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6480 (G > A)

General info

Mitimpact ID
MI.3106
Chr
chrM
Start
6480
Ref
G
Alt
A
Gene symbol
MT-CO1 Extended gene annotation
Gene position
577
Gene start
5904
Gene end
7445
Gene strand
+
Codon substitution
GTC/ATC
AA pos
193
AA ref
V
AA alt
I
Functional effect
missense
OMIM ID
516030
HGVS
NC_012920.1:g.6480G>A
HGNC ID
7419
RC complex
IV
Ensembl gene ID
ENSG00000198804
Ensembl protein ID
ENSP00000354499
Ensembl transcript ID
ENST00000361624
Uniprot ID
P00395
Uniprot name
COX1_HUMAN
Ncbi gene ID
4512
Ncbi protein ID
YP_003024028.1
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Conservation

PhyloP 100v
3.228 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.029 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
Disease automatic 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
High 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
9666
Clinvar ALLELEID
24705
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

mondo:mondo:0009068, medgen:c5435656, omim:220110, orphanet:254905
Clinvar CLNDN
Leigh syndrome;

cytochrome-c oxidase deficiency disease
Clinvar CLNSIG
Benign
MITOMAP Allele
6480G>A
MITOMAP Disease Clinical info
Prostate cancer / enriched in poag cohort
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.2552%
MITOMAP General GenBank Seqs
156
MITOMAP General GenBank Curated refs
19370763 21978175 19267350 27217714 17406640 19022198 15647368 21457906 9832034
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56425
Gnomad AC hom
183
Gnomad AF hom
0.0032432
Gnomad AC het
7
Gnomad AF het
0.000124
Gnomad filter
Pass
HelixMTdb AC hom
499
HelixMTdb AF hom
0.0025461
HelixMTdb AC het
16
HelixMTdb AF het
8.16e-05
HelixMTdb mean ARF
0.31154
HelixMTdb max ARF
0.79452
ToMMo JPN54K AC
35
ToMMo JPN54K AF
0.000645
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs199476128

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
5.49 CPD variant frequency
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

6480 (G > C)

General info

Mitimpact ID
MI.3108
Chr
chrM
Start
6480
Ref
G
Alt
C
Gene symbol
MT-CO1 Extended gene annotation
Gene position
577
Gene start
5904
Gene end
7445
Gene strand
+
Codon substitution
GTC/CTC
AA pos
193
AA ref
V
AA alt
L
Functional effect
missense
OMIM ID
516030
HGVS
NC_012920.1:g.6480G>C
HGNC ID
7419
RC complex
IV
Ensembl gene ID
ENSG00000198804
Ensembl protein ID
ENSP00000354499
Ensembl transcript ID
ENST00000361624
Uniprot ID
P00395
Uniprot name
COX1_HUMAN
Ncbi gene ID
4512
Ncbi protein ID
YP_003024028.1
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Powered by MitoWheel

Conservation

PhyloP 100v
3.228 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.029 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
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
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
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
6480G>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
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
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
.

6480 (G > T)

