Logo MitImpact
Home Description Output legend Molecular Dynamics How to cite License

5302 (T > C)

General info

Mitimpact ID
MI.14512
Chr
chrM
Start
5302
Ref
T
Alt
C
Gene symbol
MT-ND2 Extended gene annotation
Gene position
833
Gene start
4470
Gene end
5511
Gene strand
+
Codon substitution
ATC/ACC
AA pos
278
AA ref
I
AA alt
T
Functional effect
missense
OMIM ID
516001
HGVS
NC_012920.1:g.5302T>C
HGNC ID
7456
RC complex
I
Ensembl gene ID
ENSG00000198763
Ensembl protein ID
ENSP00000355046
Ensembl transcript ID
ENST00000361453
Uniprot ID
P03891
Uniprot name
NU2M_HUMAN
Ncbi gene ID
4536
Ncbi protein ID
YP_003024027.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.257 Conservation Score
PhyloP 470way
0.458 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
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
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
Neutral 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
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
235811
Clinvar ALLELEID
237470
Clinvar CLNDISDB
Medgen:cn517202;

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

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
5302T>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0851%
MITOMAP General GenBank Seqs
52
MITOMAP General GenBank Curated refs
32094358 21281460 11938495 12840039 17496137
MITOMAP Variant Class
polymorphism
Gnomad AN
56415
Gnomad AC hom
52
Gnomad AF hom
0.0009217
Gnomad AC het
4
Gnomad AF het
7.09e-05
Gnomad filter
Pass
HelixMTdb AC hom
267
HelixMTdb AF hom
0.0013623
HelixMTdb AC het
11
HelixMTdb AF het
5.61e-05
HelixMTdb mean ARF
0.4111099
HelixMTdb max ARF
0.92248
ToMMo JPN54K AC
19
ToMMo JPN54K AF
0.00035
ToMMo JPN54K AN
54301
COSMIC 90
.
dbSNP 156
rs878853115

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
.

5302 (T > A)

General info

Mitimpact ID
MI.14510
Chr
chrM
Start
5302
Ref
T
Alt
A
Gene symbol
MT-ND2 Extended gene annotation
Gene position
833
Gene start
4470
Gene end
5511
Gene strand
+
Codon substitution
ATC/AAC
AA pos
278
AA ref
I
AA alt
N
Functional effect
missense
OMIM ID
516001
HGVS
NC_012920.1:g.5302T>A
HGNC ID
7456
RC complex
I
Ensembl gene ID
ENSG00000198763
Ensembl protein ID
ENSP00000355046
Ensembl transcript ID
ENST00000361453
Uniprot ID
P03891
Uniprot name
NU2M_HUMAN
Ncbi gene ID
4536
Ncbi protein ID
YP_003024027.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.257 Conservation Score
PhyloP 470way
0.458 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
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 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
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
Neutral 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
5302T>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
.

5302 (T > G)

