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15746 (A > G)

General info

Mitimpact ID
MI.10456
Chr
chrM
Start
15746
Ref
A
Alt
G
Gene symbol
MT-CYB Extended gene annotation
Gene position
1000
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
ATT/GTT
AA pos
334
AA ref
I
AA alt
V
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15746A>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
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Conservation

PhyloP 100v
0.456 Conservation Score
PhyloP 470way
0.623 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.066 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
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
Neutral Score and details of the predictor
PhD-SNP
Neutral Score and details of the predictor

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
Neutral Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
High 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
235623
Clinvar ALLELEID
237304
Clinvar CLNDISDB
Medgen:cn517202;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Not provided;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
15746A>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
3.4138%
MITOMAP General GenBank Seqs
2087
MITOMAP General GenBank Curated refs
17152068 11130070 23144833 21281460 16855009 16060290 20304802 16714301 15466285 16120329 15984912 24002810 19733221 12840039 15372108 19818876 18800376 15890885
MITOMAP Variant Class
polymorphism
Gnomad AN
56431
Gnomad AC hom
133
Gnomad AF hom
0.0023568
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
483
HelixMTdb AF hom
0.0024644
HelixMTdb AC het
4
HelixMTdb AF het
2.04e-05
HelixMTdb mean ARF
0.43167
HelixMTdb max ARF
0.70183
ToMMo JPN54K AC
217
ToMMo JPN54K AF
0.003996
ToMMo JPN54K AN
54302
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
.

15746 (A > C)

General info

Mitimpact ID
MI.10457
Chr
chrM
Start
15746
Ref
A
Alt
C
Gene symbol
MT-CYB Extended gene annotation
Gene position
1000
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
ATT/CTT
AA pos
334
AA ref
I
AA alt
L
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15746A>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
0.456 Conservation Score
PhyloP 470way
0.623 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.066 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
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
Medium 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
15746A>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56432
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Npg
HelixMTdb AC hom
4
HelixMTdb AF hom
2.04e-05
HelixMTdb AC het
0
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
.

15746 (A > T)

General info

Mitimpact ID
MI.10458
Chr
chrM
Start
15746
Ref
A
Alt
T
Gene symbol
MT-CYB Extended gene annotation
Gene position
1000
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
ATT/TTT
AA pos
334
AA ref
I
AA alt
F
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15746A>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
0.456 Conservation Score
PhyloP 470way
0.623 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.066 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
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
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
.
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
.
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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
15746A>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
.
~ 15746 (A/G) 15746 (A/C) 15746 (A/T)
~ 15746 (ATT/GTT) 15746 (ATT/CTT) 15746 (ATT/TTT)
MitImpact id MI.10456 MI.10457 MI.10458
Chr chrM chrM chrM
Start 15746 15746 15746
Ref A A A
Alt G 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 1000 1000 1000
Gene start 14747 14747 14747
Gene end 15887 15887 15887
Gene strand + + +
Codon substitution ATT/GTT ATT/CTT ATT/TTT
AA position 334 334 334
AA ref I I I
AA alt V L F
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516020 516020 516020
HGVS NC_012920.1:g.15746A>G NC_012920.1:g.15746A>C NC_012920.1:g.15746A>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 0.456 0.456 0.456
PhyloP 470Way 0.623 0.623 0.623
PhastCons 100V 0 0 0
PhastCons 470Way 0.066 0.066 0.066
PolyPhen2 benign benign possibly_damaging
PolyPhen2 score 0 0.06 0.45
SIFT neutral neutral neutral
SIFT score 0.58 1.0 0.63
SIFT4G Tolerated Damaging Damaging
SIFT4G score 0.266 0.031 0.022
VEST Neutral Neutral Neutral
VEST pvalue 0.52 0.28 0.18
VEST FDR 0.6 0.45 0.45
Mitoclass.1 neutral neutral damaging
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.71 0.62 0.67
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 0.0867 0.0946 0.2086
CADD Neutral Neutral Neutral
CADD score 0.277887 2.233057 2.253703
CADD phred 5.477 17.73 17.86
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score -0.38 -0.89 -2.15
MutationAssessor low neutral medium
MutationAssessor score 1.09 0.64 2.575
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.94 0.902 0.846
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.894 0.712 0.548
MLC Neutral Neutral Neutral
MLC score 0.26338343 0.26338343 0.26338343
PANTHER score 0.303 . .
PhD-SNP score 0.209 . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.35 0.3 0.22
APOGEE2 Benign Benign Likely-benign
APOGEE2 score 0.001716577087828 0.0161343242482998 0.0850695119428826
CAROL neutral neutral neutral
CAROL score 0.42 0.06 0.38
Condel deleterious deleterious deleterious
Condel score 0.79 0.97 0.59
COVEC WMV neutral neutral .
COVEC WMV score -6 -6 0
MtoolBox neutral neutral neutral
MtoolBox DS 0.08 0.12 0.37
DEOGEN2 . . .
DEOGEN2 score . . .
DEOGEN2 converted rankscore . . .
Meta-SNP Neutral . .
Meta-SNP score 0.268 . .
PolyPhen2 transf high impact medium impact medium impact
PolyPhen2 transf score 2.07 0.38 -0.65
SIFT_transf medium impact high impact medium impact
SIFT transf score 0.3 1.85 0.35
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score -0.27 -0.41 1.32
CHASM Neutral Neutral Neutral
CHASM pvalue 0.39 0.46 0.49
CHASM FDR 0.8 0.8 0.8
ClinVar id 235623.0 . .
ClinVar Allele id 237304.0 . .
ClinVar CLNDISDB MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN not_provided|Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 3.4138% 0.0016% .
MITOMAP General GenBank Seqs 2087 1 .
MITOMAP General Curated refs 17152068;11130070;23144833;21281460;16855009;16060290;20304802;16714301;15466285;16120329;15984912;24002810;19733221;12840039;15372108;19818876;18800376;15890885 . .
MITOMAP Variant Class polymorphism polymorphism .
gnomAD 3.1 AN 56431.0 56432.0 .
gnomAD 3.1 AC Homo 133.0 0.0 .
gnomAD 3.1 AF Hom 0.00235686 0.0 .
gnomAD 3.1 AC Het 0.0 0.0 .
gnomAD 3.1 AF Het 0.0 0.0 .
gnomAD 3.1 filter PASS npg .
HelixMTdb AC Hom 483.0 4.0 .
HelixMTdb AF Hom 0.0024644996 2.0409934e-05 .
HelixMTdb AC Het 4.0 0.0 .
HelixMTdb AF Het 2.0409934e-05 0.0 .
HelixMTdb mean ARF 0.43167 . .
HelixMTdb max ARF 0.70183 . .
ToMMo 54KJPN AC 217 . .
ToMMo 54KJPN AF 0.003996 . .
ToMMo 54KJPN AN 54302 . .
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