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8414 (C > A)

General info

Mitimpact ID
MI.1549
Chr
chrM
Start
8414
Ref
C
Alt
A
Gene symbol
MT-ATP8 Extended gene annotation
Gene position
49
Gene start
8366
Gene end
8572
Gene strand
+
Codon substitution
CTC/ATC
AA pos
17
AA ref
L
AA alt
I
Functional effect
missense
OMIM ID
516070
HGVS
NC_012920.1:g.8414C>A
HGNC ID
7415
RC complex
V
Ensembl gene ID
ENSG00000228253
Ensembl protein ID
ENSP00000355265
Ensembl transcript ID
ENST00000361851
Uniprot ID
P03928
Uniprot name
ATP8_HUMAN
Ncbi gene ID
4509
Ncbi protein ID
YP_003024030.1
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Conservation

PhyloP 100v
-0.243 Conservation Score
PhyloP 470way
-2.036 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.002 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
Polymorphism 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
.
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
Benign 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
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
8414C>A
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
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
HelixMTdb AC hom
2
HelixMTdb AF hom
1.02e-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
.

8414 (C > G)

General info

Mitimpact ID
MI.1548
Chr
chrM
Start
8414
Ref
C
Alt
G
Gene symbol
MT-ATP8 Extended gene annotation
Gene position
49
Gene start
8366
Gene end
8572
Gene strand
+
Codon substitution
CTC/GTC
AA pos
17
AA ref
L
AA alt
V
Functional effect
missense
OMIM ID
516070
HGVS
NC_012920.1:g.8414C>G
HGNC ID
7415
RC complex
V
Ensembl gene ID
ENSG00000228253
Ensembl protein ID
ENSP00000355265
Ensembl transcript ID
ENST00000361851
Uniprot ID
P03928
Uniprot name
ATP8_HUMAN
Ncbi gene ID
4509
Ncbi protein ID
YP_003024030.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.243 Conservation Score
PhyloP 470way
-2.036 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.002 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
Polymorphism 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
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic 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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
8414C>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
.

8414 (C > T)

General info

Mitimpact ID
MI.1547
Chr
chrM
Start
8414
Ref
C
Alt
T
Gene symbol
MT-ATP8 Extended gene annotation
Gene position
49
Gene start
8366
Gene end
8572
Gene strand
+
Codon substitution
CTC/TTC
AA pos
17
AA ref
L
AA alt
F
Functional effect
missense
OMIM ID
516070
HGVS
NC_012920.1:g.8414C>T
HGNC ID
7415
RC complex
V
Ensembl gene ID
ENSG00000228253
Ensembl protein ID
ENSP00000355265
Ensembl transcript ID
ENST00000361851
Uniprot ID
P03928
Uniprot name
ATP8_HUMAN
Ncbi gene ID
4509
Ncbi protein ID
YP_003024030.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.243 Conservation Score
PhyloP 470way
-2.036 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.002 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
Polymorphism 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
.
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
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
692850
Clinvar ALLELEID
681386
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
8414C>T
MITOMAP Disease Clinical info
Increased risk of t2dm and high altitude polycythemia (hapc) in haplogroup d4 / longevity
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
3.7737%
MITOMAP General GenBank Seqs
2307
MITOMAP General GenBank Curated refs
19370763 19460299 21978175 31478599 25941154 18545700 33420243 15262184 21878127 15126279 19497304 19818876 19703591 18194667 15708009 24467713 23304069 7521328 11938495 15638829 21122100 7646496 16714301 1346260 24470521 10909988 16895436 8728098 24498190 8037701 24062162 19733221 35801081 24667788 19167085 29343773 34433719 17300996 18386806 8016139 2025303 10803467 19324017 16624503 12375058 18639500 15670746 10996007 16955413 24002810 15896721 18468491 22333566 16364244 16048457 20067846 17341440 30446962 22487888
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56433
Gnomad AC hom
507
Gnomad AF hom
0.0089841
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
1976
HelixMTdb AF hom
0.0100825
HelixMTdb AC het
6
HelixMTdb AF het
3.06e-05
HelixMTdb mean ARF
0.86386
HelixMTdb max ARF
0.92683
ToMMo JPN54K AC
19227
ToMMo JPN54K AF
0.354075
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs28358884