General info

Mitimpact ID
MI.14511
Chr
chrM
Start
5302
Ref
T
Alt
G
Gene symbol
MT-ND2 Extended gene annotation
Gene position
833
Gene start
4470
Gene end
5511
Gene strand
+
Codon substitution
ATC/AGC
AA pos
278
AA ref
I
AA alt
S
Functional effect
missense
OMIM ID
516001
HGVS
NC_012920.1:g.5302T>G
HGNC ID
7456
RC complex
I
Ensembl gene ID
ENSG00000198763
Ensembl protein ID
ENSP00000355046
Ensembl transcript ID
ENST00000361453
Uniprot ID
P03891
Uniprot name
NU2M_HUMAN
Ncbi gene ID
4536
Ncbi protein ID
YP_003024027.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.257 Conservation Score
PhyloP 470way
0.458 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
Pathogenic 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 pathogenic Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging 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
Neutral 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
5302T>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
.
~ 5302 (T/C) 5302 (T/A) 5302 (T/G)
~ 5302 (ATC/ACC) 5302 (ATC/AAC) 5302 (ATC/AGC)
MitImpact id MI.14512 MI.14510 MI.14511
Chr chrM chrM chrM
Start 5302 5302 5302
Ref T T T
Alt C A G
Gene symbol MT-ND2 MT-ND2 MT-ND2
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2
Gene position 833 833 833
Gene start 4470 4470 4470
Gene end 5511 5511 5511
Gene strand + + +
Codon substitution ATC/ACC ATC/AAC ATC/AGC
AA position 278 278 278
AA ref I I I
AA alt T N S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516001 516001 516001
HGVS NC_012920.1:g.5302T>C NC_012920.1:g.5302T>A NC_012920.1:g.5302T>G
HGNC id 7456 7456 7456
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198763 ENSG00000198763 ENSG00000198763
Ensembl transcript id ENST00000361453 ENST00000361453 ENST00000361453
Ensembl protein id ENSP00000355046 ENSP00000355046 ENSP00000355046
Uniprot id P03891 P03891 P03891
Uniprot name NU2M_HUMAN NU2M_HUMAN NU2M_HUMAN
Ncbi gene id 4536 4536 4536
Ncbi protein id YP_003024027.1 YP_003024027.1 YP_003024027.1
PhyloP 100V 0.257 0.257 0.257
PhyloP 470Way 0.458 0.458 0.458
PhastCons 100V 0 0 0
PhastCons 470Way 0.003 0.003 0.003
PolyPhen2 benign benign benign
PolyPhen2 score 0.0 0.14 0.06
SIFT neutral neutral neutral
SIFT score 0.75 0.24 0.68
SIFT4G Tolerated Damaging Damaging
SIFT4G score 0.426 0.011 0.024
VEST Neutral Neutral Pathogenic
VEST pvalue 0.12 0.09 0.03
VEST FDR 0.4 0.35 0.35
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.06 0.77 0.4
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 I278T I278N I278S
fathmm Tolerated Tolerated Tolerated
fathmm score 4.64 4.59 4.62
fathmm converted rankscore 0.01799 0.01885 0.01834
AlphaMissense ambiguous likely_pathogenic likely_pathogenic
AlphaMissense score 0.4012 0.7265 0.6022
CADD Neutral Deleterious Neutral
CADD score 0.006074 2.614109 2.382222
CADD phred 2.644 20.3 18.7
PROVEAN Damaging Damaging Damaging
PROVEAN score -2.51 -4.2 -3.23
MutationAssessor neutral medium low
MutationAssessor score 0.39 2.26 1.505
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.99 0.886 0.876
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.958 0.454 0.742
MLC Neutral Neutral Neutral
MLC score 0.15154807 0.15154807 0.15154807
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.33 0.39 0.26
APOGEE2 Benign VUS- Likely-benign
APOGEE2 score 0.0475913558979478 0.331188639801388 0.210092053555236
CAROL neutral neutral neutral
CAROL score 0.24 0.72 0.24
Condel deleterious deleterious deleterious
Condel score 0.88 0.55 0.81
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -6
MtoolBox neutral neutral neutral
MtoolBox DS 0.09 0.26 0.17
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.065341 0.08356 0.069578
DEOGEN2 converted rankscore 0.32663 0.37083 0.33743
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score 1.95 -0.08 0.3
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.47 -0.07 0.39
MutationAssessor transf low impact medium impact medium impact
MutationAssessor transf score -1.3 0.42 -0.16
CHASM Neutral Neutral Neutral
CHASM pvalue 0.35 0.28 0.27
CHASM FDR 0.8 0.8 0.8
ClinVar id 235811.0 . .
ClinVar Allele id 237470.0 . .
ClinVar CLNDISDB MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN not_provided|Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 0.0851% . .
MITOMAP General GenBank Seqs 52 . .
MITOMAP General Curated refs 32094358;21281460;11938495;12840039;17496137 . .
MITOMAP Variant Class polymorphism . .
gnomAD 3.1 AN 56415.0 . .
gnomAD 3.1 AC Homo 52.0 . .
gnomAD 3.1 AF Hom 0.000921741 . .
gnomAD 3.1 AC Het 4.0 . .
gnomAD 3.1 AF Het 7.09031e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 267.0 . .
HelixMTdb AF Hom 0.0013623631 . .
HelixMTdb AC Het 11.0 . .
HelixMTdb AF Het 5.6127315e-05 . .
HelixMTdb mean ARF 0.41111 . .
HelixMTdb max ARF 0.92248 . .
ToMMo 54KJPN AC 19 . .
ToMMo 54KJPN AF 0.00035 . .
ToMMo 54KJPN AN 54301 . .
COSMIC 90 . . .
dbSNP 156 id rs878853115 . .
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