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6489 (C > A)

General info

Mitimpact ID
MI.3124
Chr
chrM
Start
6489
Ref
C
Alt
A
Gene symbol
MT-CO1 Extended gene annotation
Gene position
586
Gene start
5904
Gene end
7445
Gene strand
+
Codon substitution
CTC/ATC
AA pos
196
AA ref
L
AA alt
I
Functional effect
missense
OMIM ID
516030
HGVS
NC_012920.1:g.6489C>A
HGNC ID
7419
RC complex
IV
Ensembl gene ID
ENSG00000198804
Ensembl protein ID
ENSP00000354499
Ensembl transcript ID
ENST00000361624
Uniprot ID
P00395
Uniprot name
COX1_HUMAN
Ncbi gene ID
4512
Ncbi protein ID
YP_003024028.1
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Conservation

PhyloP 100v
0.084 Conservation Score
PhyloP 470way
0.353 Conservation Score
PhastCons 100v
0.002 Conservation Score
PhastCons 470way
0.043 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 automatic Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Ambiguous Score and details of the predictor
CADD
Deleterious 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
Neutral Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor

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
Neutral Score and details of the meta-predictor

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
9670
Clinvar ALLELEID
24709
Clinvar CLNDISDB
Medgen:c4016602;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Cytochrome c oxidase i deficiency;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
6489C>A
MITOMAP Disease Clinical info
Co1 deficiency with epilepsia partialis continua
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.1472%
MITOMAP General GenBank Seqs
90
MITOMAP General GenBank Curated refs
19370763 12140182 11938495 21457906 21063443 31152278 29253894
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56432
Gnomad AC hom
185
Gnomad AF hom
0.0032782
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
740
HelixMTdb AF hom
0.0037758
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.1319799
HelixMTdb max ARF
0.1319799
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs28461189

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
L
CPD AA alt
I
Aln pos
199
RefSeq protein ID
NP_007512
Species name
Glis glis
Ncbi taxon ID
41261

6489 (C > G)

General info

Mitimpact ID
MI.3123
Chr
chrM
Start
6489
Ref
C
Alt
G
Gene symbol
MT-CO1 Extended gene annotation
Gene position
586
Gene start
5904
Gene end
7445
Gene strand
+
Codon substitution
CTC/GTC
AA pos
196
AA ref
L
AA alt
V
Functional effect
missense
OMIM ID
516030
HGVS
NC_012920.1:g.6489C>G
HGNC ID
7419
RC complex
IV
Ensembl gene ID
ENSG00000198804
Ensembl protein ID
ENSP00000354499
Ensembl transcript ID
ENST00000361624
Uniprot ID
P00395
Uniprot name
COX1_HUMAN
Ncbi gene ID
4512
Ncbi protein ID
YP_003024028.1
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Powered by MitoWheel

Conservation

PhyloP 100v
0.084 Conservation Score
PhyloP 470way
0.353 Conservation Score
PhastCons 100v
0.002 Conservation Score
PhastCons 470way
0.043 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 automatic Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Ambiguous Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Tolerated 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-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
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
6489C>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
rs28461189

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
.

6489 (C > T)

