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10237 (T > C)

General info

Mitimpact ID
MI.15348
Chr
chrM
Start
10237
Ref
T
Alt
C
Gene symbol
MT-ND3 Extended gene annotation
Gene position
179
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
ATT/ACT
AA pos
60
AA ref
I
AA alt
T
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10237T>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
7.73 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.729 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
Medium 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
Pathogenic Score and details of the meta-predictor
APOGEE2
Vus+ 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
Damaging 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
65508
Clinvar ALLELEID
76416
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104
Clinvar CLNDN
Leigh syndrome;

leber optic atrophy
Clinvar CLNSIG
Benign
MITOMAP Allele
10237T>C
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.1636%
MITOMAP General GenBank Seqs
100
MITOMAP General GenBank Curated refs
12227465 35773337 29987491 20301353 11349229 19818876
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56415
Gnomad AC hom
101
Gnomad AF hom
0.0017903
Gnomad AC het
9
Gnomad AF het
0.0001595
Gnomad filter
Pass
HelixMTdb AC hom
240
HelixMTdb AF hom
0.0012245
HelixMTdb AC het
20
HelixMTdb AF het
0.000102
HelixMTdb mean ARF
0.37099
HelixMTdb max ARF
0.92537
ToMMo JPN54K AC
22
ToMMo JPN54K AF
0.000405
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs1556423787

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
0.15 CPD variant frequency
AA ref
I
CPD AA alt
T
Aln pos
62
RefSeq protein ID
YP_001542749
Species name
Melursus ursinus
Ncbi taxon ID
9636

10237 (T > A)

General info

Mitimpact ID
MI.15346
Chr
chrM
Start
10237
Ref
T
Alt
A
Gene symbol
MT-ND3 Extended gene annotation
Gene position
179
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
ATT/AAT
AA pos
60
AA ref
I
AA alt
N
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10237T>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
7.73 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.729 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably 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
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
Medium 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
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
Damaging 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
10237T>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
.

10237 (T > G)

General info

Mitimpact ID
MI.15347
Chr
chrM
Start
10237
Ref
T
Alt
G
Gene symbol
MT-ND3 Extended gene annotation
Gene position
179
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
ATT/AGT
AA pos
60
AA ref
I
AA alt
S
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10237T>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
7.73 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.729 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
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
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
Damaging 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
10237T>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
.
~ 10237 (T/C) 10237 (T/A) 10237 (T/G)
~ 10237 (ATT/ACT) 10237 (ATT/AAT) 10237 (ATT/AGT)
MitImpact id MI.15348 MI.15346 MI.15347
Chr chrM chrM chrM
Start 10237 10237 10237
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 179 179 179
Gene start 10059 10059 10059
Gene end 10404 10404 10404
Gene strand + + +
Codon substitution ATT/ACT ATT/AAT ATT/AGT
AA position 60 60 60
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.10237T>C NC_012920.1:g.10237T>A NC_012920.1:g.10237T>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 7.73 7.73 7.73
PhyloP 470Way 0.666 0.666 0.666
PhastCons 100V 1 1 1
PhastCons 470Way 0.729 0.729 0.729
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 0.96 0.99 0.97
SIFT neutral deleterious deleterious
SIFT score 0.09 0.03 0.04
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.0 0.0 0.0
VEST Neutral Neutral Pathogenic
VEST pvalue 0.06 0.06 0.03
VEST FDR 0.35 0.35 0.35
Mitoclass.1 damaging damaging damaging
SNPDryad Pathogenic Pathogenic Pathogenic
SNPDryad score 0.99 0.99 0.96
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 1.2294e-05 0.999989 0.999987
MutationTaster converted rankscore 0.18198 0.18198 0.18198
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE I60T I60N I60S
fathmm Tolerated Tolerated Tolerated
fathmm score 0.71 0.68 0.69
fathmm converted rankscore 0.51228 0.51952 0.51714
AlphaMissense likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.7616 0.8865 0.82
CADD Deleterious Deleterious Deleterious
CADD score 3.328455 4.370003 4.245742
CADD phred 22.9 24.1 23.9
PROVEAN Damaging Damaging Damaging
PROVEAN score -4.68 -6.62 -5.64
MutationAssessor medium medium high
MutationAssessor score 3.165 3.275 3.965
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.428 0.496 0.546
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.366 0.312 0.384
MLC Deleterious Deleterious Deleterious
MLC score 0.84552478 0.84552478 0.84552478
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.79 0.57 0.64
APOGEE2 VUS+ Likely-pathogenic Likely-pathogenic
APOGEE2 score 0.66612962264102 0.718058628588794 0.72683396070325
CAROL deleterious deleterious deleterious
CAROL score 0.98 1.0 0.99
Condel neutral neutral neutral
Condel score 0.07 0.02 0.04
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 2 6 6
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.77 0.83 0.81
DEOGEN2 Damaging Damaging Damaging
DEOGEN2 score 0.740706 0.777587 0.787414
DEOGEN2 converted rankscore 0.92816 0.94099 0.94444
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -1.96 -2.52 -2.08
SIFT_transf medium impact medium impact medium impact
SIFT transf score -0.37 -0.65 -0.58
MutationAssessor transf high impact high impact high impact
MutationAssessor transf score 2.43 2.52 3.16
CHASM Neutral Neutral Neutral
CHASM pvalue 0.28 0.34 0.28
CHASM FDR 0.8 0.8 0.8
ClinVar id 65508.0 . .
ClinVar Allele id 76416.0 . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 . .
ClinVar CLNDN Leigh_syndrome|Leber_optic_atrophy . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info LHON . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.1636% . .
MITOMAP General GenBank Seqs 100 . .
MITOMAP General Curated refs 12227465;35773337;29987491;20301353;11349229;19818876 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56415.0 . .
gnomAD 3.1 AC Homo 101.0 . .
gnomAD 3.1 AF Hom 0.0017903 . .
gnomAD 3.1 AC Het 9.0 . .
gnomAD 3.1 AF Het 0.000159532 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 240.0 . .
HelixMTdb AF Hom 0.001224596 . .
HelixMTdb AC Het 20.0 . .
HelixMTdb AF Het 0.00010204967 . .
HelixMTdb mean ARF 0.37099 . .
HelixMTdb max ARF 0.92537 . .
ToMMo 54KJPN AC 22 . .
ToMMo 54KJPN AF 0.000405 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs1556423787 . .
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