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15257 (G > A)

General info

Mitimpact ID
MI.9409
Chr
chrM
Start
15257
Ref
G
Alt
A
Gene symbol
MT-CYB Extended gene annotation
Gene position
511
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GAC/AAC
AA pos
171
AA ref
D
AA alt
N
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15257G>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
6.103 Conservation Score
PhyloP 470way
0.641 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.191 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
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
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
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
Neutral Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
Disease Score and details of the meta-predictor

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
9674
Clinvar ALLELEID
24713
Clinvar CLNDISDB
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
Clinvar CLNDN
Leber optic atrophy;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
15257G>A
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Conflicting reports
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
1.5278%
MITOMAP General GenBank Seqs
934
MITOMAP General GenBank Curated refs
19370763 10520236 18668590 1634041 20656066 8417984 19005266 21457906 21067478 16532388 32887465 11349229 11935318 1463007 10545708 22561905 7760326 32094358 7814218 7977345 16326035 7901141 7710535 8321540 7733466 9561330 14978686 11938495 17406640 1732158 8076942 19151382 23304069 8240104 11571560 8163275 8213820 15247418 16404693 16901986 19527690 8899049 7635294 9719386 16773565 18931934 9302261 21288980 19076426 10424809 7770132 24069186 19427920 8053461 11464242 8680405 17003408 7599218 18647627 16050984 15060117 29486301 23563965 12150954 9150158 12483296 8600429 8755941 1764087 30369864 11339587
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56424
Gnomad AC hom
719
Gnomad AF hom
0.0127428
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
3511
HelixMTdb AF hom
0.0179148
HelixMTdb AC het
17
HelixMTdb AF het
8.67e-05
HelixMTdb mean ARF
0.51444
HelixMTdb max ARF
0.91429
ToMMo JPN54K AC
19
ToMMo JPN54K AF
0.00035
ToMMo JPN54K AN
54302
COSMIC 90
COSM1138306
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
.

15257 (G > C)

General info

Mitimpact ID
MI.9410
Chr
chrM
Start
15257
Ref
G
Alt
C
Gene symbol
MT-CYB Extended gene annotation
Gene position
511
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GAC/CAC
AA pos
171
AA ref
D
AA alt
H
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15257G>C
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
6.103 Conservation Score
PhyloP 470way
0.641 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.191 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Pathogenic 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
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
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
Vus 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
.
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
15257G>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
.

15257 (G > T)

