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14766 (C > T)

General info

Mitimpact ID
MI.8357
Chr
chrM
Start
14766
Ref
C
Alt
T
Gene symbol
MT-CYB Extended gene annotation
Gene position
20
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
ACT/ATT
AA pos
7
AA ref
T
AA alt
I
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.14766C>T
HGNC ID
7427
RC complex
III
Ensembl gene ID
ENSG00000198727
Ensembl protein ID
ENSP00000354554
Ensembl transcript ID
ENST00000361789
Uniprot ID
P00156
Uniprot name
CYB_HUMAN
Ncbi gene ID
4519
Ncbi protein ID
YP_003024038.1
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Conservation

PhyloP 100v
0.116 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.528 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
Neutral 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
Tolerated 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
Neutral 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
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
.
SIFT transf
.
MutationAssessor transf
.
CHASM
Neutral Score and details of the cancer-specific predictor

Databases of Frequencies and Phenotypes

Clinvar ID
140587
Clinvar ALLELEID
150279
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

mondo:mondo:0016419, medgen:c0346153, omim:114480, orphanet:227535
Clinvar CLNDN
Leigh syndrome;

familial cancer of breast
Clinvar CLNSIG
Benign
MITOMAP Allele
14766C>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
75.5848%
MITOMAP General GenBank Seqs
46208
MITOMAP General GenBank Curated refs
10453733 18619472 9384601 19732751 15465027 1323207 19497304 24467713 15922297 12112111 8254046 18590963 16901986 18806273 23756438 31358833 24470521 18712405 32943110 12725556 19076426 18603265 12192017 20939899 15896721 20153673 20691156 11179019 19370763 21281460 19022198 9792552 16532388 11349229 20566709 33420243 18495510 18402672 15771256 10508508 16721903 17454741 1757091 19167085 11464242 16172508 20304802 19398658 29486301 18639500 17331239 10329023 17264866 21978175 19050702 18477584 18223312 19188198 20728388 9545392 22561905 12271374 32094358 17698030 19026397 17406640 19062322 11517423 31152278 15286228 17085680 7635294 10909988 16895436 16773565 18931934 19427920 9412783 7726182 19555656 12464729 8213825 22333566 16950817 16048457 10960495 19460299 7987332 17429907 11820805 18691441 19394449 19818876 17434142 15591266 20627642 23304069 11938495 15015132 16714301 17620140 19733221 24667788 24069186 15932126 17967805 16050984 8910895 18386806 19324017 12937995 15466077 17072496
MITOMAP Variant Class
polymorphism
Gnomad AN
56086
Gnomad AC hom
39641
Gnomad AF hom
0.7067899
Gnomad AC het
3
Gnomad AF het
5.34e-05
Gnomad filter
Pass
HelixMTdb AC hom
114700
HelixMTdb AF hom
0.5852548
HelixMTdb AC het
34
HelixMTdb AF het
0.0001734
HelixMTdb mean ARF
0.78326
HelixMTdb max ARF
0.97
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
0.74 CPD variant frequency
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

14766 (C > A)

General info

Mitimpact ID
MI.8356
Chr
chrM
Start
14766
Ref
C
Alt
A
Gene symbol
MT-CYB Extended gene annotation
Gene position
20
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
ACT/AAT
AA pos
7
AA ref
T
AA alt
N
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.14766C>A
HGNC ID
7427
RC complex
III
Ensembl gene ID
ENSG00000198727
Ensembl protein ID
ENSP00000354554
Ensembl transcript ID
ENST00000361789
Uniprot ID
P00156
Uniprot name
CYB_HUMAN
Ncbi gene ID
4519
Ncbi protein ID
YP_003024038.1
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Conservation

PhyloP 100v
0.116 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.528 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
.
fathmm
.
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
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
Neutral 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
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
.
SIFT transf
.
MutationAssessor transf
.
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
14766C>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
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
.
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
8480
ToMMo JPN54K AF
0.313876
ToMMo JPN54K AN
27017
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
.

14766 (C > G)

