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14459 (G > A)

General info

Mitimpact ID
MI.23738
Chr
chrM
Start
14459
Ref
G
Alt
A
Gene symbol
MT-ND6 Extended gene annotation
Gene position
215
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
GCG/GTG
AA pos
72
AA ref
A
AA alt
V
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14459G>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
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Powered by MitoWheel

Conservation

PhyloP 100v
4.419 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.976 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
Medium 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
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
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
Disease Score and details of the meta-predictor

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
9689
Clinvar ALLELEID
24728
Clinvar CLNDISDB
Mondo:mondo:0044970, medgen:c0751651, orphanet:68380;

mondo:mondo:0010772, medgen:c1839040, omim:500001, orphanet:99718;

human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

medgen:c1838951
Clinvar CLNDN
Mitochondrial disease;

leber optic atrophy and dystonia;

leber optic atrophy;

leigh syndrome;

leigh syndrome due to mitochondrial complex i deficiency
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
14459G>A
MITOMAP Disease Clinical info
Ldyt / leigh disease / dystonia / carotid atherosclerosis risk
MITOMAP Disease Status
Cfrm [p]
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
0.0049%
MITOMAP General GenBank Seqs
3
MITOMAP General GenBank Curated refs
10426138 18674747 29670672 37038312 28429146 30461153 30128709 10072046 7654063 7760326 14520659 10894222 18402672 21067478 28951770 19714555 15972314 21749722 32220313 23847141 24398099 33717984 29253894 31221418 22879922 8622678 14735585 26741492 20301353 12205655 19268652 8680405 14735584 32045392 8016139 20064630 15126312 23874496 25834827 29987491 21364701 30095618 21457906 37587338 29408632
MITOMAP Variant Class
disease
Gnomad AN
56432
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
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.1428599
HelixMTdb max ARF
0.1428599
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs199476105

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
.

14459 (G > C)

General info

Mitimpact ID
MI.23740
Chr
chrM
Start
14459
Ref
G
Alt
C
Gene symbol
MT-ND6 Extended gene annotation
Gene position
215
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
GCG/GGG
AA pos
72
AA ref
A
AA alt
G
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14459G>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
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Powered by MitoWheel

Conservation

PhyloP 100v
4.419 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.976 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
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
Damaging 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
Pathogenic Score and details of the meta-predictor
APOGEE2
Vus+ Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
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
14459G>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
56431
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Npg
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
.

14459 (G > T)