General info

Mitimpact ID
MI.3107
Chr
chrM
Start
6480
Ref
G
Alt
T
Gene symbol
MT-CO1 Extended gene annotation
Gene position
577
Gene start
5904
Gene end
7445
Gene strand
+
Codon substitution
GTC/TTC
AA pos
193
AA ref
V
AA alt
F
Functional effect
missense
OMIM ID
516030
HGVS
NC_012920.1:g.6480G>T
HGNC ID
7419
RC complex
IV
Ensembl gene ID
ENSG00000198804
Ensembl protein ID
ENSP00000354499
Ensembl transcript ID
ENST00000361624
Uniprot ID
P00395
Uniprot name
COX1_HUMAN
Ncbi gene ID
4512
Ncbi protein ID
YP_003024028.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.228 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.029 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly 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
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
Deleterious 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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
6480G>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
.
~ 6480 (G/A) 6480 (G/C) 6480 (G/T)
~ 6480 (GTC/ATC) 6480 (GTC/CTC) 6480 (GTC/TTC)
MitImpact id MI.3106 MI.3108 MI.3107
Chr chrM chrM chrM
Start 6480 6480 6480
Ref G G G
Alt A C T
Gene symbol MT-CO1 MT-CO1 MT-CO1
Extended annotation mitochondrially encoded cytochrome c oxidase I mitochondrially encoded cytochrome c oxidase I mitochondrially encoded cytochrome c oxidase I
Gene position 577 577 577
Gene start 5904 5904 5904
Gene end 7445 7445 7445
Gene strand + + +
Codon substitution GTC/ATC GTC/CTC GTC/TTC
AA position 193 193 193
AA ref V V V
AA alt I L F
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516030 516030 516030
HGVS NC_012920.1:g.6480G>A NC_012920.1:g.6480G>C NC_012920.1:g.6480G>T
HGNC id 7419 7419 7419
Respiratory Chain complex IV IV IV
Ensembl gene id ENSG00000198804 ENSG00000198804 ENSG00000198804
Ensembl transcript id ENST00000361624 ENST00000361624 ENST00000361624
Ensembl protein id ENSP00000354499 ENSP00000354499 ENSP00000354499
Uniprot id P00395 P00395 P00395
Uniprot name COX1_HUMAN COX1_HUMAN COX1_HUMAN
Ncbi gene id 4512 4512 4512
Ncbi protein id YP_003024028.1 YP_003024028.1 YP_003024028.1
PhyloP 100V 3.228 3.228 3.228
PhyloP 470Way 0.458 0.458 0.458
PhastCons 100V 1 1 1
PhastCons 470Way 0.029 0.029 0.029
PolyPhen2 benign benign possibly_damaging
PolyPhen2 score 0.0 0.01 0.53
SIFT neutral neutral neutral
SIFT score 0.72 0.34 0.83
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 1.0 0.645 0.245
VEST Neutral Neutral Neutral
VEST pvalue 0.52 0.39 0.27
VEST FDR 0.6 0.55 0.55
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.04 0.49 0.87
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 0.000156619 0.999473 0.994257
MutationTaster converted rankscore 0.20103 0.21134 0.23556
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE V193I V193L V193F
fathmm Tolerated Tolerated Tolerated
fathmm score 2.87 2.81 2.69
fathmm converted rankscore 0.10386 0.10975 0.12268
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.0754 0.2257 0.1634
CADD Neutral Neutral Neutral
CADD score -1.10388 -0.206353 0.634887
CADD phred 0.01 1.065 8.395
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score 0.35 -0.4 -1.74
MutationAssessor neutral low neutral
MutationAssessor score -0.68 0.895 0.215
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.754 0.666 0.648
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.916 0.634 0.626
MLC Neutral Neutral Neutral
MLC score 0.48690325 0.48690325 0.48690325
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.42 0.49 0.35
APOGEE2 Benign Benign Likely-benign
APOGEE2 score 0.0071823314946833 0.0603742675984873 0.155963765980278
CAROL neutral neutral neutral
CAROL score 0.28 0.65 0.44
Condel deleterious deleterious deleterious
Condel score 0.86 0.67 0.65
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -3
MtoolBox neutral neutral deleterious
MtoolBox DS 0.11 0.15 0.54
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.011356 0.018325 0.039761
DEOGEN2 converted rankscore 0.10143 0.14790 0.25301
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf high impact medium impact medium impact
PolyPhen2 transf score 2.07 1.12 -0.81
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.42 0.03 0.58
MutationAssessor transf low impact medium impact medium impact
MutationAssessor transf score -2.04 -0.84 -0.91
CHASM Neutral Neutral Neutral
CHASM pvalue 0.76 0.53 0.58
CHASM FDR 0.9 0.9 0.9
ClinVar id 9666.0 . .
ClinVar Allele id 24705.0 . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0009068,MedGen:C5435656,OMIM:220110,Orphanet:254905 . .
ClinVar CLNDN Leigh_syndrome|Cytochrome-c_oxidase_deficiency_disease . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info Prostate Cancer / enriched in POAG cohort . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.2552% . .
MITOMAP General GenBank Seqs 156 . .
MITOMAP General Curated refs 19370763;21978175;19267350;27217714;17406640;19022198;15647368;21457906;9832034 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56425.0 56432.0 .
gnomAD 3.1 AC Homo 183.0 0.0 .
gnomAD 3.1 AF Hom 0.00324324 0.0 .
gnomAD 3.1 AC Het 7.0 0.0 .
gnomAD 3.1 AF Het 0.000124058 0.0 .
gnomAD 3.1 filter PASS npg .
HelixMTdb AC Hom 499.0 . .
HelixMTdb AF Hom 0.0025461393 . .
HelixMTdb AC Het 16.0 . .
HelixMTdb AF Het 8.163974e-05 . .
HelixMTdb mean ARF 0.31154 . .
HelixMTdb max ARF 0.79452 . .
ToMMo 54KJPN AC 35 . .
ToMMo 54KJPN AF 0.000645 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs199476128 . .
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