human_Phenotype_Ontology:HP:0000266,Human_Phenotype_Ontology:HP:0001354,Human_Phenotype_Ontology:HP:0002315,MedGen:C0018681|Human_Phenotype_Ontology:HP:0012443,MedGen:C4021085|Human_Phenotype_Ontology:HP:0002321,MedGen:C0042571|Human_Phenotype_Ontology:HP:0001133,Human_Phenotype_Ontology:HP:0007887,Human_Phenotype_Ontology:HP:0007981,MedGen:C0235095 . .
ClinVar CLNDN Cognitive_impairment|Muscle_spasm|Paresthesia|Headache|Abnormal_brain_morphology|Vertigo|Constriction_of_peripheral_visual_field . .
ClinVar CLNSIG Uncertain_significance . .
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 0.0033% . .
MITOMAP General GenBank Seqs 2 . .
MITOMAP General Curated refs . . .
MITOMAP Variant Class polymorphism . .
gnomAD 3.1 AN 56434.0 . .
gnomAD 3.1 AC Homo 0.0 . .
gnomAD 3.1 AF Hom 0.0 . .
gnomAD 3.1 AC Het 1.0 . .
gnomAD 3.1 AF Het 1.77198e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 8.0 . .
HelixMTdb AF Hom 4.081987e-05 . .
HelixMTdb AC Het 3.0 . .
HelixMTdb AF Het 1.530745e-05 . .
HelixMTdb mean ARF 0.17234 . .
HelixMTdb max ARF 0.19048 . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs1556424448 . .
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