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14568 (C > T)

General info

Mitimpact ID
MI.23971
Chr
chrM
Start
14568
Ref
C
Alt
T
Gene symbol
MT-ND6 Extended gene annotation
Gene position
106
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
GGT/AGT
AA pos
36
AA ref
G
AA alt
S
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14568C>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
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Conservation

PhyloP 100v
2.344 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0.907 Conservation Score
PhastCons 470way
0.336 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
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
Ambiguous 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
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
Neutral 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
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
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
Neutral 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
65515
Clinvar ALLELEID
76423
Clinvar CLNDISDB
Mondo:mondo:0044970, medgen:c0751651, orphanet:68380;

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

leber optic atrophy
Clinvar CLNSIG
Likely pathogenic
MITOMAP Allele
14568C>T
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Cfrm [lp]
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.0098%
MITOMAP General GenBank Seqs
6
MITOMAP General GenBank Curated refs
22879922 29253894 12150954 20064630 15972314 19319978 20301353 12324878 9177303 10447650
MITOMAP Variant Class
disease
Gnomad AN
56434
Gnomad AC hom
1
Gnomad AF hom
1.77e-05
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
2
HelixMTdb AF hom
1.02e-05
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.32326
HelixMTdb max ARF
0.32326
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs397515506

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
.

14568 (C > A)

General info

Mitimpact ID
MI.23970
Chr
chrM
Start
14568
Ref
C
Alt
A
Gene symbol
MT-ND6 Extended gene annotation
Gene position
106
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
GGT/TGT
AA pos
36
AA ref
G
AA alt
C
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14568C>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
2.344 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0.907 Conservation Score
PhastCons 470way
0.336 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
Medium Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Damaging 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
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
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
14568C>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56433
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
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.1465799
HelixMTdb max ARF
0.1465799
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
COSM1138273
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
.

14568 (C > G)

General info

Mitimpact ID
MI.23969
Chr
chrM
Start
14568
Ref
C
Alt
G
Gene symbol
MT-ND6 Extended gene annotation
Gene position
106
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
GGT/CGT
AA pos
36
AA ref
G
AA alt
R
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14568C>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
2.344 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0.907 Conservation Score
PhastCons 470way
0.336 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
Medium Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Damaging 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
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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
14568C>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
.
~ 14568 (C/T) 14568 (C/A) 14568 (C/G)
~ 14568 (GGT/AGT) 14568 (GGT/TGT) 14568 (GGT/CGT)
MitImpact id MI.23971 MI.23970 MI.23969
Chr chrM chrM chrM
Start 14568 14568 14568
Ref C C C
Alt T 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 106 106 106
Gene start 14149 14149 14149
Gene end 14673 14673 14673
Gene strand - - -
Codon substitution GGT/AGT GGT/TGT GGT/CGT
AA position 36 36 36
AA ref G G G
AA alt S C R
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516006 516006 516006
HGVS NC_012920.1:g.14568C>T NC_012920.1:g.14568C>A NC_012920.1:g.14568C>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 2.344 2.344 2.344
PhyloP 470Way 0.65 0.65 0.65
PhastCons 100V 0.907 0.907 0.907
PhastCons 470Way 0.336 0.336 0.336
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1 1 1
SIFT neutral neutral neutral
SIFT score 0.64 0.23 0.33
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.036 0.001 0.0
VEST Neutral Neutral Neutral
VEST pvalue 0.42 0.21 0.13
VEST FDR 0.55 0.45 0.4
Mitoclass.1 neutral damaging damaging
SNPDryad Pathogenic Pathogenic Pathogenic
SNPDryad score 1.0 0.97 1.0
MutationTaster Disease Disease Disease
MutationTaster score 1 1 1
MutationTaster converted rankscore 0.81001 0.81001 0.81001
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE R1M R1M R1M
fathmm Tolerated Tolerated Tolerated
fathmm score 2.47 2.31 2.29
fathmm converted rankscore 0.14783 0.16794 0.17113
AlphaMissense ambiguous likely_pathogenic likely_pathogenic
AlphaMissense score 0.5263 0.8987 0.9918
CADD Deleterious Deleterious Deleterious
CADD score 4.270399 4.536784 3.986131
CADD phred 24.0 24.3 23.6
PROVEAN Damaging Damaging Damaging
PROVEAN score -5.99 -8.98 -7.98
MutationAssessor neutral medium medium
MutationAssessor score 0.565 2.19 2.995
EFIN SP Damaging Neutral Neutral
EFIN SP score 0.266 0.672 0.612
EFIN HD Damaging Damaging Damaging
EFIN HD score 0.228 0.274 0.26
MLC Neutral Neutral Neutral
MLC score 0.13377392 0.13377392 0.13377392
PANTHER score 0.225 . .
PhD-SNP score 0.704 . .
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.9 0.53 0.57
APOGEE2 Likely-pathogenic VUS+ Likely-pathogenic
APOGEE2 score 0.834105016797609 0.711721415386645 0.75963680264494
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 1.0
Condel neutral neutral neutral
Condel score 0.32 0.12 0.17
COVEC WMV neutral deleterious deleterious
COVEC WMV score -2 1 2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.73 0.88 0.89
DEOGEN2 Damaging Damaging Damaging
DEOGEN2 score 0.530048 0.573241 0.69744
DEOGEN2 converted rankscore 0.83721 0.85905 0.91258
Meta-SNP Neutral . .
Meta-SNP score 0.352 . .
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 0.35 -0.09 0.04
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 0.3 1.58 1.88
CHASM Neutral Neutral Neutral
CHASM pvalue 0.77 0.79 0.76
CHASM FDR 0.85 0.85 0.85
ClinVar id 65515.0 . .
ClinVar Allele id 76423.0 . .
ClinVar CLNDISDB MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 . .
ClinVar CLNDN Mitochondrial_disease|Leber_optic_atrophy . .
ClinVar CLNSIG Likely_pathogenic . .
MITOMAP Disease Clinical info LHON . .
MITOMAP Disease Status Cfrm [LP] . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.0098% 0.0% .
MITOMAP General GenBank Seqs 6 0 .
MITOMAP General Curated refs 22879922;29253894;12150954;20064630;15972314;19319978;20301353;12324878;9177303;10447650 . .
MITOMAP Variant Class disease polymorphism .
gnomAD 3.1 AN 56434.0 56433.0 .
gnomAD 3.1 AC Homo 1.0 0.0 .
gnomAD 3.1 AF Hom 1.77198e-05 0.0 .
gnomAD 3.1 AC Het 1.0 0.0 .
gnomAD 3.1 AF Het 1.77198e-05 0.0 .
gnomAD 3.1 filter PASS npg .
HelixMTdb AC Hom 2.0 0.0 .
HelixMTdb AF Hom 1.0204967e-05 0.0 .
HelixMTdb AC Het 1.0 1.0 .
HelixMTdb AF Het 5.1024836e-06 5.1024836e-06 .
HelixMTdb mean ARF 0.32326 0.14658 .
HelixMTdb max ARF 0.32326 0.14658 .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . COSM1138273 .
dbSNP 156 id rs397515506 . .
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