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5244 (G > A)

General info

Mitimpact ID
MI.14380
Chr
chrM
Start
5244
Ref
G
Alt
A
Gene symbol
MT-ND2 Extended gene annotation
Gene position
775
Gene start
4470
Gene end
5511
Gene strand
+
Codon substitution
GGC/AGC
AA pos
259
AA ref
G
AA alt
S
Functional effect
missense
OMIM ID
516001
HGVS
NC_012920.1:g.5244G>A
HGNC ID
7456
RC complex
I
Ensembl gene ID
ENSG00000198763
Ensembl protein ID
ENSP00000355046
Ensembl transcript ID
ENST00000361453
Uniprot ID
P03891
Uniprot name
NU2M_HUMAN
Ncbi gene ID
4536
Ncbi protein ID
YP_003024027.1
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Powered by MitoWheel

Conservation

PhyloP 100v
5.445 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
1 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
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
Disease automatic 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
Damaging Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Pathogenic 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
Deleterious 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
Disease Score and details of the meta-predictor

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
9717
Clinvar ALLELEID
24756
Clinvar CLNDISDB
Human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104
Clinvar CLNDN
Leber optic atrophy
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
5244G>A
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported [vus]
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
7760326 1634041 15972314 7770132 20301353 7599218 21457906 8680405
MITOMAP Variant Class
disease
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
rs199476115

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
.

5244 (G > C)

General info

Mitimpact ID
MI.14379
Chr
chrM
Start
5244
Ref
G
Alt
C
Gene symbol
MT-ND2 Extended gene annotation
Gene position
775
Gene start
4470
Gene end
5511
Gene strand
+
Codon substitution
GGC/CGC
AA pos
259
AA ref
G
AA alt
R
Functional effect
missense
OMIM ID
516001
HGVS
NC_012920.1:g.5244G>C
HGNC ID
7456
RC complex
I
Ensembl gene ID
ENSG00000198763
Ensembl protein ID
ENSP00000355046
Ensembl transcript ID
ENST00000361453
Uniprot ID
P03891
Uniprot name
NU2M_HUMAN
Ncbi gene ID
4536
Ncbi protein ID
YP_003024027.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
5.445 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
1 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
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
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
Damaging Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Likely-pathogenic 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
Deleterious 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
High 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
5244G>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
.

5244 (G > T)

