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9966 (G > C)

General info

Mitimpact ID
MI.8268
Chr
chrM
Start
9966
Ref
G
Alt
C
Gene symbol
MT-CO3 Extended gene annotation
Gene position
760
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GTC/CTC
AA pos
254
AA ref
V
AA alt
L
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9966G>C
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
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Conservation

PhyloP 100v
0.072 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
0.006 Conservation Score
PhastCons 470way
0.964 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
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
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
693253
Clinvar ALLELEID
681789
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
9966G>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
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
2
HelixMTdb AF het
1.02e-05
HelixMTdb mean ARF
0.45467
HelixMTdb max ARF
0.48077
ToMMo JPN54K AC
3
ToMMo JPN54K AF
5.5e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs200809063

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
.

9966 (G > A)

General info

Mitimpact ID
MI.8266
Chr
chrM
Start
9966
Ref
G
Alt
A
Gene symbol
MT-CO3 Extended gene annotation
Gene position
760
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GTC/ATC
AA pos
254
AA ref
V
AA alt
I
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9966G>A
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
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Powered by MitoWheel

Conservation

PhyloP 100v
0.072 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
0.006 Conservation Score
PhastCons 470way
0.964 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
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
377020
Clinvar ALLELEID
363898
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

medgen:cn517202
Clinvar CLNDN
Leigh syndrome;

not provided
Clinvar CLNSIG
Benign/likely benign
MITOMAP Allele
9966G>A
MITOMAP Disease Clinical info
Lhon possible helper variant
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
Nr/nr
MITOMAP General GenBank Freq
0.6559%
MITOMAP General GenBank Seqs
401
MITOMAP General GenBank Curated refs
32094358 21041797 8016139 12802679 1910259 17893651 29444077 19026397 15896721 1757091 17406640 24667788 20691156 19732751 29208909 20454697 16901986 9443868
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56402
Gnomad AC hom
447
Gnomad AF hom
0.0079252
Gnomad AC het
6
Gnomad AF het
0.0001063
Gnomad filter
Pass
HelixMTdb AC hom
1092
HelixMTdb AF hom
0.0055719
HelixMTdb AC het
29
HelixMTdb AF het
0.0001479
HelixMTdb mean ARF
0.30146
HelixMTdb max ARF
0.74809
ToMMo JPN54K AC
103
ToMMo JPN54K AF
0.001897
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs200809063

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
.

9966 (G > T)