General info

Mitimpact ID
MI.9408
Chr
chrM
Start
15257
Ref
G
Alt
T
Gene symbol
MT-CYB Extended gene annotation
Gene position
511
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GAC/TAC
AA pos
171
AA ref
D
AA alt
Y
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15257G>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
6.103 Conservation Score
PhyloP 470way
0.641 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.191 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Pathogenic Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
.
fathmm
.
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
High 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
Vus 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
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
.
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
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
15257G>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
.
~ 15257 (G/A) 15257 (G/C) 15257 (G/T)
~ 15257 (GAC/AAC) 15257 (GAC/CAC) 15257 (GAC/TAC)
MitImpact id MI.9409 MI.9410 MI.9408
Chr chrM chrM chrM
Start 15257 15257 15257
Ref G G G
Alt A C T
Gene symbol MT-CYB MT-CYB MT-CYB
Extended annotation mitochondrially encoded cytochrome b mitochondrially encoded cytochrome b mitochondrially encoded cytochrome b
Gene position 511 511 511
Gene start 14747 14747 14747
Gene end 15887 15887 15887
Gene strand + + +
Codon substitution GAC/AAC GAC/CAC GAC/TAC
AA position 171 171 171
AA ref D D D
AA alt N H Y
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516020 516020 516020
HGVS NC_012920.1:g.15257G>A NC_012920.1:g.15257G>C NC_012920.1:g.15257G>T
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 6.103 6.103 6.103
PhyloP 470Way 0.641 0.641 0.641
PhastCons 100V 1 1 1
PhastCons 470Way 0.191 0.191 0.191
PolyPhen2 benign possibly_damaging possibly_damaging
PolyPhen2 score 0.01 0.69 0.88
SIFT neutral neutral neutral
SIFT score 0.35 0.55 1.0
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.01 0.0 0.0
VEST Neutral Pathogenic Pathogenic
VEST pvalue 0.32 0.05 0.03
VEST FDR 0.5 0.35 0.35
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Neutral Pathogenic
SNPDryad score 0.25 0.89 0.97
MutationTaster . . .
MutationTaster score . . .
MutationTaster converted rankscore . . .
MutationTaster model . . .
MutationTaster AAE . . .
fathmm . . .
fathmm score . . .
fathmm converted rankscore . . .
AlphaMissense likely_benign ambiguous ambiguous
AlphaMissense score 0.1231 0.4486 0.4619
CADD Deleterious Deleterious Deleterious
CADD score 3.856216 3.528702 3.852538
CADD phred 23.5 23.1 23.4
PROVEAN Damaging Damaging Damaging
PROVEAN score -3.57 -5.31 -6.97
MutationAssessor medium medium high
MutationAssessor score 2.045 3.265 3.815
EFIN SP Damaging Neutral Neutral
EFIN SP score 0.494 0.874 0.906
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.526 0.35 0.434
MLC Neutral Neutral Neutral
MLC score 0.33918764 0.33918764 0.33918764
PANTHER score 0.342 . .
PhD-SNP score 0.843 . .
APOGEE1 Neutral Neutral Pathogenic
APOGEE1 score 0.43 0.38 0.53
APOGEE2 Likely-benign VUS VUS
APOGEE2 score 0.1739002642373 0.467541768414673 0.541440263575936
CAROL neutral neutral neutral
CAROL score 0.64 0.65 0.88
Condel deleterious neutral deleterious
Condel score 0.67 0.43 0.56
COVEC WMV neutral deleterious deleterious
COVEC WMV score -3 1 1
MtoolBox neutral deleterious deleterious
MtoolBox DS 0.24 0.64 0.83
DEOGEN2 . . .
DEOGEN2 score . . .
DEOGEN2 converted rankscore . . .
Meta-SNP Disease . .
Meta-SNP score 0.601 . .
PolyPhen2 transf medium impact low impact low impact
PolyPhen2 transf score 1.13 -1.06 -1.54
SIFT_transf medium impact medium impact high impact
SIFT transf score 0.08 0.27 1.85
MutationAssessor transf medium impact high impact high impact
MutationAssessor transf score 0.62 2.69 3.07
CHASM Neutral Neutral Neutral
CHASM pvalue 0.76 0.43 0.12
CHASM FDR 0.85 0.8 0.8
ClinVar id 9674.0 . .
ClinVar Allele id 24713.0 . .
ClinVar CLNDISDB 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 . .
ClinVar CLNDN Leber_optic_atrophy|Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info LHON . .
MITOMAP Disease Status Conflicting reports . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 1.5278% . .
MITOMAP General GenBank Seqs 934 . .
MITOMAP General Curated refs 19370763;10520236;18668590;1634041;20656066;8417984;19005266;21457906;21067478;16532388;32887465;11349229;11935318;1463007;10545708;22561905;7760326;32094358;7814218;7977345;16326035;7901141;7710535;8321540;7733466;9561330;14978686;11938495;17406640;1732158;8076942;19151382;23304069;8240104;11571560;8163275;8213820;15247418;16404693;16901986;19527690;8899049;7635294;9719386;16773565;18931934;9302261;21288980;19076426;10424809;7770132;24069186;19427920;8053461;11464242;8680405;17003408;7599218;18647627;16050984;15060117;29486301;23563965;12150954;9150158;12483296;8600429;8755941;1764087;30369864;11339587 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56424.0 . .
gnomAD 3.1 AC Homo 719.0 . .
gnomAD 3.1 AF Hom 0.0127428 . .
gnomAD 3.1 AC Het 1.0 . .
gnomAD 3.1 AF Het 1.7723e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 3511.0 . .
HelixMTdb AF Hom 0.017914819 . .
HelixMTdb AC Het 17.0 . .
HelixMTdb AF Het 8.674222e-05 . .
HelixMTdb mean ARF 0.51444 . .
HelixMTdb max ARF 0.91429 . .
ToMMo 54KJPN AC 19 . .
ToMMo 54KJPN AF 0.00035 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 COSM1138306 . .
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