General info

Mitimpact ID
MI.3125
Chr
chrM
Start
6489
Ref
C
Alt
T
Gene symbol
MT-CO1 Extended gene annotation
Gene position
586
Gene start
5904
Gene end
7445
Gene strand
+
Codon substitution
CTC/TTC
AA pos
196
AA ref
L
AA alt
F
Functional effect
missense
OMIM ID
516030
HGVS
NC_012920.1:g.6489C>T
HGNC ID
7419
RC complex
IV
Ensembl gene ID
ENSG00000198804
Ensembl protein ID
ENSP00000354499
Ensembl transcript ID
ENST00000361624
Uniprot ID
P00395
Uniprot name
COX1_HUMAN
Ncbi gene ID
4512
Ncbi protein ID
YP_003024028.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.084 Conservation Score
PhyloP 470way
0.353 Conservation Score
PhastCons 100v
0.002 Conservation Score
PhastCons 470way
0.043 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
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
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
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
Low 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
6489C>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
.
~ 6489 (C/A) 6489 (C/G) 6489 (C/T)
~ 6489 (CTC/ATC) 6489 (CTC/GTC) 6489 (CTC/TTC)
MitImpact id MI.3124 MI.3123 MI.3125
Chr chrM chrM chrM
Start 6489 6489 6489
Ref C C C
Alt A G T
Gene symbol MT-CO1 MT-CO1 MT-CO1
Extended annotation mitochondrially encoded cytochrome c oxidase I mitochondrially encoded cytochrome c oxidase I mitochondrially encoded cytochrome c oxidase I
Gene position 586 586 586
Gene start 5904 5904 5904
Gene end 7445 7445 7445
Gene strand + + +
Codon substitution CTC/ATC CTC/GTC CTC/TTC
AA position 196 196 196
AA ref L L L
AA alt I V F
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516030 516030 516030
HGVS NC_012920.1:g.6489C>A NC_012920.1:g.6489C>G NC_012920.1:g.6489C>T
HGNC id 7419 7419 7419
Respiratory Chain complex IV IV IV
Ensembl gene id ENSG00000198804 ENSG00000198804 ENSG00000198804
Ensembl transcript id ENST00000361624 ENST00000361624 ENST00000361624
Ensembl protein id ENSP00000354499 ENSP00000354499 ENSP00000354499
Uniprot id P00395 P00395 P00395
Uniprot name COX1_HUMAN COX1_HUMAN COX1_HUMAN
Ncbi gene id 4512 4512 4512
Ncbi protein id YP_003024028.1 YP_003024028.1 YP_003024028.1
PhyloP 100V 0.084 0.084 0.084
PhyloP 470Way 0.353 0.353 0.353
PhastCons 100V 0.002 0.002 0.002
PhastCons 470Way 0.043 0.043 0.043
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 0.99 1.0
SIFT neutral neutral deleterious
SIFT score 0.13 0.17 0.0
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.02 0.018 0.008
VEST Neutral Neutral Neutral
VEST pvalue 0.29 0.39 0.32
VEST FDR 0.55 0.55 0.55
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.54 0.66 0.87
MutationTaster Disease automatic Disease automatic Polymorphism
MutationTaster score 0.00478171 0.00858714 0.957962
MutationTaster converted rankscore 0.23345 0.24037 0.26242
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE L196I L196V L196F
fathmm Tolerated Tolerated Tolerated
fathmm score 2.67 2.61 2.46
fathmm converted rankscore 0.12473 0.13095 0.14907
AlphaMissense ambiguous ambiguous likely_pathogenic
AlphaMissense score 0.4418 0.4332 0.8942
CADD Deleterious Deleterious Deleterious
CADD score 4.042451 3.400184 3.955454
CADD phred 23.7 23.0 23.6
PROVEAN Tolerated Tolerated Damaging
PROVEAN score -1.51 -2.33 -3.35
MutationAssessor low medium high
MutationAssessor score 1.66 2.305 4.04
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.186 0.346 0.322
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.466 0.334 0.346
MLC Deleterious Deleterious Deleterious
MLC score 0.53974289 0.53974289 0.53974289
PANTHER score 0.372 . .
PhD-SNP score 0.759 . .
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.81 0.53 0.56
APOGEE2 VUS- Likely-benign VUS-
APOGEE2 score 0.328936150923727 0.200735343572161 0.378722165268338
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 1.0
Condel neutral neutral neutral
Condel score 0.07 0.09 0.0
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 1 1 6
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.73 0.71 0.79
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.04386 0.130126 0.164602
DEOGEN2 converted rankscore 0.26635 0.45884 0.51012
Meta-SNP Neutral . .
Meta-SNP score 0.482 . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.58 -2.64 -3.58
SIFT_transf medium impact medium impact low impact
SIFT transf score -0.27 -0.19 -1.48
MutationAssessor transf medium impact medium impact high impact
MutationAssessor transf score 0.89 1.12 2.99
CHASM Neutral Neutral Neutral
CHASM pvalue 0.57 0.43 0.36
CHASM FDR 0.9 0.9 0.9
ClinVar id 9670.0 . .
ClinVar Allele id 24709.0 . .
ClinVar CLNDISDB MedGen:C4016602|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN Cytochrome_c_oxidase_I_deficiency|Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info CO1 deficiency with epilepsia partialis continua . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het -/+ ./. ./.
MITOMAP General GenBank Freq 0.1472% . .
MITOMAP General GenBank Seqs 90 . .
MITOMAP General Curated refs 19370763;12140182;11938495;21457906;21063443;31152278;29253894 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56432.0 . .
gnomAD 3.1 AC Homo 185.0 . .
gnomAD 3.1 AF Hom 0.00327828 . .
gnomAD 3.1 AC Het 0.0 . .
gnomAD 3.1 AF Het 0.0 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 740.0 . .
HelixMTdb AF Hom 0.0037758376 . .
HelixMTdb AC Het 1.0 . .
HelixMTdb AF Het 5.1024836e-06 . .
HelixMTdb mean ARF 0.13198 . .
HelixMTdb max ARF 0.13198 . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs28461189 rs28461189 .
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