General info

Mitimpact ID
MI.14378
Chr
chrM
Start
5244
Ref
G
Alt
T
Gene symbol
MT-ND2 Extended gene annotation
Gene position
775
Gene start
4470
Gene end
5511
Gene strand
+
Codon substitution
GGC/TGC
AA pos
259
AA ref
G
AA alt
C
Functional effect
missense
OMIM ID
516001
HGVS
NC_012920.1:g.5244G>T
HGNC ID
7456
RC complex
I
Ensembl gene ID
ENSG00000198763
Ensembl protein ID
ENSP00000355046
Ensembl transcript ID
ENST00000361453
Uniprot ID
P03891
Uniprot name
NU2M_HUMAN
Ncbi gene ID
4536
Ncbi protein ID
YP_003024027.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
5.445 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
1 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
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
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
Damaging Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral Score and details of the meta-predictor
APOGEE2
Likely-pathogenic 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
Deleterious 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
High 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
5244G>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
.
~ 5244 (G/A) 5244 (G/C) 5244 (G/T)
~ 5244 (GGC/AGC) 5244 (GGC/CGC) 5244 (GGC/TGC)
MitImpact id MI.14380 MI.14379 MI.14378
Chr chrM chrM chrM
Start 5244 5244 5244
Ref G G G
Alt A C T
Gene symbol MT-ND2 MT-ND2 MT-ND2
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2
Gene position 775 775 775
Gene start 4470 4470 4470
Gene end 5511 5511 5511
Gene strand + + +
Codon substitution GGC/AGC GGC/CGC GGC/TGC
AA position 259 259 259
AA ref G G G
AA alt S R C
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516001 516001 516001
HGVS NC_012920.1:g.5244G>A NC_012920.1:g.5244G>C NC_012920.1:g.5244G>T
HGNC id 7456 7456 7456
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198763 ENSG00000198763 ENSG00000198763
Ensembl transcript id ENST00000361453 ENST00000361453 ENST00000361453
Ensembl protein id ENSP00000355046 ENSP00000355046 ENSP00000355046
Uniprot id P03891 P03891 P03891
Uniprot name NU2M_HUMAN NU2M_HUMAN NU2M_HUMAN
Ncbi gene id 4536 4536 4536
Ncbi protein id YP_003024027.1 YP_003024027.1 YP_003024027.1
PhyloP 100V 5.445 5.445 5.445
PhyloP 470Way 0.602 0.602 0.602
PhastCons 100V 1 1 1
PhastCons 470Way 0.003 0.003 0.003
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0 1.0
SIFT neutral neutral neutral
SIFT score 0.4 0.35 0.18
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.0 0.0 0.0
VEST Pathogenic Pathogenic Pathogenic
VEST pvalue 0.05 0.03 0.03
VEST FDR 0.35 0.35 0.35
Mitoclass.1 damaging damaging damaging
SNPDryad Pathogenic Pathogenic Pathogenic
SNPDryad score 0.98 1.0 0.96
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 1.35488e-06 0.999999 0.999999
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE G259S G259R G259C
fathmm Tolerated Tolerated Tolerated
fathmm score 4.31 4.24 4.21
fathmm converted rankscore 0.02412 0.02590 0.02664
AlphaMissense likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.9241 0.9957 0.9846
CADD Deleterious Deleterious Deleterious
CADD score 4.229313 4.01898 4.207468
CADD phred 23.9 23.6 23.9
PROVEAN Damaging Damaging Damaging
PROVEAN score -5.75 -7.66 -8.62
MutationAssessor high high high
MutationAssessor score 4.64 5.19 5.19
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.266 0.512 0.436
EFIN HD Damaging Damaging Damaging
EFIN HD score 0.018 0.018 0.016
MLC Deleterious Deleterious Deleterious
MLC score 0.94043093 0.94043093 0.94043093
PANTHER score 0.541 . .
PhD-SNP score 0.909 . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.77 0.37 0.43
APOGEE2 Pathogenic Likely-pathogenic Likely-pathogenic
APOGEE2 score 0.94623846483892 0.841364059778341 0.889971658472212
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 1.0
Condel neutral neutral neutral
Condel score 0.2 0.18 0.09
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 2 2 2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.83 0.9 0.88
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.175001 0.398026 0.38207
DEOGEN2 converted rankscore 0.52444 0.75623 0.74424
Meta-SNP Disease . .
Meta-SNP score 0.712 . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.54 -3.54 -3.54
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.11 0.06 -0.16
MutationAssessor transf medium impact high impact high impact
MutationAssessor transf score 1.95 2.23 2.23
CHASM Neutral Neutral Neutral
CHASM pvalue 0.7 0.66 0.24
CHASM FDR 0.85 0.8 0.8
ClinVar id 9717.0 . .
ClinVar Allele id 24756.0 . .
ClinVar CLNDISDB Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 . .
ClinVar CLNDN Leber_optic_atrophy . .
ClinVar CLNSIG Pathogenic . .
MITOMAP Disease Clinical info LHON . .
MITOMAP Disease Status Reported [VUS] . .
MITOMAP Disease Hom/Het -/+ ./. ./.
MITOMAP General GenBank Freq 0.0% . .
MITOMAP General GenBank Seqs 0 . .
MITOMAP General Curated refs 7760326;1634041;15972314;7770132;20301353;7599218;21457906;8680405 . .
MITOMAP Variant Class disease . .
gnomAD 3.1 AN 56432.0 . .
gnomAD 3.1 AC Homo 0.0 . .
gnomAD 3.1 AF Hom 0.0 . .
gnomAD 3.1 AC Het 0.0 . .
gnomAD 3.1 AF Het 0.0 . .
gnomAD 3.1 filter npg . .
HelixMTdb AC Hom . . .
HelixMTdb AF Hom . . .
HelixMTdb AC Het . . .
HelixMTdb AF Het . . .
HelixMTdb mean ARF . . .
HelixMTdb max ARF . . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs199476115 . .
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