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10084 (T > C)

General info

Mitimpact ID
MI.15016
Chr
chrM
Start
10084
Ref
T
Alt
C
Gene symbol
MT-ND3 Extended gene annotation
Gene position
26
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
ATC/ACC
AA pos
9
AA ref
I
AA alt
T
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10084T>C
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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Conservation

PhyloP 100v
-0.638 Conservation Score
PhyloP 470way
-0.466 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.003 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
Deleterious 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
235627
Clinvar ALLELEID
237308
Clinvar CLNDISDB
Medgen:cn517202;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Not provided;

leigh syndrome
Clinvar CLNSIG
Benign/likely benign
MITOMAP Allele
10084T>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.9029%
MITOMAP General GenBank Seqs
552
MITOMAP General GenBank Curated refs
11406419 19370763 21978175 22110754 11349229 18545700 15465027 29208909 22561905 11938495 19026397 19151382 16404693 16714301 12802679 16773565 28387361 19167085 21041797 10205264 20067846
MITOMAP Variant Class
polymorphism
Gnomad AN
56418
Gnomad AC hom
292
Gnomad AF hom
0.0051756
Gnomad AC het
4
Gnomad AF het
7.08e-05
Gnomad filter
Pass
HelixMTdb AC hom
1139
HelixMTdb AF hom
0.0058117
HelixMTdb AC het
13
HelixMTdb AF het
6.63e-05
HelixMTdb mean ARF
0.6093499
HelixMTdb max ARF
0.90909
ToMMo JPN54K AC
540
ToMMo JPN54K AF
0.009944
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs41487950

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
.

10084 (T > A)

General info

Mitimpact ID
MI.15015
Chr
chrM
Start
10084
Ref
T
Alt
A
Gene symbol
MT-ND3 Extended gene annotation
Gene position
26
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
ATC/AAC
AA pos
9
AA ref
I
AA alt
N
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10084T>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
-0.638 Conservation Score
PhyloP 470way
-0.466 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.003 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
Neutral 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
High 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
Deleterious Score and details of the meta-predictor
COVEC WMV
Deleterious 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
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
10084T>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
.

10084 (T > G)

General info

Mitimpact ID
MI.15014
Chr
chrM
Start
10084
Ref
T
Alt
G
Gene symbol
MT-ND3 Extended gene annotation
Gene position
26
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
ATC/AGC
AA pos
9
AA ref
I
AA alt
S
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10084T>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
-0.638 Conservation Score
PhyloP 470way
-0.466 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.003 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
Neutral Score and details of the predictor
MitoClass 1
Damaging 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
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
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
10084T>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
.
~ 10084 (T/C) 10084 (T/A) 10084 (T/G)
~ 10084 (ATC/ACC) 10084 (ATC/AAC) 10084 (ATC/AGC)
MitImpact id MI.15016 MI.15015 MI.15014
Chr chrM chrM chrM
Start 10084 10084 10084
Ref T T T
Alt C A G
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 26 26 26
Gene start 10059 10059 10059
Gene end 10404 10404 10404
Gene strand + + +
Codon substitution ATC/ACC ATC/AAC ATC/AGC
AA position 9 9 9
AA ref I I I
AA alt T N S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516002 516002 516002
HGVS NC_012920.1:g.10084T>C NC_012920.1:g.10084T>A NC_012920.1:g.10084T>G
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 -0.638 -0.638 -0.638
PhyloP 470Way -0.466 -0.466 -0.466
PhastCons 100V 0 0 0
PhastCons 470Way 0.003 0.003 0.003
PolyPhen2 benign benign benign
PolyPhen2 score 0.0 0.01 0.01
SIFT neutral deleterious neutral
SIFT score 0.35 0.03 0.21
SIFT4G Tolerated Damaging Damaging
SIFT4G score 0.336 0.0 0.001
VEST Neutral Neutral Neutral
VEST pvalue 0.15 0.1 0.07
VEST FDR 0.4 0.4 0.35
Mitoclass.1 neutral damaging damaging
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.12 0.53 0.47
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 I9T I9N I9S
fathmm Tolerated Tolerated Tolerated
fathmm score 1.75 1.69 1.73
fathmm converted rankscore 0.26152 0.27032 0.26445
AlphaMissense likely_benign ambiguous likely_benign
AlphaMissense score 0.1699 0.3444 0.2652
CADD Neutral Neutral Neutral
CADD score -0.283767 2.401936 2.111229
CADD phred 0.723 18.83 16.93
PROVEAN Tolerated Damaging Damaging
PROVEAN score -0.96 -3.74 -2.78
MutationAssessor low high medium
MutationAssessor score 1.055 4.0 2.68
EFIN SP Neutral Damaging Neutral
EFIN SP score 0.92 0.6 0.652
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.978 0.356 0.378
MLC Deleterious Deleterious Deleterious
MLC score 0.53117267 0.53117267 0.53117267
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.37 0.34 0.35
APOGEE2 Benign VUS VUS
APOGEE2 score 0.0519239128185471 0.49698660166635 0.439621396827079
CAROL neutral neutral neutral
CAROL score 0.65 0.97 0.79
Condel deleterious deleterious deleterious
Condel score 0.68 0.51 0.6
COVEC WMV neutral deleterious neutral
COVEC WMV score -6 2 -3
MtoolBox neutral neutral neutral
MtoolBox DS 0.1 0.2 0.16
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.036692 0.286491 0.096765
DEOGEN2 converted rankscore 0.24197 0.65928 0.39890
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score 1.99 1.09 1.09
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.04 -0.65 -0.13
MutationAssessor transf medium impact high impact medium impact
MutationAssessor transf score 0.08 2.2 1.3
CHASM Neutral Neutral Neutral
CHASM pvalue 0.31 0.3 0.26
CHASM FDR 0.8 0.8 0.8
ClinVar id 235627.0 . .
ClinVar Allele id 237308.0 . .
ClinVar CLNDISDB MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN not_provided|Leigh_syndrome . .
ClinVar CLNSIG Benign/Likely_benign . .
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 0.9029% . .
MITOMAP General GenBank Seqs 552 . .
MITOMAP General Curated refs 11406419;19370763;21978175;22110754;11349229;18545700;15465027;29208909;22561905;11938495;19026397;19151382;16404693;16714301;12802679;16773565;28387361;19167085;21041797;10205264;20067846 . .
MITOMAP Variant Class polymorphism . .
gnomAD 3.1 AN 56418.0 . .
gnomAD 3.1 AC Homo 292.0 . .
gnomAD 3.1 AF Hom 0.00517565 . .
gnomAD 3.1 AC Het 4.0 . .
gnomAD 3.1 AF Het 7.08994e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 1139.0 . .
HelixMTdb AF Hom 0.0058117285 . .
HelixMTdb AC Het 13.0 . .
HelixMTdb AF Het 6.6332286e-05 . .
HelixMTdb mean ARF 0.60935 . .
HelixMTdb max ARF 0.90909 . .
ToMMo 54KJPN AC 540 . .
ToMMo 54KJPN AF 0.009944 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs41487950 . .
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