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6261 (G > A)

General info

Mitimpact ID
MI.2647
Chr
chrM
Start
6261
Ref
G
Alt
A
Gene symbol
MT-CO1 Extended gene annotation
Gene position
358
Gene start
5904
Gene end
7445
Gene strand
+
Codon substitution
GCC/ACC
AA pos
120
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516030
HGVS
NC_012920.1:g.6261G>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
7.692 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.73 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
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
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
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
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
235718
Clinvar ALLELEID
237398
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
6261G>A
MITOMAP Disease Clinical info
Prostate cancer / lhon
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.8113%
MITOMAP General GenBank Seqs
496
MITOMAP General GenBank Curated refs
10720328 21978175 18477584 17021933 18495510 32094358 15466285 11938495 31152278 16901986 12749053 19267350 16172508 17003408 31817256 15254257 21041797 15647368 16892079
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56365
Gnomad AC hom
401
Gnomad AF hom
0.0071143
Gnomad AC het
10
Gnomad AF het
0.0001774
Gnomad filter
Pass
HelixMTdb AC hom
1501
HelixMTdb AF hom
0.0076588
HelixMTdb AC het
30
HelixMTdb AF het
0.000153
HelixMTdb mean ARF
0.33124
HelixMTdb max ARF
0.89598
ToMMo JPN54K AC
95
ToMMo JPN54K AF
0.001749
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs201262114

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
A
CPD AA alt
T
Aln pos
123
RefSeq protein ID
YP_006460519
Species name
Pygathrix nigripes
Ncbi taxon ID
310352

6261 (G > C)

General info

Mitimpact ID
MI.2646
Chr
chrM
Start
6261
Ref
G
Alt
C
Gene symbol
MT-CO1 Extended gene annotation
Gene position
358
Gene start
5904
Gene end
7445
Gene strand
+
Codon substitution
GCC/CCC
AA pos
120
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516030
HGVS
NC_012920.1:g.6261G>C
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
7.692 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.73 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
Ambiguous 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
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
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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
6261G>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56428
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.84574
HelixMTdb max ARF
0.84574
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
.

6261 (G > T)

General info

Mitimpact ID
MI.2648
Chr
chrM
Start
6261
Ref
G
Alt
T
Gene symbol
MT-CO1 Extended gene annotation
Gene position
358
Gene start
5904
Gene end
7445
Gene strand
+
Codon substitution
GCC/TCC
AA pos
120
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516030
HGVS
NC_012920.1:g.6261G>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
7.692 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.73 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
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
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
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
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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
6261G>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0049%
MITOMAP General GenBank Seqs
3
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
5
HelixMTdb AF hom
2.55e-05
HelixMTdb AC het
0
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
.
~ 6261 (G/A) 6261 (G/C) 6261 (G/T)
~ 6261 (GCC/ACC) 6261 (GCC/CCC) 6261 (GCC/TCC)
MitImpact id MI.2647 MI.2646 MI.2648
Chr chrM chrM chrM
Start 6261 6261 6261
Ref G G G
Alt A C 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 358 358 358
Gene start 5904 5904 5904
Gene end 7445 7445 7445
Gene strand + + +
Codon substitution GCC/ACC GCC/CCC GCC/TCC
AA position 120 120 120
AA ref A A A
AA alt T P S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516030 516030 516030
HGVS NC_012920.1:g.6261G>A NC_012920.1:g.6261G>C NC_012920.1:g.6261G>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 7.692 7.692 7.692
PhyloP 470Way 0.458 0.458 0.458
PhastCons 100V 1 1 1
PhastCons 470Way 0.73 0.73 0.73
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 0.99 1.0 0.99
SIFT neutral neutral neutral
SIFT score 0.15 0.11 0.66
SIFT4G Tolerated Damaging Tolerated
SIFT4G score 0.118 0.011 1.0
VEST Neutral Neutral Neutral
VEST pvalue 0.38 0.2 0.32
VEST FDR 0.55 0.55 0.55
Mitoclass.1 damaging damaging neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.2 0.85 0.64
MutationTaster Disease Disease Disease
MutationTaster score 0.91373 0.973718 0.820995
MutationTaster converted rankscore 0.36481 0.39046 0.34776
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE A120T A120P A120S
fathmm Tolerated Tolerated Tolerated
fathmm score 2.82 2.77 2.82
fathmm converted rankscore 0.10871 0.11407 0.10871
AlphaMissense likely_benign ambiguous likely_benign
AlphaMissense score 0.1247 0.5038 0.0817
CADD Neutral Neutral Neutral
CADD score 1.079795 2.129352 -1.000265
CADD phred 11.11 17.05 0.016
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score 0.27 -1.11 1.09
MutationAssessor neutral low neutral
MutationAssessor score 0.465 1.86 -1.03
EFIN SP Neutral Damaging Neutral
EFIN SP score 0.612 0.588 0.684
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.568 0.348 0.834
MLC Neutral Neutral Neutral
MLC score 0.36513972 0.36513972 0.36513972
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.69 0.48 0.46
APOGEE2 Likely-benign Likely-benign Benign
APOGEE2 score 0.0934824695836723 0.221143729548438 0.0354716983298786
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 0.99
Condel neutral neutral neutral
Condel score 0.08 0.06 0.34
COVEC WMV neutral neutral neutral
COVEC WMV score -2 -2 -2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.66 0.82 0.64
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.005769 0.026944 0.004515
DEOGEN2 converted rankscore 0.05219 0.19836 0.03917
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -2.64 -3.58 -2.64
SIFT_transf medium impact medium impact medium impact
SIFT transf score -0.23 -0.31 0.35
MutationAssessor transf low impact medium impact low impact
MutationAssessor transf score -1.47 0.21 -2.76
CHASM Neutral Neutral Neutral
CHASM pvalue 0.68 0.68 0.73
CHASM FDR 0.9 0.9 0.9
ClinVar id 235718.0 . .
ClinVar Allele id 237398.0 . .
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 Prostate Cancer / LHON . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.8113% 0.0% 0.0049%
MITOMAP General GenBank Seqs 496 0 3
MITOMAP General Curated refs 10720328;21978175;18477584;17021933;18495510;32094358;15466285;11938495;31152278;16901986;12749053;19267350;16172508;17003408;31817256;15254257;21041797;15647368;16892079 . .
MITOMAP Variant Class polymorphism;disease polymorphism polymorphism
gnomAD 3.1 AN 56365.0 56428.0 .
gnomAD 3.1 AC Homo 401.0 0.0 .
gnomAD 3.1 AF Hom 0.00711434 0.0 .
gnomAD 3.1 AC Het 10.0 1.0 .
gnomAD 3.1 AF Het 0.000177415 1.77217e-05 .
gnomAD 3.1 filter PASS PASS .
HelixMTdb AC Hom 1501.0 0.0 5.0
HelixMTdb AF Hom 0.0076588276 0.0 2.5512418e-05
HelixMTdb AC Het 30.0 1.0 0.0
HelixMTdb AF Het 0.0001530745 5.1024836e-06 0.0
HelixMTdb mean ARF 0.33124 0.84574 .
HelixMTdb max ARF 0.89598 0.84574 .
ToMMo 54KJPN AC 95 . .
ToMMo 54KJPN AF 0.001749 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs201262114 . .
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