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11984 (T > C)

General info

Mitimpact ID
MI.18890
Chr
chrM
Start
11984
Ref
T
Alt
C
Gene symbol
MT-ND4 Extended gene annotation
Gene position
1225
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
TAC/CAC
AA pos
409
AA ref
Y
AA alt
H
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11984T>C
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
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Powered by MitoWheel

Conservation

PhyloP 100v
-0.018 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.611 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
Damaging 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
Deleterious 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
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
155888
Clinvar ALLELEID
165637
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
11984T>C
MITOMAP Disease Clinical info
Leigh syndrome
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.1031%
MITOMAP General GenBank Seqs
63
MITOMAP General GenBank Curated refs
17022785 19370763 19043581
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56431
Gnomad AC hom
55
Gnomad AF hom
0.0009746
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
88
HelixMTdb AF hom
0.000449
HelixMTdb AC het
3
HelixMTdb AF het
1.53e-05
HelixMTdb mean ARF
0.21577
HelixMTdb max ARF
0.33803
ToMMo JPN54K AC
67
ToMMo JPN54K AF
0.001234
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs200911567

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
.

11984 (T > A)

General info

Mitimpact ID
MI.18891
Chr
chrM
Start
11984
Ref
T
Alt
A
Gene symbol
MT-ND4 Extended gene annotation
Gene position
1225
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
TAC/AAC
AA pos
409
AA ref
Y
AA alt
N
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11984T>A
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.018 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.611 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Deleterious 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
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 benign Score and details of the predictor
CADD
Deleterious 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
Deleterious 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
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
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
11984T>A
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
.

11984 (T > G)

General info

Mitimpact ID
MI.18889
Chr
chrM
Start
11984
Ref
T
Alt
G
Gene symbol
MT-ND4 Extended gene annotation
Gene position
1225
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
TAC/GAC
AA pos
409
AA ref
Y
AA alt
D
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11984T>G
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.018 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.611 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Deleterious 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 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
Damaging Score and details of the predictor
Mutation Assessor
High 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
Deleterious 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
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
Medium impact Score and details of the cancer-specific predictor
SIFT transf
Low 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
11984T>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
.
~ 11984 (T/C) 11984 (T/A) 11984 (T/G)
~ 11984 (TAC/CAC) 11984 (TAC/AAC) 11984 (TAC/GAC)
MitImpact id MI.18890 MI.18891 MI.18889
Chr chrM chrM chrM
Start 11984 11984 11984
Ref T T T
Alt C A G
Gene symbol MT-ND4 MT-ND4 MT-ND4
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4
Gene position 1225 1225 1225
Gene start 10760 10760 10760
Gene end 12137 12137 12137
Gene strand + + +
Codon substitution TAC/CAC TAC/AAC TAC/GAC
AA position 409 409 409
AA ref Y Y Y
AA alt H N D
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516003 516003 516003
HGVS NC_012920.1:g.11984T>C NC_012920.1:g.11984T>A NC_012920.1:g.11984T>G
HGNC id 7459 7459 7459
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198886 ENSG00000198886 ENSG00000198886
Ensembl transcript id ENST00000361381 ENST00000361381 ENST00000361381
Ensembl protein id ENSP00000354961 ENSP00000354961 ENSP00000354961
Uniprot id P03905 P03905 P03905
Uniprot name NU4M_HUMAN NU4M_HUMAN NU4M_HUMAN
Ncbi gene id 4538 4538 4538
Ncbi protein id YP_003024035.1 YP_003024035.1 YP_003024035.1
PhyloP 100V -0.018 -0.018 -0.018
PhyloP 470Way 0.666 0.666 0.666
PhastCons 100V 0 0 0
PhastCons 470Way 0.611 0.611 0.611
PolyPhen2 benign possibly_damaging possibly_damaging
PolyPhen2 score 0.01 0.44 0.6
SIFT neutral deleterious deleterious
SIFT score 0.09 0.02 0.0
SIFT4G Tolerated Damaging Damaging
SIFT4G score 0.245 0.013 0.003
VEST Neutral Neutral Pathogenic
VEST pvalue 0.19 0.07 0.03
VEST FDR 0.45 0.35 0.35
Mitoclass.1 neutral damaging damaging
SNPDryad Neutral Pathogenic Pathogenic
SNPDryad score 0.42 0.92 1.0
MutationTaster Disease automatic Polymorphism Disease
MutationTaster score 8.62866e-08 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.81001
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE Y409H Y409N Y409D
fathmm Tolerated Tolerated Tolerated
fathmm score 2.54 2.56 2.54
fathmm converted rankscore 0.13916 0.13673 0.13916
AlphaMissense likely_benign likely_benign ambiguous
AlphaMissense score 0.1322 0.22 0.5343
CADD Neutral Deleterious Deleterious
CADD score 2.310205 4.058638 3.999341
CADD phred 18.23 23.7 23.6
PROVEAN Damaging Damaging Damaging
PROVEAN score -2.69 -6.79 -7.88
MutationAssessor neutral medium high
MutationAssessor score 0.51 2.435 3.59
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.754 0.698 0.702
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.834 0.648 0.406
MLC Deleterious Deleterious Deleterious
MLC score 0.54499366 0.54499366 0.54499366
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.43 0.42 0.46
APOGEE2 Likely-benign VUS VUS+
APOGEE2 score 0.154682915713149 0.422100549136351 0.626256532869418
CAROL neutral neutral deleterious
CAROL score 0.91 0.98 1.0
Condel deleterious neutral neutral
Condel score 0.54 0.29 0.2
COVEC WMV neutral deleterious deleterious
COVEC WMV score -6 4 5
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.76 0.76 0.79
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.116026 0.133926 0.247871
DEOGEN2 converted rankscore 0.43506 0.46488 0.61758
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score 1.16 -0.62 -0.88
SIFT_transf medium impact medium impact low impact
SIFT transf score -0.36 -0.75 -1.48
MutationAssessor transf low impact medium impact high impact
MutationAssessor transf score -1.03 1.71 2.4
CHASM Neutral Neutral Neutral
CHASM pvalue 0.17 0.2 0.14
CHASM FDR 0.8 0.8 0.8
ClinVar id 155888.0 . .
ClinVar Allele id 165637.0 . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info Leigh Syndrome . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.1031% . .
MITOMAP General GenBank Seqs 63 . .
MITOMAP General Curated refs 17022785;19370763;19043581 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56431.0 . .
gnomAD 3.1 AC Homo 55.0 . .
gnomAD 3.1 AF Hom 0.000974642 . .
gnomAD 3.1 AC Het 1.0 . .
gnomAD 3.1 AF Het 1.77208e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 88.0 . .
HelixMTdb AF Hom 0.00044901852 . .
HelixMTdb AC Het 3.0 . .
HelixMTdb AF Het 1.530745e-05 . .
HelixMTdb mean ARF 0.21577 . .
HelixMTdb max ARF 0.33803 . .
ToMMo 54KJPN AC 67 . .
ToMMo 54KJPN AF 0.001234 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs200911567 . .
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