General info

Mitimpact ID
MI.8267
Chr
chrM
Start
9966
Ref
G
Alt
T
Gene symbol
MT-CO3 Extended gene annotation
Gene position
760
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GTC/TTC
AA pos
254
AA ref
V
AA alt
F
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9966G>T
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.072 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
0.006 Conservation Score
PhastCons 470way
0.964 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
Pathogenic Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic 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
Neutral Score and details of the predictor
PROVEAN
Damaging 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
Vus- 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
9966G>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
.
~ 9966 (G/C) 9966 (G/A) 9966 (G/T)
~ 9966 (GTC/CTC) 9966 (GTC/ATC) 9966 (GTC/TTC)
MitImpact id MI.8268 MI.8266 MI.8267
Chr chrM chrM chrM
Start 9966 9966 9966
Ref G G G
Alt C A T
Gene symbol MT-CO3 MT-CO3 MT-CO3
Extended annotation mitochondrially encoded cytochrome c oxidase III mitochondrially encoded cytochrome c oxidase III mitochondrially encoded cytochrome c oxidase III
Gene position 760 760 760
Gene start 9207 9207 9207
Gene end 9990 9990 9990
Gene strand + + +
Codon substitution GTC/CTC GTC/ATC GTC/TTC
AA position 254 254 254
AA ref V V V
AA alt L I F
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516050 516050 516050
HGVS NC_012920.1:g.9966G>C NC_012920.1:g.9966G>A NC_012920.1:g.9966G>T
HGNC id 7422 7422 7422
Respiratory Chain complex IV IV IV
Ensembl gene id ENSG00000198938 ENSG00000198938 ENSG00000198938
Ensembl transcript id ENST00000362079 ENST00000362079 ENST00000362079
Ensembl protein id ENSP00000354982 ENSP00000354982 ENSP00000354982
Uniprot id P00414 P00414 P00414
Uniprot name COX3_HUMAN COX3_HUMAN COX3_HUMAN
Ncbi gene id 4514 4514 4514
Ncbi protein id YP_003024032.1 YP_003024032.1 YP_003024032.1
PhyloP 100V 0.072 0.072 0.072
PhyloP 470Way 0.848 0.848 0.848
PhastCons 100V 0.006 0.006 0.006
PhastCons 470Way 0.964 0.964 0.964
PolyPhen2 benign benign benign
PolyPhen2 score 0.0 0.0 0.13
SIFT neutral neutral neutral
SIFT score 0.54 0.59 0.48
SIFT4G Tolerated Tolerated Damaging
SIFT4G score 0.105 1.0 0.001
VEST Neutral Neutral Pathogenic
VEST pvalue 0.19 0.34 0.05
VEST FDR 0.45 0.5 0.35
Mitoclass.1 neutral neutral damaging
SNPDryad Neutral Neutral Pathogenic
SNPDryad score 0.71 0.06 0.97
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 0.999998 0.999999 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE V254L V254I V254F
fathmm Tolerated Tolerated Tolerated
fathmm score 2.14 2.22 1.97
fathmm converted rankscore 0.19450 0.18248 0.22067
AlphaMissense likely_benign likely_benign ambiguous
AlphaMissense score 0.2922 0.0941 0.3651
CADD Neutral Neutral Neutral
CADD score 0.549726 -0.852828 1.991966
CADD phred 7.8 0.033 16.16
PROVEAN Tolerated Tolerated Damaging
PROVEAN score -1.12 0.19 -2.83
MutationAssessor neutral neutral medium
MutationAssessor score 0.78 -0.295 2.295
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.75 0.918 0.634
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.79 0.962 0.446
MLC Neutral Neutral Neutral
MLC score 0.3126622 0.3126622 0.3126622
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.37 0.4 0.34
APOGEE2 Likely-benign Benign VUS-
APOGEE2 score 0.122556348662775 0.0391874415659705 0.314087969437017
CAROL neutral neutral neutral
CAROL score 0.46 0.41 0.43
Condel deleterious deleterious deleterious
Condel score 0.77 0.8 0.68
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -6
MtoolBox neutral neutral neutral
MtoolBox DS 0.12 0.07 0.27
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.030553 0.011579 0.094519
DEOGEN2 converted rankscore 0.21631 0.10309 0.39432
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf high impact high impact medium impact
PolyPhen2 transf score 2.05 2.05 -0.07
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.23 0.28 0.17
MutationAssessor transf low impact low impact medium impact
MutationAssessor transf score -1.12 -1.29 0.28
CHASM Neutral Neutral Neutral
CHASM pvalue 0.54 0.73 0.33
CHASM FDR 0.8 0.85 0.8
ClinVar id 693253.0 377020.0 .
ClinVar Allele id 681789.0 363898.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MedGen:CN517202 .
ClinVar CLNDN Leigh_syndrome Leigh_syndrome|not_provided .
ClinVar CLNSIG Uncertain_significance Benign/Likely_benign .
MITOMAP Disease Clinical info . LHON possible helper variant .
MITOMAP Disease Status . Reported .
MITOMAP Disease Hom/Het ./. nr/nr ./.
MITOMAP General GenBank Freq 0.0016% 0.6559% .
MITOMAP General GenBank Seqs 1 401 .
MITOMAP General Curated refs . 32094358;21041797;8016139;12802679;1910259;17893651;29444077;19026397;15896721;1757091;17406640;24667788;20691156;19732751;29208909;20454697;16901986;9443868 .
MITOMAP Variant Class polymorphism polymorphism;disease .
gnomAD 3.1 AN 56432.0 56402.0 .
gnomAD 3.1 AC Homo 1.0 447.0 .
gnomAD 3.1 AF Hom 1.77204e-05 0.00792525 .
gnomAD 3.1 AC Het 0.0 6.0 .
gnomAD 3.1 AF Het 0.0 0.000106379 .
gnomAD 3.1 filter PASS PASS .
HelixMTdb AC Hom 0.0 1092.0 .
HelixMTdb AF Hom 0.0 0.005571912 .
HelixMTdb AC Het 2.0 29.0 .
HelixMTdb AF Het 1.0204967e-05 0.00014797202 .
HelixMTdb mean ARF 0.45467 0.30146 .
HelixMTdb max ARF 0.48077 0.74809 .
ToMMo 54KJPN AC 3 103 .
ToMMo 54KJPN AF 5.5e-05 0.001897 .
ToMMo 54KJPN AN 54302 54302 .
COSMIC 90 . . .
dbSNP 156 id rs200809063 rs200809063 .
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