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4048 (G > A)

General info

Mitimpact ID
MI.12306
Chr
chrM
Start
4048
Ref
G
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
742
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GAC/AAC
AA pos
248
AA ref
D
AA alt
N
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4048G>A
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
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Conservation

PhyloP 100v
-0.796 Conservation Score
PhyloP 470way
-0.326 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.0 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
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
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
692416
Clinvar ALLELEID
680952
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
4048G>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
1.5376%
MITOMAP General GenBank Seqs
940
MITOMAP General GenBank Curated refs
21281460 21741027 22110754 19022198 18545700 19818876 15126279 11507041 20045353 17434142 21099167 24467713 23304069 19026397 12406974 19527690 16714301 16895436 24667788 19167085 17257906 12436196 21041797 18639500 31798871 17259400 31797714 17072496 20067846 22487888
MITOMAP Variant Class
polymorphism
Gnomad AN
56404
Gnomad AC hom
329
Gnomad AF hom
0.0058329
Gnomad AC het
10
Gnomad AF het
0.0001772
Gnomad filter
Pass
HelixMTdb AC hom
677
HelixMTdb AF hom
0.0034543
HelixMTdb AC het
45
HelixMTdb AF het
0.0002296
HelixMTdb mean ARF
0.65295
HelixMTdb max ARF
0.92063
ToMMo JPN54K AC
2911
ToMMo JPN54K AF
0.053608
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs201629275

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
.

4048 (G > C)

General info

Mitimpact ID
MI.12307
Chr
chrM
Start
4048
Ref
G
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
742
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GAC/CAC
AA pos
248
AA ref
D
AA alt
H
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4048G>C
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
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Powered by MitoWheel

Conservation

PhyloP 100v
-0.796 Conservation Score
PhyloP 470way
-0.326 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.0 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
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
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
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
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
4048G>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
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
2
HelixMTdb AF het
1.02e-05
HelixMTdb mean ARF
0.18908
HelixMTdb max ARF
0.21053
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
.

4048 (G > T)

General info

Mitimpact ID
MI.12305
Chr
chrM
Start
4048
Ref
G
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
742
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GAC/TAC
AA pos
248
AA ref
D
AA alt
Y
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4048G>T
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.796 Conservation Score
PhyloP 470way
-0.326 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.0 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
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
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
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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
4048G>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
.
~ 4048 (G/A) 4048 (G/C) 4048 (G/T)
~ 4048 (GAC/AAC) 4048 (GAC/CAC) 4048 (GAC/TAC)
MitImpact id MI.12306 MI.12307 MI.12305
Chr chrM chrM chrM
Start 4048 4048 4048
Ref G G G
Alt A C T
Gene symbol MT-ND1 MT-ND1 MT-ND1
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1
Gene position 742 742 742
Gene start 3307 3307 3307
Gene end 4262 4262 4262
Gene strand + + +
Codon substitution GAC/AAC GAC/CAC GAC/TAC
AA position 248 248 248
AA ref D D D
AA alt N H Y
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516000 516000 516000
HGVS NC_012920.1:g.4048G>A NC_012920.1:g.4048G>C NC_012920.1:g.4048G>T
HGNC id 7455 7455 7455
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198888 ENSG00000198888 ENSG00000198888
Ensembl transcript id ENST00000361390 ENST00000361390 ENST00000361390
Ensembl protein id ENSP00000354687 ENSP00000354687 ENSP00000354687
Uniprot id P03886 P03886 P03886
Uniprot name NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN
Ncbi gene id 4535 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1 YP_003024026.1
PhyloP 100V -0.796 -0.796 -0.796
PhyloP 470Way -0.326 -0.326 -0.326
PhastCons 100V 0 0 0
PhastCons 470Way 0.0 0.0 0.0
PolyPhen2 benign benign benign
PolyPhen2 score 0.0 0.26 0.23
SIFT neutral neutral neutral
SIFT score 0.37 0.51 0.98
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 0.991 0.537 1.0
VEST Neutral Neutral Neutral
VEST pvalue 0.38 0.12 0.08
VEST FDR 0.5 0.4 0.35
Mitoclass.1 neutral damaging neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.02 0.0 0.04
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1.0 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE D248N D248H D248Y
fathmm Tolerated Tolerated Tolerated
fathmm score 2.81 2.76 2.75
fathmm converted rankscore 0.10975 0.11515 0.11622
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.0905 0.1839 0.1963
CADD Neutral Neutral Neutral
CADD score 0.259303 -0.008611 -0.419914
CADD phred 5.291 2.504 0.346
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score 1.51 0.36 -0.16
MutationAssessor neutral neutral neutral
MutationAssessor score -1.355 0.425 -0.93
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.834 0.796 0.878
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.938 0.782 0.874
MLC Deleterious Deleterious Deleterious
MLC score 0.62091858 0.62091858 0.62091858
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.34 0.31 0.25
APOGEE2 Benign Likely-benign Likely-benign
APOGEE2 score 0.017936055343837 0.139251548607529 0.0634609585936633
CAROL neutral neutral neutral
CAROL score 0.63 0.39 0.18
Condel deleterious deleterious deleterious
Condel score 0.69 0.63 0.88
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -6
MtoolBox neutral neutral neutral
MtoolBox DS 0.07 0.18 0.32
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.005364 0.011572 0.00607
DEOGEN2 converted rankscore 0.04811 0.10309 0.05507
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf high impact medium impact medium impact
PolyPhen2 transf score 2.07 -0.32 -0.26
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.15 0.29 1.22
MutationAssessor transf low impact medium impact low impact
MutationAssessor transf score -2.17 -0.46 -1.03
CHASM Neutral Neutral Neutral
CHASM pvalue 0.62 0.32 0.14
CHASM FDR 0.8 0.8 0.8
ClinVar id 692416.0 . .
ClinVar Allele id 680952.0 . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 1.5376% 0.0% .
MITOMAP General GenBank Seqs 940 0 .
MITOMAP General Curated refs 21281460;21741027;22110754;19022198;18545700;19818876;15126279;11507041;20045353;17434142;21099167;24467713;23304069;19026397;12406974;19527690;16714301;16895436;24667788;19167085;17257906;12436196;21041797;18639500;31798871;17259400;31797714;17072496;20067846;22487888 . .
MITOMAP Variant Class polymorphism polymorphism .
gnomAD 3.1 AN 56404.0 . .
gnomAD 3.1 AC Homo 329.0 . .
gnomAD 3.1 AF Hom 0.00583292 . .
gnomAD 3.1 AC Het 10.0 . .
gnomAD 3.1 AF Het 0.000177292 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 677.0 0.0 .
HelixMTdb AF Hom 0.0034543811 0.0 .
HelixMTdb AC Het 45.0 2.0 .
HelixMTdb AF Het 0.00022961175 1.0204967e-05 .
HelixMTdb mean ARF 0.65295 0.18908 .
HelixMTdb max ARF 0.92063 0.21053 .
ToMMo 54KJPN AC 2911 . .
ToMMo 54KJPN AF 0.053608 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs201629275 . .
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