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7965 (T > C)

General info

Mitimpact ID
MI.6000
Chr
chrM
Start
7965
Ref
T
Alt
C
Gene symbol
MT-CO2 Extended gene annotation
Gene position
380
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
TTC/TCC
AA pos
127
AA ref
F
AA alt
S
Functional effect
missense
OMIM ID
516040
HGVS
NC_012920.1:g.7965T>C
HGNC ID
7421
RC complex
IV
Ensembl gene ID
ENSG00000198712
Ensembl protein ID
ENSP00000354876
Ensembl transcript ID
ENST00000361739
Uniprot ID
P00403
Uniprot name
COX2_HUMAN
Ncbi gene ID
4513
Ncbi protein ID
YP_003024029.1
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Conservation

PhyloP 100v
3.451 Conservation Score
PhyloP 470way
-1.177 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.002 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
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
Deleterious 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
Likely-benign Score and details of the meta-predictor
CAROL
Deleterious 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
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
440835
Clinvar ALLELEID
434458
Clinvar CLNDISDB
Mondo:mondo:0009068, medgen:c5435656, omim:220110, orphanet:254905
Clinvar CLNDN
Cytochrome-c oxidase deficiency disease
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
7965T>C
MITOMAP Disease Clinical info
Hepatic failure / cox deficiency
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
./+
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
28802248 30461153
MITOMAP Variant Class
disease
Gnomad AN
56428
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
3
HelixMTdb AF het
1.53e-05
HelixMTdb mean ARF
0.3438899
HelixMTdb max ARF
0.77305
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs1556423369

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
.

7965 (T > A)

General info

Mitimpact ID
MI.6001
Chr
chrM
Start
7965
Ref
T
Alt
A
Gene symbol
MT-CO2 Extended gene annotation
Gene position
380
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
TTC/TAC
AA pos
127
AA ref
F
AA alt
Y
Functional effect
missense
OMIM ID
516040
HGVS
NC_012920.1:g.7965T>A
HGNC ID
7421
RC complex
IV
Ensembl gene ID
ENSG00000198712
Ensembl protein ID
ENSP00000354876
Ensembl transcript ID
ENST00000361739
Uniprot ID
P00403
Uniprot name
COX2_HUMAN
Ncbi gene ID
4513
Ncbi protein ID
YP_003024029.1
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Powered by MitoWheel

Conservation

PhyloP 100v
3.451 Conservation Score
PhyloP 470way
-1.177 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.002 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
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
Deleterious 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
7965T>A
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
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
3
HelixMTdb AF hom
1.53e-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
.

7965 (T > G)

