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7664 (G > A)

General info

Mitimpact ID
MI.5351
Chr
chrM
Start
7664
Ref
G
Alt
A
Gene symbol
MT-CO2 Extended gene annotation
Gene position
79
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
GCC/ACC
AA pos
27
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516040
HGVS
NC_012920.1:g.7664G>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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Conservation

PhyloP 100v
0.122 Conservation Score
PhyloP 470way
-0.26 Conservation Score
PhastCons 100v
0.001 Conservation Score
PhastCons 470way
0.152 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
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
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
Tolerated Score and details of the meta-predictor
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
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
692756
Clinvar ALLELEID
681291
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
7664G>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.1325%
MITOMAP General GenBank Seqs
81
MITOMAP General GenBank Curated refs
21041797 24467713 16895436 20304802 16714301
MITOMAP Variant Class
polymorphism
Gnomad AN
56416
Gnomad AC hom
21
Gnomad AF hom
0.0003722
Gnomad AC het
7
Gnomad AF het
0.000124
Gnomad filter
Pass
HelixMTdb AC hom
84
HelixMTdb AF hom
0.0004286
HelixMTdb AC het
22
HelixMTdb AF het
0.0001122
HelixMTdb mean ARF
0.23966
HelixMTdb max ARF
0.77011
ToMMo JPN54K AC
351
ToMMo JPN54K AF
0.006464
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs879139393

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
.

7664 (G > C)

General info

Mitimpact ID
MI.5350
Chr
chrM
Start
7664
Ref
G
Alt
C
Gene symbol
MT-CO2 Extended gene annotation
Gene position
79
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
GCC/CCC
AA pos
27
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516040
HGVS
NC_012920.1:g.7664G>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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Powered by MitoWheel

Conservation

PhyloP 100v
0.122 Conservation Score
PhyloP 470way
-0.26 Conservation Score
PhastCons 100v
0.001 Conservation Score
PhastCons 470way
0.152 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
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely pathogenic 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
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
.
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
.
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
7664G>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
.

7664 (G > T)

General info

Mitimpact ID
MI.5349
Chr
chrM
Start
7664
Ref
G
Alt
T
Gene symbol
MT-CO2 Extended gene annotation
Gene position
79
Gene start
7586
Gene end
8269
Gene strand
+
Codon substitution
GCC/TCC
AA pos
27
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516040
HGVS
NC_012920.1:g.7664G>T
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
0.122 Conservation Score
PhyloP 470way
-0.26 Conservation Score
PhastCons 100v
0.001 Conservation Score
PhastCons 470way
0.152 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
Damaging 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
Low 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
.
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
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
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
692755
Clinvar ALLELEID
681292
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
7664G>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
56433
Gnomad AC hom
3
Gnomad AF hom
5.31e-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
rs879139393

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
.
~ 7664 (G/A) 7664 (G/C) 7664 (G/T)
~ 7664 (GCC/ACC) 7664 (GCC/CCC) 7664 (GCC/TCC)
MitImpact id MI.5351 MI.5350 MI.5349
Chr chrM chrM chrM
Start 7664 7664 7664
Ref G G G
Alt A C T
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 79 79 79
Gene start 7586 7586 7586
Gene end 8269 8269 8269
Gene strand + + +
Codon substitution GCC/ACC GCC/CCC GCC/TCC
AA position 27 27 27
AA ref A A A
AA alt T P S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516040 516040 516040
HGVS NC_012920.1:g.7664G>A NC_012920.1:g.7664G>C NC_012920.1:g.7664G>T
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 0.122 0.122 0.122
PhyloP 470Way -0.26 -0.26 -0.26
PhastCons 100V 0.001 0.001 0.001
PhastCons 470Way 0.152 0.152 0.152
PolyPhen2 benign possibly_damaging benign
PolyPhen2 score 0.02 0.74 0.34
SIFT neutral neutral neutral
SIFT score 0.66 0.3 0.53
SIFT4G Tolerated Damaging Tolerated
SIFT4G score 0.76 0.003 0.064
VEST Neutral Neutral Neutral
VEST pvalue 0.48 0.13 0.48
VEST FDR 0.55 0.4 0.55
Mitoclass.1 neutral damaging damaging
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.01 0.69 0.48
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 0.999971 0.999899 0.999987
MutationTaster converted rankscore 0.18612 0.19781 0.18198
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE A27T A27P A27S
fathmm Tolerated Tolerated Tolerated
fathmm score 1.57 1.42 1.47
fathmm converted rankscore 0.29342 0.33189 0.31987
AlphaMissense likely_benign likely_pathogenic likely_benign
AlphaMissense score 0.1431 0.9895 0.1888
CADD Neutral Deleterious Neutral
CADD score 0.010945 3.539456 0.783856
CADD phred 2.692 23.1 9.364
PROVEAN Tolerated Damaging Tolerated
PROVEAN score -0.57 -3.37 -1.41
MutationAssessor neutral high low
MutationAssessor score 0.115 3.65 1.42
EFIN SP Neutral Damaging Damaging
EFIN SP score 0.794 0.422 0.54
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.952 0.318 0.586
MLC Neutral Neutral Neutral
MLC score 0.1348301 0.1348301 0.1348301
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.3 0.44 0.36
APOGEE2 Benign VUS Likely-benign
APOGEE2 score 0.0142738980339124 0.517106439561567 0.137600712217345
CAROL neutral neutral neutral
CAROL score 0.3 0.79 0.39
Condel deleterious neutral deleterious
Condel score 0.82 0.28 0.6
COVEC WMV neutral . neutral
COVEC WMV score -6 0 -6
MtoolBox neutral deleterious neutral
MtoolBox DS 0.12 0.79 0.34
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.025483 0.201109 0.029018
DEOGEN2 converted rankscore 0.19048 0.55889 0.20885
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact low impact medium impact
PolyPhen2 transf score 0.86 -1.14 -0.45
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.36 0 0.23
MutationAssessor transf low impact medium impact medium impact
MutationAssessor transf score -1.15 1.92 0.18
CHASM Neutral Neutral Neutral
CHASM pvalue 0.61 0.71 0.71
CHASM FDR 0.8 0.85 0.85
ClinVar id 692756.0 . 692755.0
ClinVar Allele id 681291.0 . 681292.0
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506
ClinVar CLNDN Leigh_syndrome . Leigh_syndrome
ClinVar CLNSIG Benign . Uncertain_significance
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 0.1325% . 0.0%
MITOMAP General GenBank Seqs 81 . 0
MITOMAP General Curated refs 21041797;24467713;16895436;20304802;16714301 . .
MITOMAP Variant Class polymorphism . polymorphism
gnomAD 3.1 AN 56416.0 . 56433.0
gnomAD 3.1 AC Homo 21.0 . 3.0
gnomAD 3.1 AF Hom 0.000372235 . 5.31604e-05
gnomAD 3.1 AC Het 7.0 . 0.0
gnomAD 3.1 AF Het 0.000124078 . 0.0
gnomAD 3.1 filter PASS . PASS
HelixMTdb AC Hom 84.0 . 9.0
HelixMTdb AF Hom 0.0004286086 . 4.5922352e-05
HelixMTdb AC Het 22.0 . 0.0
HelixMTdb AF Het 0.00011225463 . 0.0
HelixMTdb mean ARF 0.23966 . .
HelixMTdb max ARF 0.77011 . .
ToMMo 54KJPN AC 351 . .
ToMMo 54KJPN AF 0.006464 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs879139393 . rs879139393
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