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10159 (C > A)

General info

Mitimpact ID
MI.15177
Chr
chrM
Start
10159
Ref
C
Alt
A
Gene symbol
MT-ND3 Extended gene annotation
Gene position
101
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/TAC
AA pos
34
AA ref
S
AA alt
Y
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10159C>A
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
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Powered by MitoWheel

Conservation

PhyloP 100v
0.639 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.75 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
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
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
Neutral 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
693268
Clinvar ALLELEID
680158
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
10159C>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0049%
MITOMAP General GenBank Seqs
3
MITOMAP General GenBank Curated refs
23463613
MITOMAP Variant Class
polymorphism
Gnomad AN
56434
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
5
HelixMTdb AF hom
2.55e-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
rs1603222701

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
.

10159 (C > G)

General info

Mitimpact ID
MI.15176
Chr
chrM
Start
10159
Ref
C
Alt
G
Gene symbol
MT-ND3 Extended gene annotation
Gene position
101
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/TGC
AA pos
34
AA ref
S
AA alt
C
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10159C>G
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.639 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.75 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
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
Deleterious 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
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
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
10159C>G
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
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
.

10159 (C > T)

General info

Mitimpact ID
MI.15175
Chr
chrM
Start
10159
Ref
C
Alt
T
Gene symbol
MT-ND3 Extended gene annotation
Gene position
101
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/TTC
AA pos
34
AA ref
S
AA alt
F
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10159C>T
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.639 Conservation Score
PhyloP 470way
0.65 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.75 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
Deleterious 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
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
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
10159C>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0115%
MITOMAP General GenBank Seqs
7
MITOMAP General GenBank Curated refs
22110754 19026397
MITOMAP Variant Class
polymorphism
Gnomad AN
56430
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
2
HelixMTdb AF hom
1.02e-05
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.13846
HelixMTdb max ARF
0.13846
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
.
~ 10159 (C/A) 10159 (C/G) 10159 (C/T)
~ 10159 (TCC/TAC) 10159 (TCC/TGC) 10159 (TCC/TTC)
MitImpact id MI.15177 MI.15176 MI.15175
Chr chrM chrM chrM
Start 10159 10159 10159
Ref C C C
Alt A G T
Gene symbol MT-ND3 MT-ND3 MT-ND3
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3
Gene position 101 101 101
Gene start 10059 10059 10059
Gene end 10404 10404 10404
Gene strand + + +
Codon substitution TCC/TAC TCC/TGC TCC/TTC
AA position 34 34 34
AA ref S S S
AA alt Y C F
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516002 516002 516002
HGVS NC_012920.1:g.10159C>A NC_012920.1:g.10159C>G NC_012920.1:g.10159C>T
HGNC id 7458 7458 7458
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198840 ENSG00000198840 ENSG00000198840
Ensembl transcript id ENST00000361227 ENST00000361227 ENST00000361227
Ensembl protein id ENSP00000355206 ENSP00000355206 ENSP00000355206
Uniprot id P03897 P03897 P03897
Uniprot name NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN
Ncbi gene id 4537 4537 4537
Ncbi protein id YP_003024033.1 YP_003024033.1 YP_003024033.1
PhyloP 100V 0.639 0.639 0.639
PhyloP 470Way 0.65 0.65 0.65
PhastCons 100V 0 0 0
PhastCons 470Way 0.75 0.75 0.75
PolyPhen2 possibly_damaging possibly_damaging possibly_damaging
PolyPhen2 score 0.66 0.73 0.47
SIFT neutral deleterious neutral
SIFT score 0.1 0.04 0.07
SIFT4G Tolerated Damaging Tolerated
SIFT4G score 0.136 0.013 0.061
VEST Neutral Neutral Neutral
VEST pvalue 0.1 0.12 0.14
VEST FDR 0.4 0.4 0.4
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.7 0.58 0.73
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1 1 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE S34Y S34C S34F
fathmm Tolerated Tolerated Tolerated
fathmm score 0.89 0.86 0.89
fathmm converted rankscore 0.45636 0.46777 0.45636
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.2201 0.2275 0.2938
CADD Neutral Deleterious Deleterious
CADD score 2.454105 3.242792 2.629306
CADD phred 19.17 22.8 20.4
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score -1.44 -1.3 -1.61
MutationAssessor low low low
MutationAssessor score 1.345 1.835 1.53
EFIN SP Neutral Damaging Damaging
EFIN SP score 0.794 0.548 0.516
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.768 0.41 0.582
MLC Deleterious Deleterious Deleterious
MLC score 0.52649526 0.52649526 0.52649526
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.37 0.42 0.45
APOGEE2 Likely-benign VUS- VUS-
APOGEE2 score 0.13750379893822 0.356683796932937 0.269501657230877
CAROL neutral neutral neutral
CAROL score 0.91 0.97 0.92
Condel neutral neutral neutral
Condel score 0.22 0.16 0.3
COVEC WMV neutral deleterious neutral
COVEC WMV score -3 4 -3
MtoolBox deleterious deleterious neutral
MtoolBox DS 0.48 0.49 0.4
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.233831 0.291657 0.279969
DEOGEN2 converted rankscore 0.60072 0.66441 0.65266
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact low impact medium impact
PolyPhen2 transf score -0.98 -1.11 -0.67
SIFT_transf medium impact medium impact medium impact
SIFT transf score -0.34 -0.58 -0.43
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 0.04 1.38 0.6
CHASM Neutral Neutral Neutral
CHASM pvalue 0.12 0.17 0.07
CHASM FDR 0.8 0.8 0.8
ClinVar id 693268.0 . .
ClinVar Allele id 680158.0 . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN Leigh_syndrome . .
ClinVar CLNSIG Uncertain_significance . .
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 0.0049% 0.0016% 0.0115%
MITOMAP General GenBank Seqs 3 1 7
MITOMAP General Curated refs 23463613 . 22110754;19026397
MITOMAP Variant Class polymorphism polymorphism polymorphism
gnomAD 3.1 AN 56434.0 . 56430.0
gnomAD 3.1 AC Homo 1.0 . 3.0
gnomAD 3.1 AF Hom 1.77198e-05 . 5.31632e-05
gnomAD 3.1 AC Het 0.0 . 0.0
gnomAD 3.1 AF Het 0.0 . 0.0
gnomAD 3.1 filter PASS . PASS
HelixMTdb AC Hom 5.0 . 2.0
HelixMTdb AF Hom 2.5512418e-05 . 1.0204967e-05
HelixMTdb AC Het 0.0 . 1.0
HelixMTdb AF Het 0.0 . 5.1024836e-06
HelixMTdb mean ARF . . 0.13846
HelixMTdb max ARF . . 0.13846
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs1603222701 . .
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