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14325 (T > C)

General info

Mitimpact ID
MI.23468
Chr
chrM
Start
14325
Ref
T
Alt
C
Gene symbol
MT-ND6 Extended gene annotation
Gene position
349
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
AAC/GAC
AA pos
117
AA ref
N
AA alt
D
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14325T>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
-3.847 Conservation Score
PhyloP 470way
0.361 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.009 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging 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
Disease automatic 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
Tolerated 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
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic 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
Neutral 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
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
65512
Clinvar ALLELEID
76420
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

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

leber optic atrophy
Clinvar CLNSIG
Benign
MITOMAP Allele
14325T>C
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.0932%
MITOMAP General GenBank Seqs
57
MITOMAP General GenBank Curated refs
21041797 24467713 15382008 29987491 20301353 31152278 12736867 16714301
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56428
Gnomad AC hom
78
Gnomad AF hom
0.0013822
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
228
HelixMTdb AF hom
0.0011633
HelixMTdb AC het
17
HelixMTdb AF het
8.67e-05
HelixMTdb mean ARF
0.46131
HelixMTdb max ARF
0.89547
ToMMo JPN54K AC
132
ToMMo JPN54K AF
0.002431
ToMMo JPN54K AN
54302
COSMIC 90
COSM1155553
dbSNP 156
rs397515505

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
0.89 CPD variant frequency
AA ref
N
CPD AA alt
D
Aln pos
126
RefSeq protein ID
YP_009025007 , YP_004935516 , YP_005087606 , YP_002791222 , YP_008999721 , YP_004123241
Species name
Trachypithecus cristatus, Apodemus agrarius, Apodemus chejuensis, Rattus praetor, Rattus niobe, Rattus lutreolus
Ncbi taxon ID
122765, 39030, 754351, 349711, 472762, 472760

14325 (T > A)

General info

Mitimpact ID
MI.23467
Chr
chrM
Start
14325
Ref
T
Alt
A
Gene symbol
MT-ND6 Extended gene annotation
Gene position
349
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
AAC/TAC
AA pos
117
AA ref
N
AA alt
Y
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14325T>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
-3.847 Conservation Score
PhyloP 470way
0.361 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.009 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
Deleterious 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
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
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
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
14325T>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
.

14325 (T > G)

General info

Mitimpact ID
MI.23466
Chr
chrM
Start
14325
Ref
T
Alt
G
Gene symbol
MT-ND6 Extended gene annotation
Gene position
349
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
AAC/CAC
AA pos
117
AA ref
N
AA alt
H
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14325T>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
-3.847 Conservation Score
PhyloP 470way
0.361 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.009 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
Tolerated 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
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
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
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
14325T>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
.
~ 14325 (T/C) 14325 (T/A) 14325 (T/G)
~ 14325 (AAC/GAC) 14325 (AAC/TAC) 14325 (AAC/CAC)
MitImpact id MI.23468 MI.23467 MI.23466
Chr chrM chrM chrM
Start 14325 14325 14325
Ref T T T
Alt C A G
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 349 349 349
Gene start 14149 14149 14149
Gene end 14673 14673 14673
Gene strand - - -
Codon substitution AAC/GAC AAC/TAC AAC/CAC
AA position 117 117 117
AA ref N N N
AA alt D Y H
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516006 516006 516006
HGVS NC_012920.1:g.14325T>C NC_012920.1:g.14325T>A NC_012920.1:g.14325T>G
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 -3.847 -3.847 -3.847
PhyloP 470Way 0.361 0.361 0.361
PhastCons 100V 0 0 0
PhastCons 470Way 0.009 0.009 0.009
PolyPhen2 possibly_damaging probably_damaging probably_damaging
PolyPhen2 score 0.49 0.94 0.91
SIFT neutral neutral neutral
SIFT score 0.42 1.0 0.56
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 0.649 0.052 0.104
VEST Neutral Neutral Neutral
VEST pvalue 0.59 0.32 0.46
VEST FDR 0.65 0.5 0.55
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.11 0.76 0.41
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 4.63429e-08 1 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model without_aae without_aae without_aae
MutationTaster AAE . . .
fathmm Tolerated Tolerated Tolerated
fathmm score 1.71 1.65 1.65
fathmm converted rankscore 0.26737 0.27650 0.27650
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.0675 0.2095 0.1226
CADD Neutral Deleterious Neutral
CADD score -0.044599 2.894288 2.255099
CADD phred 2.178 21.8 17.87
PROVEAN Tolerated Damaging Tolerated
PROVEAN score 0.7 -2.72 -1.41
MutationAssessor neutral neutral neutral
MutationAssessor score 0.205 -1.05 0.345
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.914 0.878 0.804
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.984 0.83 0.64
MLC Neutral Neutral Neutral
MLC score 0.26259883 0.26259883 0.26259883
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.54 0.28 0.27
APOGEE2 Benign Likely-benign Likely-benign
APOGEE2 score 0.0187627764746114 0.17280501327238 0.208094692610728
CAROL neutral neutral neutral
CAROL score 0.56 0.94 0.9
Condel neutral deleterious neutral
Condel score 0.47 0.53 0.33
COVEC WMV neutral neutral deleterious
COVEC WMV score -3 -2 1
MtoolBox neutral deleterious deleterious
MtoolBox DS 0.4 0.72 0.64
DEOGEN2 Tolerated Damaging Tolerated
DEOGEN2 score 0.190626 0.587173 0.369743
DEOGEN2 converted rankscore 0.54522 0.86571 0.73440
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact low impact low impact
PolyPhen2 transf score -0.78 -1.89 -1.72
SIFT_transf medium impact high impact medium impact
SIFT transf score 0.13 1.87 0.27
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score -0.34 0.39 0.68
CHASM Neutral Neutral Neutral
CHASM pvalue 0.65 0.63 0.54
CHASM FDR 0.8 0.8 0.8
ClinVar id 65512.0 . .
ClinVar Allele id 76420.0 . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 . .
ClinVar CLNDN Leigh_syndrome|Leber_optic_atrophy . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info LHON . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.0932% . .
MITOMAP General GenBank Seqs 57 . .
MITOMAP General Curated refs 21041797;24467713;15382008;29987491;20301353;31152278;12736867;16714301 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56428.0 . .
gnomAD 3.1 AC Homo 78.0 . .
gnomAD 3.1 AF Hom 0.00138229 . .
gnomAD 3.1 AC Het 1.0 . .
gnomAD 3.1 AF Het 1.77217e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 228.0 . .
HelixMTdb AF Hom 0.0011633663 . .
HelixMTdb AC Het 17.0 . .
HelixMTdb AF Het 8.674222e-05 . .
HelixMTdb mean ARF 0.46131 . .
HelixMTdb max ARF 0.89547 . .
ToMMo 54KJPN AC 132 . .
ToMMo 54KJPN AF 0.002431 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 COSM1155553 . .
dbSNP 156 id rs397515505 . .
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