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8408 (C > T)

General info

Mitimpact ID
MI.1535
Chr
chrM
Start
8408
Ref
C
Alt
T
Gene symbol
MT-ATP8 Extended gene annotation
Gene position
43
Gene start
8366
Gene end
8572
Gene strand
+
Codon substitution
CCC/TCC
AA pos
15
AA ref
P
AA alt
S
Functional effect
missense
OMIM ID
516070
HGVS
NC_012920.1:g.8408C>T
HGNC ID
7415
RC complex
V
Ensembl gene ID
ENSG00000228253
Ensembl protein ID
ENSP00000355265
Ensembl transcript ID
ENST00000361851
Uniprot ID
P03928
Uniprot name
ATP8_HUMAN
Ncbi gene ID
4509
Ncbi protein ID
YP_003024030.1
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Conservation

PhyloP 100v
-2.084 Conservation Score
PhyloP 470way
-0.513 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.003 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
.
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
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
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
Low 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
930945
Clinvar ALLELEID
920080
Clinvar CLNDISDB
.
Clinvar CLNDN
See cases
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
8408C>T
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
56434
Gnomad AC hom
1
Gnomad AF hom
1.77e-05
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
9
HelixMTdb AF hom
4.59e-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
rs2068708846

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
.

8408 (C > A)

General info

Mitimpact ID
MI.1534
Chr
chrM
Start
8408
Ref
C
Alt
A
Gene symbol
MT-ATP8 Extended gene annotation
Gene position
43
Gene start
8366
Gene end
8572
Gene strand
+
Codon substitution
CCC/ACC
AA pos
15
AA ref
P
AA alt
T
Functional effect
missense
OMIM ID
516070
HGVS
NC_012920.1:g.8408C>A
HGNC ID
7415
RC complex
V
Ensembl gene ID
ENSG00000228253
Ensembl protein ID
ENSP00000355265
Ensembl transcript ID
ENST00000361851
Uniprot ID
P03928
Uniprot name
ATP8_HUMAN
Ncbi gene ID
4509
Ncbi protein ID
YP_003024030.1
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Powered by MitoWheel

Conservation

PhyloP 100v
-2.084 Conservation Score
PhyloP 470way
-0.513 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.003 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
.
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
Likely-benign 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
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
Low 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
8408C>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
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
1
HelixMTdb AF hom
5.1e-06
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
.

8408 (C > G)

