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9478 (T > A)

General info

Mitimpact ID
MI.7208
Chr
chrM
Start
9478
Ref
T
Alt
A
Gene symbol
MT-CO3 Extended gene annotation
Gene position
272
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GTT/GAT
AA pos
91
AA ref
V
AA alt
D
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9478T>A
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
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Conservation

PhyloP 100v
2.151 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.989 Conservation Score
PhastCons 470way
0.67 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
Medium 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
9478T>A
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
56431
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
.

9478 (T > C)

General info

Mitimpact ID
MI.7210
Chr
chrM
Start
9478
Ref
T
Alt
C
Gene symbol
MT-CO3 Extended gene annotation
Gene position
272
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GTT/GCT
AA pos
91
AA ref
V
AA alt
A
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9478T>C
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
2.151 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.989 Conservation Score
PhastCons 470way
0.67 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
Neutral 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
Neutral 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
Pathogenic 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
Deleterious Score and details of the meta-predictor
COVEC WMV
Neutral Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
High 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
155885
Clinvar ALLELEID
165634
Clinvar CLNDISDB
Medgen:cn169374;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Not specified;

leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
9478T>C
MITOMAP Disease Clinical info
Leigh disease
MITOMAP Disease Status
Reported [vus]
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.036%
MITOMAP General GenBank Seqs
22
MITOMAP General GenBank Curated refs
20525945 23301511 24448545 29253894
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56427
Gnomad AC hom
127
Gnomad AF hom
0.0022507
Gnomad AC het
2
Gnomad AF het
3.54e-05
Gnomad filter
Pass
HelixMTdb AC hom
53
HelixMTdb AF hom
0.0002704
HelixMTdb AC het
3
HelixMTdb AF het
1.53e-05
HelixMTdb mean ARF
0.53379
HelixMTdb max ARF
0.74603
ToMMo JPN54K AC
4
ToMMo JPN54K AF
7.4e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs587776437

Residue interaction

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

Compensated Pathogenic Deviations

Frequency
1.34 CPD variant frequency
AA ref
V
CPD AA alt
A
Aln pos
91
RefSeq protein ID
YP_002884232 , YP_026110 , YP_637016 , YP_659440 , YP_007024936 , NP_944756 , YP_007001310 , YP_637068 , YP_423955
Species name
Macaca fascicularis, Macaca mulatta, Phascolarctos cinereus, Semnopithecus entellus, Trachypithecus vetulus, Monodon monoceros, Globicephala melas, Phalanger vestitus, Lipotes vexillifer
Ncbi taxon ID
9541, 9544, 38626, 88029, 54137, 40151, 9731, 175809, 118797

9478 (T > G)

General info

Mitimpact ID
MI.7209
Chr
chrM
Start
9478
Ref
T
Alt
G
Gene symbol
MT-CO3 Extended gene annotation
Gene position
272
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GTT/GGT
AA pos
91
AA ref
V
AA alt
G
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9478T>G
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
2.151 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0.989 Conservation Score
PhastCons 470way
0.67 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
Ambiguous Score and details of the predictor
CADD
Neutral 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
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
Deleterious Score and details of the meta-predictor
MtoolBox
Neutral Score and details of the meta-predictor
DEOGEN2
Tolerated Score and details of the meta-predictor
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
Medium 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
693171
Clinvar ALLELEID
681707
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
9478T>G
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
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
rs587776437