Residue interaction

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

Compensated Pathogenic Deviations

Frequency
23.41 CPD variant frequency
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.
~ 8414 (C/A) 8414 (C/G) 8414 (C/T)
~ 8414 (CTC/ATC) 8414 (CTC/GTC) 8414 (CTC/TTC)
MitImpact id MI.1549 MI.1548 MI.1547
Chr chrM chrM chrM
Start 8414 8414 8414
Ref C C C
Alt A G T
Gene symbol MT-ATP8 MT-ATP8 MT-ATP8
Extended annotation mitochondrially encoded ATP synthase membrane subunit 8 mitochondrially encoded ATP synthase membrane subunit 8 mitochondrially encoded ATP synthase membrane subunit 8
Gene position 49 49 49
Gene start 8366 8366 8366
Gene end 8572 8572 8572
Gene strand + + +
Codon substitution CTC/ATC CTC/GTC CTC/TTC
AA position 17 17 17
AA ref L L L
AA alt I V F
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516070 516070 516070
HGVS NC_012920.1:g.8414C>A NC_012920.1:g.8414C>G NC_012920.1:g.8414C>T
HGNC id 7415 7415 7415
Respiratory Chain complex V V V
Ensembl gene id ENSG00000228253 ENSG00000228253 ENSG00000228253
Ensembl transcript id ENST00000361851 ENST00000361851 ENST00000361851
Ensembl protein id ENSP00000355265 ENSP00000355265 ENSP00000355265
Uniprot id P03928 P03928 P03928
Uniprot name ATP8_HUMAN ATP8_HUMAN ATP8_HUMAN
Ncbi gene id 4509 4509 4509
Ncbi protein id YP_003024030.1 YP_003024030.1 YP_003024030.1
PhyloP 100V -0.243 -0.243 -0.243
PhyloP 470Way -2.036 -2.036 -2.036
PhastCons 100V 0 0 0
PhastCons 470Way 0.002 0.002 0.002
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 0.97 0.97 0.99
SIFT neutral neutral neutral
SIFT score 0.35 0.15 0.31
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 1.0 0.213 0.155
VEST Neutral Neutral Neutral
VEST pvalue 0.67403744 0.67403744 0.51005936
VEST FDR 0.85 0.85 0.85
Mitoclass.1 neutral damaging neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.11 0.24 0.12
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1 1 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE L17I L17V L17F
fathmm Tolerated Tolerated Tolerated
fathmm score 1.82 1.75 1.71
fathmm converted rankscore 0.25018 0.26152 0.26737
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.0878 0.1081 0.1011
CADD Neutral Neutral Neutral
CADD score 2.334719 2.046087 2.424327
CADD phred 18.39 16.51 18.98
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score 0.13 -0.69 -1.98
MutationAssessor . low .
MutationAssessor score . 1.315 .
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.99 0.996 0.998
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.928 0.934 0.788
MLC Neutral Neutral Neutral
MLC score 0.01297604 0.01297604 0.01297604
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.51 0.59 0.58
APOGEE2 Benign Benign Likely-benign
APOGEE2 score 0.0148751430306985 0.0601795700273695 0.062326488098504
CAROL neutral deleterious deleterious
CAROL score 0.97 0.99 0.99
Condel neutral neutral neutral
Condel score 0.19 0.09 0.16
COVEC WMV neutral neutral neutral
COVEC WMV score -2 -2 -2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.68 0.71 0.71
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.010577 0.018955 0.032167
DEOGEN2 converted rankscore 0.09538 0.15187 0.22369
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -2.19 -2.19 -2.65
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.14 -0.13 0.1
MutationAssessor transf low impact medium impact medium impact
MutationAssessor transf score -1.58 -0.24 -0.2
CHASM Neutral Neutral Neutral
CHASM pvalue 0.57 0.62 0.65
CHASM FDR 0.85 0.85 0.85
ClinVar id . . 692850.0
ClinVar Allele id . . 681386.0
ClinVar CLNDISDB . . MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506
ClinVar CLNDN . . Leigh_syndrome
ClinVar CLNSIG . . Benign
MITOMAP Disease Clinical info . . Increased risk of T2DM and high altitude polycythemia (HAPC) in haplogroup D4 / Longevity
MITOMAP Disease Status . . Reported
MITOMAP Disease Hom/Het ./. ./. +/-
MITOMAP General GenBank Freq 0.0% . 3.7737%
MITOMAP General GenBank Seqs 0 . 2307
MITOMAP General Curated refs . . 19370763;19460299;21978175;31478599;25941154;18545700;33420243;15262184;21878127;15126279;19497304;19818876;19703591;18194667;15708009;24467713;23304069;7521328;11938495;15638829;21122100;7646496;16714301;1346260;24470521;10909988;16895436;8728098;24498190;8037701;24062162;19733221;35801081;24667788;19167085;29343773;34433719;17300996;18386806;8016139;2025303;10803467;19324017;16624503;12375058;18639500;15670746;10996007;16955413;24002810;15896721;18468491;22333566;16364244;16048457;20067846;17341440;30446962;22487888
MITOMAP Variant Class polymorphism . polymorphism;disease
gnomAD 3.1 AN . . 56433.0
gnomAD 3.1 AC Homo . . 507.0
gnomAD 3.1 AF Hom . . 0.0089841
gnomAD 3.1 AC Het . . 0.0
gnomAD 3.1 AF Het . . 0.0
gnomAD 3.1 filter . . PASS
HelixMTdb AC Hom 2.0 . 1976.0
HelixMTdb AF Hom 1.0204967e-05 . 0.0100825075
HelixMTdb AC Het 0.0 . 6.0
HelixMTdb AF Het 0.0 . 3.06149e-05
HelixMTdb mean ARF . . 0.86386
HelixMTdb max ARF . . 0.92683
ToMMo 54KJPN AC . . 19227
ToMMo 54KJPN AF . . 0.354075
ToMMo 54KJPN AN . . 54302
COSMIC 90 . . .
dbSNP 156 id . . rs28358884
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