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14000 (T > A)

General info

Mitimpact ID
MI.22795
Chr
chrM
Start
14000
Ref
T
Alt
A
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1664
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
CTA/CAA
AA pos
555
AA ref
L
AA alt
Q
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.14000T>A
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
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Conservation

PhyloP 100v
0.227 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.064 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
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
Neutral Score and details of the meta-predictor
COVEC WMV
Neutral 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
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
235700
Clinvar ALLELEID
237380
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
14000T>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
1.0747%
MITOMAP General GenBank Seqs
657
MITOMAP General GenBank Curated refs
21041797 11938495 30242360
MITOMAP Variant Class
polymorphism
Gnomad AN
56421
Gnomad AC hom
1524
Gnomad AF hom
0.0270112
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
850
HelixMTdb AF hom
0.0043371
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.89394
HelixMTdb max ARF
0.89394
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs28359185

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
.

14000 (T > C)

General info

Mitimpact ID
MI.22796
Chr
chrM
Start
14000
Ref
T
Alt
C
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1664
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
CTA/CCA
AA pos
555
AA ref
L
AA alt
P
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.14000T>C
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
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Powered by MitoWheel

Conservation

PhyloP 100v
0.227 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.064 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
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
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
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
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
14000T>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56429
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
rs28359185

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
.

14000 (T > G)

General info

Mitimpact ID
MI.22794
Chr
chrM
Start
14000
Ref
T
Alt
G
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1664
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
CTA/CGA
AA pos
555
AA ref
L
AA alt
R
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.14000T>G
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.227 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.064 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
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
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
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
14000T>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
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
.

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
.
~ 14000 (T/A) 14000 (T/C) 14000 (T/G)
~ 14000 (CTA/CAA) 14000 (CTA/CCA) 14000 (CTA/CGA)
MitImpact id MI.22795 MI.22796 MI.22794
Chr chrM chrM chrM
Start 14000 14000 14000
Ref T T T
Alt A C G
Gene symbol MT-ND5 MT-ND5 MT-ND5
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5
Gene position 1664 1664 1664
Gene start 12337 12337 12337
Gene end 14148 14148 14148
Gene strand + + +
Codon substitution CTA/CAA CTA/CCA CTA/CGA
AA position 555 555 555
AA ref L L L
AA alt Q P R
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516005 516005 516005
HGVS NC_012920.1:g.14000T>A NC_012920.1:g.14000T>C NC_012920.1:g.14000T>G
HGNC id 7461 7461 7461
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198786 ENSG00000198786 ENSG00000198786
Ensembl transcript id ENST00000361567 ENST00000361567 ENST00000361567
Ensembl protein id ENSP00000354813 ENSP00000354813 ENSP00000354813
Uniprot id P03915 P03915 P03915
Uniprot name NU5M_HUMAN NU5M_HUMAN NU5M_HUMAN
Ncbi gene id 4540 4540 4540
Ncbi protein id YP_003024036.1 YP_003024036.1 YP_003024036.1
PhyloP 100V 0.227 0.227 0.227
PhyloP 470Way 0.666 0.666 0.666
PhastCons 100V 0 0 0
PhastCons 470Way 0.064 0.064 0.064
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 0.95 0.96 0.95
SIFT neutral neutral neutral
SIFT score 0.31 0.21 0.35
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 0.833 0.083 0.145
VEST Neutral Neutral Neutral
VEST pvalue 0.2 0.15 0.21
VEST FDR 0.45 0.4 0.45
Mitoclass.1 neutral damaging neutral
SNPDryad Neutral Pathogenic Neutral
SNPDryad score 0.75 0.92 0.82
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1.0 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE L555Q L555P L555R
fathmm Tolerated Tolerated Tolerated
fathmm score 1.74 1.46 1.54
fathmm converted rankscore 0.26301 0.32238 0.30133
AlphaMissense likely_benign likely_pathogenic likely_benign
AlphaMissense score 0.167 0.8746 0.3365
CADD Neutral Deleterious Deleterious
CADD score 1.989311 2.970207 3.139664
CADD phred 16.14 22.1 22.6
PROVEAN Damaging Damaging Damaging
PROVEAN score -2.99 -4.14 -3.38
MutationAssessor low high medium
MutationAssessor score 1.055 3.75 2.55
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.832 0.606 0.776
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.87 0.326 0.75
MLC Neutral Neutral Neutral
MLC score 0.25592975 0.25592975 0.25592975
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.36 0.3 0.31
APOGEE2 Likely-benign VUS+ VUS-
APOGEE2 score 0.0692758864780254 0.59952324580358 0.270082074204329
CAROL neutral neutral neutral
CAROL score 0.96 0.98 0.96
Condel neutral neutral neutral
Condel score 0.18 0.13 0.2
COVEC WMV neutral deleterious deleterious
COVEC WMV score -2 1 1
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.68 0.81 0.72
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.062882 0.126271 0.067968
DEOGEN2 converted rankscore 0.32031 0.45254 0.33336
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -1.96 -2.06 -1.96
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.04 -0.09 0.08
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score -0.23 1.88 1.05
CHASM Neutral Neutral Neutral
CHASM pvalue 0.48 0.44 0.55
CHASM FDR 0.8 0.8 0.8
ClinVar id 235700.0 . .
ClinVar Allele id 237380.0 . .
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 1.0747% 0.0016% .
MITOMAP General GenBank Seqs 657 1 .
MITOMAP General Curated refs 21041797;11938495;30242360 . .
MITOMAP Variant Class polymorphism polymorphism .
gnomAD 3.1 AN 56421.0 56429.0 56433.0
gnomAD 3.1 AC Homo 1524.0 0.0 0.0
gnomAD 3.1 AF Hom 0.0270112 0.0 0.0
gnomAD 3.1 AC Het 0.0 0.0 0.0
gnomAD 3.1 AF Het 0.0 0.0 0.0
gnomAD 3.1 filter PASS npg npg
HelixMTdb AC Hom 850.0 . .
HelixMTdb AF Hom 0.004337111 . .
HelixMTdb AC Het 1.0 . .
HelixMTdb AF Het 5.1024836e-06 . .
HelixMTdb mean ARF 0.89394 . .
HelixMTdb max ARF 0.89394 . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs28359185 rs28359185 .
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