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9438 (G > A)

General info

Mitimpact ID
MI.7123
Chr
chrM
Start
9438
Ref
G
Alt
A
Gene symbol
MT-CO3 Extended gene annotation
Gene position
232
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GGC/AGC
AA pos
78
AA ref
G
AA alt
S
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9438G>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
2.254 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.993 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
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
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
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
Neutral 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
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
Neutral Score and details of the meta-predictor

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
9651
Clinvar ALLELEID
24690
Clinvar CLNDISDB
Human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leber optic atrophy;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
9438G>A
MITOMAP Disease Clinical info
Lhon / gout
MITOMAP Disease Status
Conflicting reports
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
1.2448%
MITOMAP General GenBank Seqs
761
MITOMAP General GenBank Curated refs
10520236 17170302 16132471 8037217 21457906 18246027 18161625 7710535 20388556 22927010 23332919 16714301 8240356 7804416 8037201 8053461 16172508 7599218 12870132 7573056 21041797 29976239 22333566 14563219 15791543 20003445 18445251
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56418
Gnomad AC hom
192
Gnomad AF hom
0.0034031
Gnomad AC het
6
Gnomad AF het
0.0001063
Gnomad filter
Pass
HelixMTdb AC hom
589
HelixMTdb AF hom
0.0030053
HelixMTdb AC het
22
HelixMTdb AF het
0.0001122
HelixMTdb mean ARF
0.39247
HelixMTdb max ARF
0.91797
ToMMo JPN54K AC
41
ToMMo JPN54K AF
0.000755
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs267606611

Residue interaction

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

Compensated Pathogenic Deviations

Frequency
2.97 CPD variant frequency
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

9438 (G > C)

General info

Mitimpact ID
MI.7124
Chr
chrM
Start
9438
Ref
G
Alt
C
Gene symbol
MT-CO3 Extended gene annotation
Gene position
232
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GGC/CGC
AA pos
78
AA ref
G
AA alt
R
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9438G>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
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Powered by MitoWheel

Conservation

PhyloP 100v
2.254 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.993 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
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
Damaging 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
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
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
9438G>C
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
.

9438 (G > T)

General info

Mitimpact ID
MI.7125
Chr
chrM
Start
9438
Ref
G
Alt
T
Gene symbol
MT-CO3 Extended gene annotation
Gene position
232
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GGC/TGC
AA pos
78
AA ref
G
AA alt
C
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9438G>T
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
2.254 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.993 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
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
Medium Score and details of the predictor
EFIN SP
Neutral Score and details of the predictor
EFIN HD
Damaging 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-pathogenic 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
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
9438G>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
.
~ 9438 (G/A) 9438 (G/C) 9438 (G/T)
~ 9438 (GGC/AGC) 9438 (GGC/CGC) 9438 (GGC/TGC)
MitImpact id MI.7123 MI.7124 MI.7125
Chr chrM chrM chrM
Start 9438 9438 9438
Ref G G G
Alt A C T
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 232 232 232
Gene start 9207 9207 9207
Gene end 9990 9990 9990
Gene strand + + +
Codon substitution GGC/AGC GGC/CGC GGC/TGC
AA position 78 78 78
AA ref G G G
AA alt S R C
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516050 516050 516050
HGVS NC_012920.1:g.9438G>A NC_012920.1:g.9438G>C NC_012920.1:g.9438G>T
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 2.254 2.254 2.254
PhyloP 470Way 0.848 0.848 0.848
PhastCons 100V 1 1 1
PhastCons 470Way 0.993 0.993 0.993
PolyPhen2 benign probably_damaging probably_damaging
PolyPhen2 score 0.1 0.98 0.99
SIFT neutral neutral neutral
SIFT score 0.41 0.36 0.18
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.033 0.0 0.0
VEST Neutral Neutral Neutral
VEST pvalue 0.23 0.09 0.07
VEST FDR 0.45 0.4 0.35
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Pathogenic Neutral
SNPDryad score 0.34 1 0.84
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 7.80213e-08 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE G78S G78R G78C
fathmm Tolerated Tolerated Tolerated
fathmm score 2.03 1.93 1.9
fathmm converted rankscore 0.20959 0.22881 0.23486
AlphaMissense likely_benign likely_pathogenic likely_pathogenic
AlphaMissense score 0.297 0.9701 0.7655
CADD Neutral Deleterious Deleterious
CADD score 2.331796 3.903941 4.059363
CADD phred 18.37 23.5 23.7
PROVEAN Damaging Damaging Damaging
PROVEAN score -4.27 -6.15 -7.29
MutationAssessor medium high medium
MutationAssessor score 2.07 4.97 3.475
EFIN SP Damaging Neutral Neutral
EFIN SP score 0.224 0.7 0.656
EFIN HD Neutral Damaging Damaging
EFIN HD score 0.59 0.154 0.158
MLC Neutral Neutral Neutral
MLC score 0.34537389 0.34537389 0.34537389
PANTHER score 0.179 . .
PhD-SNP score 0.876 . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.93 0.47 0.4
APOGEE2 VUS VUS+ Likely-pathogenic
APOGEE2 score 0.43836995239623 0.62705388853292 0.762712124442482
CAROL neutral deleterious deleterious
CAROL score 0.53 0.98 1
Condel deleterious neutral neutral
Condel score 0.66 0.19 0.1
COVEC WMV neutral deleterious deleterious
COVEC WMV score -3 2 2
MtoolBox neutral deleterious deleterious
MtoolBox DS 0.27 0.86 0.87
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.112244 0.141234 0.192005
DEOGEN2 converted rankscore 0.42836 0.47618 0.54702
Meta-SNP Neutral . .
Meta-SNP score 0.238 . .
PolyPhen2 transf medium impact low impact low impact
PolyPhen2 transf score 0.06 -2.51 -2.81
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.1 0.05 -0.18
MutationAssessor transf medium impact high impact high impact
MutationAssessor transf score 0.74 2.12 2.03
CHASM Neutral Neutral Neutral
CHASM pvalue 0.46 0.43 0.08
CHASM FDR 0.8 0.8 0.8
ClinVar id 9651.0 . .
ClinVar Allele id 24690.0 . .
ClinVar CLNDISDB Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN Leber_optic_atrophy|Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info LHON / gout . .
MITOMAP Disease Status Conflicting reports . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 1.2448% . .
MITOMAP General GenBank Seqs 761 . .
MITOMAP General Curated refs 10520236;17170302;16132471;8037217;21457906;18246027;18161625;7710535;20388556;22927010;23332919;16714301;8240356;7804416;8037201;8053461;16172508;7599218;12870132;7573056;21041797;29976239;22333566;14563219;15791543;20003445;18445251 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56418.0 . .
gnomAD 3.1 AC Homo 192.0 . .
gnomAD 3.1 AF Hom 0.00340317 . .
gnomAD 3.1 AC Het 6.0 . .
gnomAD 3.1 AF Het 0.000106349 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 589.0 . .
HelixMTdb AF Hom 0.0030053628 . .
HelixMTdb AC Het 22.0 . .
HelixMTdb AF Het 0.00011225463 . .
HelixMTdb mean ARF 0.39247 . .
HelixMTdb max ARF 0.91797 . .
ToMMo 54KJPN AC 41 . .
ToMMo 54KJPN AF 0.000755 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs267606611 . .
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