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
.
~ 9478 (T/A) 9478 (T/C) 9478 (T/G)
~ 9478 (GTT/GAT) 9478 (GTT/GCT) 9478 (GTT/GGT)
MitImpact id MI.7208 MI.7210 MI.7209
Chr chrM chrM chrM
Start 9478 9478 9478
Ref T T T
Alt A C G
Gene symbol MT-CO3 MT-CO3 MT-CO3
Extended annotation mitochondrially encoded cytochrome c oxidase III mitochondrially encoded cytochrome c oxidase III mitochondrially encoded cytochrome c oxidase III
Gene position 272 272 272
Gene start 9207 9207 9207
Gene end 9990 9990 9990
Gene strand + + +
Codon substitution GTT/GAT GTT/GCT GTT/GGT
AA position 91 91 91
AA ref V V V
AA alt D A G
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516050 516050 516050
HGVS NC_012920.1:g.9478T>A NC_012920.1:g.9478T>C NC_012920.1:g.9478T>G
HGNC id 7422 7422 7422
Respiratory Chain complex IV IV IV
Ensembl gene id ENSG00000198938 ENSG00000198938 ENSG00000198938
Ensembl transcript id ENST00000362079 ENST00000362079 ENST00000362079
Ensembl protein id ENSP00000354982 ENSP00000354982 ENSP00000354982
Uniprot id P00414 P00414 P00414
Uniprot name COX3_HUMAN COX3_HUMAN COX3_HUMAN
Ncbi gene id 4514 4514 4514
Ncbi protein id YP_003024032.1 YP_003024032.1 YP_003024032.1
PhyloP 100V 2.151 2.151 2.151
PhyloP 470Way 0.666 0.666 0.666
PhastCons 100V 0.989 0.989 0.989
PhastCons 470Way 0.67 0.67 0.67
PolyPhen2 benign benign benign
PolyPhen2 score 0.25 0.0 0.12
SIFT deleterious neutral deleterious
SIFT score 0.02 0.36 0.01
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.0 0.026 0.0
VEST Pathogenic Neutral Pathogenic
VEST pvalue 0.03 0.13 0.05
VEST FDR 0.35 0.4 0.35
Mitoclass.1 damaging neutral damaging
SNPDryad Pathogenic Neutral Pathogenic
SNPDryad score 0.97 0.37 0.96
MutationTaster Polymorphism Disease automatic Polymorphism
MutationTaster score 0.999952 1.59637e-05 0.999984
MutationTaster converted rankscore 0.19072 0.18198 0.18198
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE V91D V91A V91G
fathmm Tolerated Tolerated Tolerated
fathmm score 1.91 2.01 1.92
fathmm converted rankscore 0.23283 0.21291 0.23082
AlphaMissense likely_pathogenic ambiguous ambiguous
AlphaMissense score 0.9487 0.5502 0.4926
CADD Deleterious Neutral Neutral
CADD score 4.274556 1.556248 2.097247
CADD phred 24.0 13.61 16.84
PROVEAN Damaging Damaging Damaging
PROVEAN score -6.04 -3.41 -6.17
MutationAssessor high medium high
MutationAssessor score 5.0 2.835 4.305
EFIN SP Damaging Neutral Damaging
EFIN SP score 0.57 0.764 0.584
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.416 0.682 0.62
MLC Neutral Neutral Neutral
MLC score 0.27388497 0.27388497 0.27388497
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Pathogenic Neutral
APOGEE1 score 0.43 0.59 0.41
APOGEE2 VUS Likely-benign Likely-benign
APOGEE2 score 0.447248615956257 0.148660450512161 0.248821684638583
CAROL neutral neutral deleterious
CAROL score 0.98 0.64 0.99
Condel neutral deleterious neutral
Condel score 0.39 0.68 0.45
COVEC WMV deleterious neutral deleterious
COVEC WMV score 2 -3 1
MtoolBox deleterious neutral neutral
MtoolBox DS 0.57 0.14 0.33
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.361944 0.110326 0.131961
DEOGEN2 converted rankscore 0.72794 0.42492 0.46176
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact high impact medium impact
PolyPhen2 transf score -0.41 2.05 -0.03
SIFT_transf medium impact medium impact medium impact
SIFT transf score -0.77 0.05 -0.95
MutationAssessor transf high impact medium impact medium impact
MutationAssessor transf score 2.73 0.86 1.12
CHASM Neutral Neutral Neutral
CHASM pvalue 0.14 0.17 0.23
CHASM FDR 0.8 0.8 0.8
ClinVar id . 155885.0 693171.0
ClinVar Allele id . 165634.0 681707.0
ClinVar CLNDISDB . MedGen:CN169374|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506
ClinVar CLNDN . not_specified|Leigh_syndrome Leigh_syndrome
ClinVar CLNSIG . Uncertain_significance Uncertain_significance
MITOMAP Disease Clinical info . Leigh Disease .
MITOMAP Disease Status . Reported [VUS] .
MITOMAP Disease Hom/Het ./. -/+ ./.
MITOMAP General GenBank Freq 0.0016% 0.036% 0.0%
MITOMAP General GenBank Seqs 1 22 0
MITOMAP General Curated refs . 20525945;23301511;24448545;29253894 .
MITOMAP Variant Class polymorphism polymorphism;disease polymorphism
gnomAD 3.1 AN 56431.0 56427.0 56428.0
gnomAD 3.1 AC Homo 0.0 127.0 0.0
gnomAD 3.1 AF Hom 0.0 0.0022507 0.0
gnomAD 3.1 AC Het 0.0 2.0 0.0
gnomAD 3.1 AF Het 0.0 3.5444e-05 0.0
gnomAD 3.1 filter npg PASS npg
HelixMTdb AC Hom . 53.0 .
HelixMTdb AF Hom . 0.00027043163 .
HelixMTdb AC Het . 3.0 .
HelixMTdb AF Het . 1.530745e-05 .
HelixMTdb mean ARF . 0.53379 .
HelixMTdb max ARF . 0.74603 .
ToMMo 54KJPN AC . 4 .
ToMMo 54KJPN AF . 7.4e-05 .
ToMMo 54KJPN AN . 54302 .
COSMIC 90 . . .
dbSNP 156 id . rs587776437 rs587776437
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