General info

Mitimpact ID
MI.5999
Chr
chrM
Start
7965
Ref
T
Alt
G
Gene symbol
MT-CO2 Extended gene annotation
Gene position
380
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
TTC/TGC
AA pos
127
AA ref
F
AA alt
C
Functional effect
missense
OMIM ID
516040
HGVS
NC_012920.1:g.7965T>G
HGNC ID
7421
RC complex
IV
Ensembl gene ID
ENSG00000198712
Ensembl protein ID
ENSP00000354876
Ensembl transcript ID
ENST00000361739
Uniprot ID
P00403
Uniprot name
COX2_HUMAN
Ncbi gene ID
4513
Ncbi protein ID
YP_003024029.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.451 Conservation Score
PhyloP 470way
-1.177 Conservation Score
PhastCons 100v
0.994 Conservation Score
PhastCons 470way
0.002 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
Neutral Score and details of the predictor
MutationTaster
Polymorphism 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
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
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
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
7965T>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
.
~ 7965 (T/C) 7965 (T/A) 7965 (T/G)
~ 7965 (TTC/TCC) 7965 (TTC/TAC) 7965 (TTC/TGC)
MitImpact id MI.6000 MI.6001 MI.5999
Chr chrM chrM chrM
Start 7965 7965 7965
Ref T T T
Alt C A G
Gene symbol MT-CO2 MT-CO2 MT-CO2
Extended annotation mitochondrially encoded cytochrome c oxidase II mitochondrially encoded cytochrome c oxidase II mitochondrially encoded cytochrome c oxidase II
Gene position 380 380 380
Gene start 7586 7586 7586
Gene end 8269 8269 8269
Gene strand + + +
Codon substitution TTC/TCC TTC/TAC TTC/TGC
AA position 127 127 127
AA ref F F F
AA alt S Y C
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516040 516040 516040
HGVS NC_012920.1:g.7965T>C NC_012920.1:g.7965T>A NC_012920.1:g.7965T>G
HGNC id 7421 7421 7421
Respiratory Chain complex IV IV IV
Ensembl gene id ENSG00000198712 ENSG00000198712 ENSG00000198712
Ensembl transcript id ENST00000361739 ENST00000361739 ENST00000361739
Ensembl protein id ENSP00000354876 ENSP00000354876 ENSP00000354876
Uniprot id P00403 P00403 P00403
Uniprot name COX2_HUMAN COX2_HUMAN COX2_HUMAN
Ncbi gene id 4513 4513 4513
Ncbi protein id YP_003024029.1 YP_003024029.1 YP_003024029.1
PhyloP 100V 3.451 3.451 3.451
PhyloP 470Way -1.177 -1.177 -1.177
PhastCons 100V 0.994 0.994 0.994
PhastCons 470Way 0.002 0.002 0.002
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 0.99 1.0
SIFT neutral neutral neutral
SIFT score 0.95 0.51 0.1
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.02 0.011 0.016
VEST Neutral Neutral Neutral
VEST pvalue 0.36 0.46 0.33
VEST FDR 0.5 0.55 0.5
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.38 0.31 0.59
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 0.998798 0.999852 0.998154
MutationTaster converted rankscore 0.21902 0.20048 0.22321
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE F127S F127Y F127C
fathmm Tolerated Tolerated Tolerated
fathmm score 2.08 2.0 1.98
fathmm converted rankscore 0.20255 0.21473 0.21865
AlphaMissense likely_benign likely_benign ambiguous
AlphaMissense score 0.1618 0.127 0.3712
CADD Deleterious Deleterious Deleterious
CADD score 4.390921 4.530299 4.198023
CADD phred 24.1 24.3 23.9
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score 2.26 0.05 -0.73
MutationAssessor neutral neutral low
MutationAssessor score -1.11 -0.55 0.805
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.684 0.734 0.664
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.712 0.746 0.452
MLC Neutral Neutral Neutral
MLC score 0.20725451 0.20725451 0.20725451
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Pathogenic Pathogenic
APOGEE1 score 0.47 0.56 0.51
APOGEE2 Likely-benign Likely-benign Likely-benign
APOGEE2 score 0.0859406186531866 0.0662448499820889 0.219206815155212
CAROL deleterious deleterious deleterious
CAROL score 1 0.99 1
Condel deleterious neutral neutral
Condel score 0.48 0.26 0.05
COVEC WMV neutral neutral neutral
COVEC WMV score -2 -2 -2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.65 0.67 0.71
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.001452 0.004587 0.009666
DEOGEN2 converted rankscore 0.00908 0.03998 0.08788
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.52 -2.58 -3.52
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.91 0.21 -0.32
MutationAssessor transf low impact low impact medium impact
MutationAssessor transf score -1.68 -1.09 0.11
CHASM Neutral Neutral Neutral
CHASM pvalue 0.3 0.38 0.27
CHASM FDR 0.8 0.8 0.8
ClinVar id 440835.0 . .
ClinVar Allele id 434458.0 . .
ClinVar CLNDISDB MONDO:MONDO:0009068,MedGen:C5435656,OMIM:220110,Orphanet:254905 . .
ClinVar CLNDN Cytochrome-c_oxidase_deficiency_disease . .
ClinVar CLNSIG Uncertain_significance . .
MITOMAP Disease Clinical info Hepatic failure / COX deficiency . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het ./+ ./. ./.
MITOMAP General GenBank Freq 0.0016% 0.0016% .
MITOMAP General GenBank Seqs 1 1 .
MITOMAP General Curated refs 28802248;30461153 . .
MITOMAP Variant Class disease polymorphism .
gnomAD 3.1 AN 56428.0 56434.0 .
gnomAD 3.1 AC Homo 1.0 1.0 .
gnomAD 3.1 AF Hom 1.77217e-05 1.77198e-05 .
gnomAD 3.1 AC Het 1.0 0.0 .
gnomAD 3.1 AF Het 1.77217e-05 0.0 .
gnomAD 3.1 filter PASS PASS .
HelixMTdb AC Hom 2.0 3.0 .
HelixMTdb AF Hom 1.0204967e-05 1.530745e-05 .
HelixMTdb AC Het 3.0 0.0 .
HelixMTdb AF Het 1.530745e-05 0.0 .
HelixMTdb mean ARF 0.34389 . .
HelixMTdb max ARF 0.77305 . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs1556423369 . .
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