General info

Mitimpact ID
MI.23739
Chr
chrM
Start
14459
Ref
G
Alt
T
Gene symbol
MT-ND6 Extended gene annotation
Gene position
215
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
GCG/GAG
AA pos
72
AA ref
A
AA alt
E
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14459G>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
4.419 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.976 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
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
Pathogenic 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
14459G>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
.
~ 14459 (G/A) 14459 (G/C) 14459 (G/T)
~ 14459 (GCG/GTG) 14459 (GCG/GGG) 14459 (GCG/GAG)
MitImpact id MI.23738 MI.23740 MI.23739
Chr chrM chrM chrM
Start 14459 14459 14459
Ref G G G
Alt A 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 215 215 215
Gene start 14149 14149 14149
Gene end 14673 14673 14673
Gene strand - - -
Codon substitution GCG/GTG GCG/GGG GCG/GAG
AA position 72 72 72
AA ref A A A
AA alt V G E
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516006 516006 516006
HGVS NC_012920.1:g.14459G>A NC_012920.1:g.14459G>C NC_012920.1:g.14459G>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 4.419 4.419 4.419
PhyloP 470Way 0.848 0.848 0.848
PhastCons 100V 1 1 1
PhastCons 470Way 0.976 0.976 0.976
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1 1 1
SIFT neutral neutral neutral
SIFT score 0.3 0.2 0.25
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.001 0.002 0.0
VEST Neutral Neutral Neutral
VEST pvalue 0.4 0.25 0.15
VEST FDR 0.5 0.45 0.4
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Neutral Pathogenic
SNPDryad score 0.81 0.8 0.99
MutationTaster Disease Polymorphism Disease
MutationTaster score 1 0.999822 1
MutationTaster converted rankscore 0.81001 0.20203 0.81001
MutationTaster model without_aae simple_aae complex_aae
MutationTaster AAE . S37R S37*
fathmm Tolerated Tolerated Tolerated
fathmm score 2.27 2.17 2.16
fathmm converted rankscore 0.17431 0.19020 0.19166
AlphaMissense likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.8611 0.7519 0.9792
CADD Deleterious Deleterious Deleterious
CADD score 4.081497 3.564245 3.883665
CADD phred 23.7 23.1 23.5
PROVEAN Damaging Damaging Damaging
PROVEAN score -3.98 -3.98 -4.98
MutationAssessor medium medium high
MutationAssessor score 3.215 3.07 3.765
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.076 0.46 0.352
EFIN HD Damaging Neutral Damaging
EFIN HD score 0.15 0.46 0.194
MLC Deleterious Deleterious Deleterious
MLC score 0.83300139 0.83300139 0.83300139
PANTHER score 0.614 . .
PhD-SNP score 0.919 . .
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.93 0.55 0.63
APOGEE2 Pathogenic VUS+ Likely-pathogenic
APOGEE2 score 0.925252754722916 0.712099908387641 0.767269110274587
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 1.0
Condel neutral neutral neutral
Condel score 0.15 0.1 0.13
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 2 2 2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.87 0.84 0.9
DEOGEN2 Damaging Damaging Damaging
DEOGEN2 score 0.613447 0.585451 0.73832
DEOGEN2 converted rankscore 0.87783 0.86490 0.92731
Meta-SNP Disease . .
Meta-SNP score 0.918 . .
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 -0.13 -0.06
MutationAssessor transf medium impact high impact high impact
MutationAssessor transf score 1.88 2.18 2.18
CHASM Neutral Neutral Neutral
CHASM pvalue 0.86 0.81 0.8
CHASM FDR 0.9 0.85 0.85
ClinVar id 9689.0 . .
ClinVar Allele id 24728.0 . .
ClinVar CLNDISDB MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MONDO:MONDO:0010772,MedGen:C1839040,OMIM:500001,Orphanet:99718|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MedGen:C1838951 . .
ClinVar CLNDN Mitochondrial_disease|Leber_optic_atrophy_and_dystonia|Leber_optic_atrophy|Leigh_syndrome|Leigh_syndrome_due_to_mitochondrial_complex_I_deficiency . .
ClinVar CLNSIG Pathogenic . .
MITOMAP Disease Clinical info LDYT / Leigh Disease / dystonia / carotid atherosclerosis risk . .
MITOMAP Disease Status Cfrm [P] . .
MITOMAP Disease Hom/Het +/+ ./. ./.
MITOMAP General GenBank Freq 0.0049% . .
MITOMAP General GenBank Seqs 3 . .
MITOMAP General Curated refs 10426138;18674747;29670672;37038312;28429146;30461153;30128709;10072046;7654063;7760326;14520659;10894222;18402672;21067478;28951770;19714555;15972314;21749722;32220313;23847141;24398099;33717984;29253894;31221418;22879922;8622678;14735585;26741492;20301353;12205655;19268652;8680405;14735584;32045392;8016139;20064630;15126312;23874496;25834827;29987491;21364701;30095618;21457906;37587338;29408632 . .
MITOMAP Variant Class disease . .
gnomAD 3.1 AN 56432.0 56431.0 .
gnomAD 3.1 AC Homo 0.0 0.0 .
gnomAD 3.1 AF Hom 0.0 0.0 .
gnomAD 3.1 AC Het 1.0 0.0 .
gnomAD 3.1 AF Het 1.77204e-05 0.0 .
gnomAD 3.1 filter PASS npg .
HelixMTdb AC Hom 0.0 . .
HelixMTdb AF Hom 0.0 . .
HelixMTdb AC Het 1.0 . .
HelixMTdb AF Het 5.1024836e-06 . .
HelixMTdb mean ARF 0.14286 . .
HelixMTdb max ARF 0.14286 . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs199476105 . .
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