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14598 (T > C)

General info

Mitimpact ID
MI.24032
Chr
chrM
Start
14598
Ref
T
Alt
C
Gene symbol
MT-ND6 Extended gene annotation
Gene position
76
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
ATT/GTT
AA pos
26
AA ref
I
AA alt
V
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14598T>C
HGNC ID
7462
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot ID
P03923
Uniprot name
NU6M_HUMAN
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
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Powered by MitoWheel

Conservation

PhyloP 100v
0.263 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.009 Conservation Score
PhastCons 470way
0.997 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
Neutral Score and details of the predictor
MutationTaster
Disease 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
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
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
Deleterious 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
374080
Clinvar ALLELEID
361108
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

human phenotype ontology:hp:0001300, medgen:c0242422;

human phenotype ontology:hp:0000618, human phenotype ontology:hp:0007839, medgen:c0456909
Clinvar CLNDN
Leigh syndrome;

parkinsonism;

blindness
Clinvar CLNSIG
Conflicting interpretations of pathogenicity
MITOMAP Allele
14598T>C
MITOMAP Disease Clinical info
Pd / ls
MITOMAP Disease Status
Reported [vus]
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.0115%
MITOMAP General GenBank Seqs
7
MITOMAP General GenBank Curated refs
24002810 23463613
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56425
Gnomad AC hom
9
Gnomad AF hom
0.0001595
Gnomad AC het
3
Gnomad AF het
5.31e-05
Gnomad filter
Pass
HelixMTdb AC hom
26
HelixMTdb AF hom
0.0001326
HelixMTdb AC het
3
HelixMTdb AF het
1.53e-05
HelixMTdb mean ARF
0.19312
HelixMTdb max ARF
0.3047599
ToMMo JPN54K AC
11
ToMMo JPN54K AF
0.000203
ToMMo JPN54K AN
54301
COSMIC 90
COSM6716806
dbSNP 156
rs1057518882

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
.

14598 (T > A)

General info

Mitimpact ID
MI.24033
Chr
chrM
Start
14598
Ref
T
Alt
A
Gene symbol
MT-ND6 Extended gene annotation
Gene position
76
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
ATT/TTT
AA pos
26
AA ref
I
AA alt
F
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14598T>A
HGNC ID
7462
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot ID
P03923
Uniprot name
NU6M_HUMAN
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
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Powered by MitoWheel

Conservation

PhyloP 100v
0.263 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.009 Conservation Score
PhastCons 470way
0.997 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
.
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
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
Deleterious 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
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
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
14598T>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
.

14598 (T > G)