General info

Mitimpact ID
MI.8358
Chr
chrM
Start
14766
Ref
C
Alt
G
Gene symbol
MT-CYB Extended gene annotation
Gene position
20
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
ACT/AGT
AA pos
7
AA ref
T
AA alt
S
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.14766C>G
HGNC ID
7427
RC complex
III
Ensembl gene ID
ENSG00000198727
Ensembl protein ID
ENSP00000354554
Ensembl transcript ID
ENST00000361789
Uniprot ID
P00156
Uniprot name
CYB_HUMAN
Ncbi gene ID
4519
Ncbi protein ID
YP_003024038.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.116 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.528 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
.
fathmm
.
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
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
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
.
SIFT transf
.
MutationAssessor transf
.
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
14766C>G
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
31358833 11820805
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
11297
ToMMo JPN54K AF
0.418144
ToMMo JPN54K AN
27017
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
.
~ 14766 (C/T) 14766 (C/A) 14766 (C/G)
~ 14766 (ACT/ATT) 14766 (ACT/AAT) 14766 (ACT/AGT)
MitImpact id MI.8357 MI.8356 MI.8358
Chr chrM chrM chrM
Start 14766 14766 14766
Ref C C C
Alt T A G
Gene symbol MT-CYB MT-CYB MT-CYB
Extended annotation mitochondrially encoded cytochrome b mitochondrially encoded cytochrome b mitochondrially encoded cytochrome b
Gene position 20 20 20
Gene start 14747 14747 14747
Gene end 15887 15887 15887
Gene strand + + +
Codon substitution ACT/ATT ACT/AAT ACT/AGT
AA position 7 7 7
AA ref T T T
AA alt I N S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516020 516020 516020
HGVS NC_012920.1:g.14766C>T NC_012920.1:g.14766C>A NC_012920.1:g.14766C>G
HGNC id 7427 7427 7427
Respiratory Chain complex III III III
Ensembl gene id ENSG00000198727 ENSG00000198727 ENSG00000198727
Ensembl transcript id ENST00000361789 ENST00000361789 ENST00000361789
Ensembl protein id ENSP00000354554 ENSP00000354554 ENSP00000354554
Uniprot id P00156 P00156 P00156
Uniprot name CYB_HUMAN CYB_HUMAN CYB_HUMAN
Ncbi gene id 4519 4519 4519
Ncbi protein id YP_003024038.1 YP_003024038.1 YP_003024038.1
PhyloP 100V 0.116 0.116 0.116
PhyloP 470Way 0.65 0.65 0.65
PhastCons 100V 0 0 0
PhastCons 470Way 0.528 0.528 0.528
PolyPhen2 benign possibly_damaging benign
PolyPhen2 score 0.01 0.48 0.11
SIFT neutral neutral neutral
SIFT score 0.21 0.54 0.72
SIFT4G Damaging Tolerated Tolerated
SIFT4G score 0.025 0.1 0.609
VEST Neutral Neutral Neutral
VEST pvalue 0.12 0.43 0.37
VEST FDR 0.4 0.55 0.5
Mitoclass.1 damaging neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.09 0.04 0.0
MutationTaster . . .
MutationTaster score . . .
MutationTaster converted rankscore . . .
MutationTaster model . . .
MutationTaster AAE . . .
fathmm . . .
fathmm score . . .
fathmm converted rankscore . . .
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.1426 0.0822 0.0813
CADD Neutral Neutral Neutral
CADD score 1.932542 0.648941 -0.637255
CADD phred 15.79 8.489 0.101
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score -2.35 -1.63 -1.05
MutationAssessor medium low neutral
MutationAssessor score 2.615 1.065 0.565
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.982 0.964 0.97
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.616 0.866 0.974
MLC Neutral Neutral Neutral
MLC score 0.12444927 0.12444927 0.12444927
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.48 0.33 0.39
APOGEE2 Benign Benign Benign
APOGEE2 score 0.0416181905425675 0.0312597764622889 0.0363865198724106
CAROL neutral neutral neutral
CAROL score 0.79 0.45 0.17
Condel deleterious deleterious deleterious
Condel score 0.6 0.53 0.81
COVEC WMV neutral neutral neutral
COVEC WMV score -4 -1 -4
MtoolBox neutral neutral neutral
MtoolBox DS 0.09 0.41 0.11
DEOGEN2 . . .
DEOGEN2 score . . .
DEOGEN2 converted rankscore . . .
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf . . .
PolyPhen2 transf score . . .
SIFT_transf . . .
SIFT transf score . . .
MutationAssessor transf . . .
MutationAssessor transf score . . .
CHASM Neutral Neutral Neutral
CHASM pvalue 0.32 0.5 0.55
CHASM FDR 0.8 0.8 0.8
ClinVar id 140587.0 . .
ClinVar Allele id 150279.0 . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0016419,MedGen:C0346153,OMIM:114480,Orphanet:227535 . .
ClinVar CLNDN Leigh_syndrome|Familial_cancer_of_breast . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 75.5848% . 0.0%
MITOMAP General GenBank Seqs 46208 . 0
MITOMAP General Curated refs 10453733;18619472;9384601;19732751;15465027;1323207;19497304;24467713;15922297;12112111;8254046;18590963;16901986;18806273;23756438;31358833;24470521;18712405;32943110;12725556;19076426;18603265;12192017;20939899;15896721;20153673;20691156;11179019;19370763;21281460;19022198;9792552;16532388;11349229;20566709;33420243;18495510;18402672;15771256;10508508;16721903;17454741;1757091;19167085;11464242;16172508;20304802;19398658;29486301;18639500;17331239;10329023;17264866;21978175;19050702;18477584;18223312;19188198;20728388;9545392;22561905;12271374;32094358;17698030;19026397;17406640;19062322;11517423;31152278;15286228;17085680;7635294;10909988;16895436;16773565;18931934;19427920;9412783;7726182;19555656;12464729;8213825;22333566;16950817;16048457;10960495;19460299;7987332;17429907;11820805;18691441;19394449;19818876;17434142;15591266;20627642;23304069;11938495;15015132;16714301;17620140;19733221;24667788;24069186;15932126;17967805;16050984;8910895;18386806;19324017;12937995;15466077;17072496 . 31358833;11820805
MITOMAP Variant Class polymorphism . polymorphism
gnomAD 3.1 AN 56086.0 56433.0 .
gnomAD 3.1 AC Homo 39641.0 0.0 .
gnomAD 3.1 AF Hom 0.7067899999999999 0.0 .
gnomAD 3.1 AC Het 3.0 0.0 .
gnomAD 3.1 AF Het 5.34893e-05 0.0 .
gnomAD 3.1 filter PASS npg .
HelixMTdb AC Hom 114700.0 . .
HelixMTdb AF Hom 0.58525485 . .
HelixMTdb AC Het 34.0 . .
HelixMTdb AF Het 0.00017348444 . .
HelixMTdb mean ARF 0.78326 . .
HelixMTdb max ARF 0.97 . .
ToMMo 54KJPN AC . 8480 11297
ToMMo 54KJPN AF . 0.313876 0.418144
ToMMo 54KJPN AN . 27017 27017
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