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3890 (G > A)

General info

Mitimpact ID
MI.11964
Chr
chrM
Start
3890
Ref
G
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
584
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
CGA/CAA
AA pos
195
AA ref
R
AA alt
Q
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3890G>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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Powered by MitoWheel

Conservation

PhyloP 100v
3.884 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
0.996 Conservation Score
PhastCons 470way
0.05 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
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
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
Neutral 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
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
.

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
155881
Clinvar ALLELEID
165630
Clinvar CLNDISDB
Medgen:cn169374;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

mondo:mondo:0044970, medgen:c0751651, orphanet:68380
Clinvar CLNDN
Not specified;

leigh syndrome;

mitochondrial disease
Clinvar CLNSIG
Likely pathogenic
MITOMAP Allele
3890G>A
MITOMAP Disease Clinical info
Progressive encephalomyopathy / leigh syndrome / optic atrophy
MITOMAP Disease Status
Cfrm [lp]
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
27798429 34390870 29987491 23847141 30095618 18504678 23246842 29253894
MITOMAP Variant Class
disease
Gnomad AN
56433
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
rs587776434

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
.

3890 (G > C)

General info

Mitimpact ID
MI.11965
Chr
chrM
Start
3890
Ref
G
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
584
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
CGA/CCA
AA pos
195
AA ref
R
AA alt
P
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3890G>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
3.884 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
0.996 Conservation Score
PhastCons 470way
0.05 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
Neutral 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
Pathogenic 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
3890G>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
.

3890 (G > T)

General info

Mitimpact ID
MI.11966
Chr
chrM
Start
3890
Ref
G
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
584
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
CGA/CTA
AA pos
195
AA ref
R
AA alt
L
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3890G>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
3.884 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
0.996 Conservation Score
PhastCons 470way
0.05 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
Neutral 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
Pathogenic 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
Deleterious 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
3890G>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
.
~ 3890 (G/A) 3890 (G/C) 3890 (G/T)
~ 3890 (CGA/CAA) 3890 (CGA/CCA) 3890 (CGA/CTA)
MitImpact id MI.11964 MI.11965 MI.11966
Chr chrM chrM chrM
Start 3890 3890 3890
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 584 584 584
Gene start 3307 3307 3307
Gene end 4262 4262 4262
Gene strand + + +
Codon substitution CGA/CAA CGA/CCA CGA/CTA
AA position 195 195 195
AA ref R R R
AA alt Q P L
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516000 516000 516000
HGVS NC_012920.1:g.3890G>A NC_012920.1:g.3890G>C NC_012920.1:g.3890G>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 3.884 3.884 3.884
PhyloP 470Way 0.602 0.602 0.602
PhastCons 100V 0.996 0.996 0.996
PhastCons 470Way 0.05 0.05 0.05
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0 1.0
SIFT neutral neutral neutral
SIFT score 0.49 0.31 0.99
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.0 0.001 0.006
VEST Neutral Pathogenic Pathogenic
VEST pvalue 0.17 0.02 0.04
VEST FDR 0.45 0.35 0.35
Mitoclass.1 damaging damaging damaging
SNPDryad Pathogenic Pathogenic Pathogenic
SNPDryad score 1.0 1.0 1.0
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 0.00265266 0.999805 0.999939
MutationTaster converted rankscore 0.22697 0.20292 0.19363
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE R195Q R195P R195L
fathmm Tolerated Tolerated Tolerated
fathmm score 1.65 1.61 1.63
fathmm converted rankscore 0.27650 0.28391 0.28002
AlphaMissense likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.8496 0.9926 0.9581
CADD Deleterious Deleterious Deleterious
CADD score 4.555087 4.301042 4.31195
CADD phred 24.4 24.0 24.0
PROVEAN Damaging Damaging Damaging
PROVEAN score -3.8 -6.66 -6.66
MutationAssessor high high high
MutationAssessor score 4.975 4.63 4.975
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.724 0.628 0.754
EFIN HD Damaging Damaging Damaging
EFIN HD score 0.096 0.056 0.09
MLC Deleterious Deleterious Deleterious
MLC score 0.93228318 0.93228318 0.93228318
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.73 0.71 0.72
APOGEE2 Pathogenic Likely-pathogenic Likely-pathogenic
APOGEE2 score 0.930881313582521 0.858072953352285 0.840449308382027
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 1.0
Condel neutral neutral deleterious
Condel score 0.25 0.16 0.5
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 2 2 2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.82 0.89 0.88
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.480654 0.497571 0.360861
DEOGEN2 converted rankscore 0.80955 0.81938 0.72703
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.57 -3.57 -3.57
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.27 0.08 1.39
MutationAssessor transf high impact high impact high impact
MutationAssessor transf score 2.79 3.1 3.1
CHASM Neutral Neutral Neutral
CHASM pvalue 0.81 0.1 0.02
CHASM FDR 0.85 0.8 0.8
ClinVar id 155881.0 . .
ClinVar Allele id 165630.0 . .
ClinVar CLNDISDB MedGen:CN169374|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380 . .
ClinVar CLNDN not_specified|Leigh_syndrome|Mitochondrial_disease . .
ClinVar CLNSIG Likely_pathogenic . .
MITOMAP Disease Clinical info Progressive Encephalomyopathy / Leigh Syndrome / Optic Atrophy . .
MITOMAP Disease Status Cfrm [LP] . .
MITOMAP Disease Hom/Het -/+ ./. ./.
MITOMAP General GenBank Freq 0.0016% . .
MITOMAP General GenBank Seqs 1 . .
MITOMAP General Curated refs 27798429;34390870;29987491;23847141;30095618;18504678;23246842;29253894 . .
MITOMAP Variant Class disease . .
gnomAD 3.1 AN 56433.0 . .
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 rs587776434 . .
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