General info

Mitimpact ID
MI.24031
Chr
chrM
Start
14598
Ref
T
Alt
G
Gene symbol
MT-ND6 Extended gene annotation
Gene position
76
Gene start
14149
Gene end
14673
Gene strand
-
Codon substitution
ATT/CTT
AA pos
26
AA ref
I
AA alt
L
Functional effect
missense
OMIM ID
516006
HGVS
NC_012920.1:g.14598T>G
HGNC ID
7462
RC complex
I
Ensembl gene ID
ENSG00000198695
Ensembl protein ID
ENSP00000354665
Ensembl transcript ID
ENST00000361681
Uniprot ID
P03923
Uniprot name
NU6M_HUMAN
Ncbi gene ID
4541
Ncbi protein ID
YP_003024037.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.263 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.009 Conservation Score
PhastCons 470way
0.997 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
Neutral Score and details of the predictor
MutationTaster
Disease 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
Low 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
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
14598T>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
.
~ 14598 (T/C) 14598 (T/A) 14598 (T/G)
~ 14598 (ATT/GTT) 14598 (ATT/TTT) 14598 (ATT/CTT)
MitImpact id MI.24032 MI.24033 MI.24031
Chr chrM chrM chrM
Start 14598 14598 14598
Ref T T T
Alt C A G
Gene symbol MT-ND6 MT-ND6 MT-ND6
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6
Gene position 76 76 76
Gene start 14149 14149 14149
Gene end 14673 14673 14673
Gene strand - - -
Codon substitution ATT/GTT ATT/TTT ATT/CTT
AA position 26 26 26
AA ref I I I
AA alt V F L
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516006 516006 516006
HGVS NC_012920.1:g.14598T>C NC_012920.1:g.14598T>A NC_012920.1:g.14598T>G
HGNC id 7462 7462 7462
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198695 ENSG00000198695 ENSG00000198695
Ensembl transcript id ENST00000361681 ENST00000361681 ENST00000361681
Ensembl protein id ENSP00000354665 ENSP00000354665 ENSP00000354665
Uniprot id P03923 P03923 P03923
Uniprot name NU6M_HUMAN NU6M_HUMAN NU6M_HUMAN
Ncbi gene id 4541 4541 4541
Ncbi protein id YP_003024037.1 YP_003024037.1 YP_003024037.1
PhyloP 100V 0.263 0.263 0.263
PhyloP 470Way 0.666 0.666 0.666
PhastCons 100V 0.009 0.009 0.009
PhastCons 470Way 0.997 0.997 0.997
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1 1 1
SIFT neutral neutral neutral
SIFT score 0.45 0.59 0.61
SIFT4G Tolerated Damaging Damaging
SIFT4G score 0.387 0.041 0.023
VEST Neutral Neutral Neutral
VEST pvalue 0.58 0.51 0.39
VEST FDR 0.65 0.6 0.5
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Pathogenic Neutral
SNPDryad score 0.15 0.93 0.62
MutationTaster Disease . Disease
MutationTaster score 1 . 1
MutationTaster converted rankscore 0.81001 . 0.81001
MutationTaster model without_aae . without_aae
MutationTaster AAE . . .
fathmm Tolerated Tolerated Tolerated
fathmm score 2.37 2.1 2.21
fathmm converted rankscore 0.15964 0.19990 0.18414
AlphaMissense likely_benign likely_pathogenic likely_benign
AlphaMissense score 0.0915 0.5657 0.2824
CADD Neutral Deleterious Neutral
CADD score -0.451492 4.159179 2.351432
CADD phred 0.29 23.8 18.5
PROVEAN Tolerated Damaging Tolerated
PROVEAN score -0.62 -3.97 -1.99
MutationAssessor low low low
MutationAssessor score 0.985 0.92 1.88
EFIN SP Neutral Neutral Damaging
EFIN SP score 0.786 0.624 0.406
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.844 0.666 0.368
MLC Deleterious Deleterious Deleterious
MLC score 0.75427002 0.75427002 0.75427002
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Pathogenic
APOGEE1 score 0.31 0.31 0.65
APOGEE2 Benign VUS- VUS+
APOGEE2 score 0.0498621622144087 0.302875209549539 0.629375553785344
CAROL deleterious deleterious deleterious
CAROL score 0.99 1.0 0.99
Condel neutral neutral neutral
Condel score 0.23 0.3 0.31
COVEC WMV neutral deleterious deleterious
COVEC WMV score -2 1 1
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.68 0.7 0.7
DEOGEN2 Tolerated Damaging Tolerated
DEOGEN2 score 0.218413 0.531547 0.410017
DEOGEN2 converted rankscore 0.58113 0.83798 0.76488
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.55 -3.55 -3.55
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.16 0.29 0.31
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 0.29 0.49 1.46
CHASM Neutral Neutral Neutral
CHASM pvalue 0.63 0.78 0.68
CHASM FDR 0.8 0.85 0.85
ClinVar id 374080.0 . .
ClinVar Allele id 361108.0 . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|Human_Phenotype_Ontology:HP:0001300,MedGen:C0242422|Human_Phenotype_Ontology:HP:0000618,Human_Phenotype_Ontology:HP:0007839,MedGen:C0456909 . .
ClinVar CLNDN Leigh_syndrome|Parkinsonism|Blindness . .
ClinVar CLNSIG Conflicting_interpretations_of_pathogenicity . .
MITOMAP Disease Clinical info PD / LS . .
MITOMAP Disease Status Reported [VUS] . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.0115% . .
MITOMAP General GenBank Seqs 7 . .
MITOMAP General Curated refs 24002810;23463613 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56425.0 . .
gnomAD 3.1 AC Homo 9.0 . .
gnomAD 3.1 AF Hom 0.000159504 . .
gnomAD 3.1 AC Het 3.0 . .
gnomAD 3.1 AF Het 5.31679e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 26.0 . .
HelixMTdb AF Hom 0.00013266457 . .
HelixMTdb AC Het 3.0 . .
HelixMTdb AF Het 1.530745e-05 . .
HelixMTdb mean ARF 0.19312 . .
HelixMTdb max ARF 0.30476 . .
ToMMo 54KJPN AC 11 . .
ToMMo 54KJPN AF 0.000203 . .
ToMMo 54KJPN AN 54301 . .
COSMIC 90 COSM6716806 . .
dbSNP 156 id rs1057518882 . .
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