General info

Mitimpact ID
MI.1536
Chr
chrM
Start
8408
Ref
C
Alt
G
Gene symbol
MT-ATP8 Extended gene annotation
Gene position
43
Gene start
8366
Gene end
8572
Gene strand
+
Codon substitution
CCC/GCC
AA pos
15
AA ref
P
AA alt
A
Functional effect
missense
OMIM ID
516070
HGVS
NC_012920.1:g.8408C>G
HGNC ID
7415
RC complex
V
Ensembl gene ID
ENSG00000228253
Ensembl protein ID
ENSP00000355265
Ensembl transcript ID
ENST00000361851
Uniprot ID
P03928
Uniprot name
ATP8_HUMAN
Ncbi gene ID
4509
Ncbi protein ID
YP_003024030.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-2.084 Conservation Score
PhyloP 470way
-0.513 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.003 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
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-benign 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
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
Low 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
8408C>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
56434
Gnomad AC hom
1
Gnomad AF hom
1.77e-05
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
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
.
~ 8408 (C/T) 8408 (C/A) 8408 (C/G)
~ 8408 (CCC/TCC) 8408 (CCC/ACC) 8408 (CCC/GCC)
MitImpact id MI.1535 MI.1534 MI.1536
Chr chrM chrM chrM
Start 8408 8408 8408
Ref C C C
Alt T A G
Gene symbol MT-ATP8 MT-ATP8 MT-ATP8
Extended annotation mitochondrially encoded ATP synthase membrane subunit 8 mitochondrially encoded ATP synthase membrane subunit 8 mitochondrially encoded ATP synthase membrane subunit 8
Gene position 43 43 43
Gene start 8366 8366 8366
Gene end 8572 8572 8572
Gene strand + + +
Codon substitution CCC/TCC CCC/ACC CCC/GCC
AA position 15 15 15
AA ref P P P
AA alt S T A
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516070 516070 516070
HGVS NC_012920.1:g.8408C>T NC_012920.1:g.8408C>A NC_012920.1:g.8408C>G
HGNC id 7415 7415 7415
Respiratory Chain complex V V V
Ensembl gene id ENSG00000228253 ENSG00000228253 ENSG00000228253
Ensembl transcript id ENST00000361851 ENST00000361851 ENST00000361851
Ensembl protein id ENSP00000355265 ENSP00000355265 ENSP00000355265
Uniprot id P03928 P03928 P03928
Uniprot name ATP8_HUMAN ATP8_HUMAN ATP8_HUMAN
Ncbi gene id 4509 4509 4509
Ncbi protein id YP_003024030.1 YP_003024030.1 YP_003024030.1
PhyloP 100V -2.084 -2.084 -2.084
PhyloP 470Way -0.513 -0.513 -0.513
PhastCons 100V 0 0 0
PhastCons 470Way 0.003 0.003 0.003
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0 0.99
SIFT neutral neutral neutral
SIFT score 0.62 0.21 0.26
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 1.0 0.313 0.261
VEST Neutral Neutral Neutral
VEST pvalue 0.60673599 0.48647755 0.41328743
VEST FDR 0.85 0.85 0.85
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.08 0.12 0.24
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1 1 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE P15S P15T P15A
fathmm Tolerated Tolerated Tolerated
fathmm score 2.2 2.06 2.06
fathmm converted rankscore 0.18570 0.20523 0.20523
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.0997 0.0836 0.0861
CADD Neutral Neutral Neutral
CADD score 1.030377 0.791828 1.025069
CADD phred 10.83 9.414 10.8
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score 2.01 0.62 0.31
MutationAssessor . . neutral
MutationAssessor score . . -0.315
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.996 0.97 0.988
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.968 0.896 0.908
MLC Neutral Neutral Neutral
MLC score 0.02082202 0.02082202 0.02082202
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Pathogenic Pathogenic
APOGEE1 score 0.4 0.56 0.6
APOGEE2 Benign Likely-benign Likely-benign
APOGEE2 score 0.039942946863516 0.0928727385535903 0.101006000264735
CAROL deleterious deleterious deleterious
CAROL score 0.99 1 0.99
Condel neutral neutral neutral
Condel score 0.31 0.11 0.14
COVEC WMV neutral neutral neutral
COVEC WMV score -2 -2 -2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.62 0.66 0.67
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.015971 0.017258 0.020819
DEOGEN2 converted rankscore 0.13294 0.14114 0.16323
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.6 -3.6 -2.65
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.41 -0.03 0.04
MutationAssessor transf low impact low impact low impact
MutationAssessor transf score -2.9 -1.39 -1.15
CHASM Neutral Neutral Neutral
CHASM pvalue 0.46 0.77 0.76
CHASM FDR 0.85 0.85 0.85
ClinVar id 930945.0 . .
ClinVar Allele id 920080.0 . .
ClinVar CLNDISDB . . .
ClinVar CLNDN See_cases . .
ClinVar CLNSIG Uncertain_significance . .
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 0.0% 0.0% .
MITOMAP General GenBank Seqs 0 0 .
MITOMAP General Curated refs . . .
MITOMAP Variant Class polymorphism polymorphism .
gnomAD 3.1 AN 56434.0 . 56434.0
gnomAD 3.1 AC Homo 1.0 . 1.0
gnomAD 3.1 AF Hom 1.77198e-05 . 1.77198e-05
gnomAD 3.1 AC Het 0.0 . 0.0
gnomAD 3.1 AF Het 0.0 . 0.0
gnomAD 3.1 filter PASS . PASS
HelixMTdb AC Hom 9.0 1.0 .
HelixMTdb AF Hom 4.5922352e-05 5.1024836e-06 .
HelixMTdb AC Het 0.0 0.0 .
HelixMTdb AF Het 0.0 0.0 .
HelixMTdb mean ARF . . .
HelixMTdb max ARF . . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs2068708846 . .
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