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11084 (A > C)

General info

Mitimpact ID
MI.17006
Chr
chrM
Start
11084
Ref
A
Alt
C
Gene symbol
MT-ND4 Extended gene annotation
Gene position
325
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
ACA/CCA
AA pos
109
AA ref
T
AA alt
P
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11084A>C
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
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Powered by MitoWheel

Conservation

PhyloP 100v
3.11 Conservation Score
PhyloP 470way
-0.008 Conservation Score
PhastCons 100v
0.998 Conservation Score
PhastCons 470way
0.024 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
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
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
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
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
11084A>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
1757091
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
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
.

11084 (A > G)

General info

Mitimpact ID
MI.17005
Chr
chrM
Start
11084
Ref
A
Alt
G
Gene symbol
MT-ND4 Extended gene annotation
Gene position
325
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
ACA/GCA
AA pos
109
AA ref
T
AA alt
A
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11084A>G
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.11 Conservation Score
PhyloP 470way
-0.008 Conservation Score
PhastCons 100v
0.998 Conservation Score
PhastCons 470way
0.024 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly 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 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
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
Neutral 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
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
High 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
9709
Clinvar ALLELEID
24748
Clinvar CLNDISDB
Mondo:mondo:0010789, medgen:c0162671, omim:540000, orphanet:550;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Juvenile myopathy, encephalopathy, lactic acidosis and stroke;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
11084A>G
MITOMAP Disease Clinical info
Ad, pd melas
MITOMAP Disease Status
Conflicting reports
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
0.3664%
MITOMAP General GenBank Seqs
224
MITOMAP General GenBank Curated refs
11843871 23563965 21099167 2043137 8213827 16895436 15505787 15533721 18468491 18691441 15972314 24667788 20067846 29987491 18545700 21457906 1323207 16714301
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56432
Gnomad AC hom
94
Gnomad AF hom
0.0016657
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
471
HelixMTdb AF hom
0.0024032
HelixMTdb AC het
2
HelixMTdb AF het
1.02e-05
HelixMTdb mean ARF
0.64334
HelixMTdb max ARF
0.85714
ToMMo JPN54K AC
3515
ToMMo JPN54K AF
0.064731
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs199476113

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
.

11084 (A > T)

General info

Mitimpact ID
MI.17004
Chr
chrM
Start
11084
Ref
A
Alt
T
Gene symbol
MT-ND4 Extended gene annotation
Gene position
325
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
ACA/TCA
AA pos
109
AA ref
T
AA alt
S
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11084A>T
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.11 Conservation Score
PhyloP 470way
-0.008 Conservation Score
PhastCons 100v
0.998 Conservation Score
PhastCons 470way
0.024 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly 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
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
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
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
Likely-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
.
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
11084A>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
.
~ 11084 (A/C) 11084 (A/G) 11084 (A/T)
~ 11084 (ACA/CCA) 11084 (ACA/GCA) 11084 (ACA/TCA)
MitImpact id MI.17006 MI.17005 MI.17004
Chr chrM chrM chrM
Start 11084 11084 11084
Ref A A A
Alt C G T
Gene symbol MT-ND4 MT-ND4 MT-ND4
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4
Gene position 325 325 325
Gene start 10760 10760 10760
Gene end 12137 12137 12137
Gene strand + + +
Codon substitution ACA/CCA ACA/GCA ACA/TCA
AA position 109 109 109
AA ref T T T
AA alt P A S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516003 516003 516003
HGVS NC_012920.1:g.11084A>C NC_012920.1:g.11084A>G NC_012920.1:g.11084A>T
HGNC id 7459 7459 7459
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198886 ENSG00000198886 ENSG00000198886
Ensembl transcript id ENST00000361381 ENST00000361381 ENST00000361381
Ensembl protein id ENSP00000354961 ENSP00000354961 ENSP00000354961
Uniprot id P03905 P03905 P03905
Uniprot name NU4M_HUMAN NU4M_HUMAN NU4M_HUMAN
Ncbi gene id 4538 4538 4538
Ncbi protein id YP_003024035.1 YP_003024035.1 YP_003024035.1
PhyloP 100V 3.11 3.11 3.11
PhyloP 470Way -0.008 -0.008 -0.008
PhastCons 100V 0.998 0.998 0.998
PhastCons 470Way 0.024 0.024 0.024
PolyPhen2 probably_damaging possibly_damaging possibly_damaging
PolyPhen2 score 0.98 0.81 0.89
SIFT deleterious neutral neutral
SIFT score 0.04 1.0 0.27
SIFT4G Damaging Tolerated Damaging
SIFT4G score 0.002 1.0 0.011
VEST Pathogenic Neutral Neutral
VEST pvalue 0.04 0.34 0.49
VEST FDR 0.35 0.5 0.55
Mitoclass.1 damaging neutral neutral
SNPDryad Pathogenic Neutral Neutral
SNPDryad score 0.97 0.59 0.62
MutationTaster Polymorphism Disease automatic Polymorphism
MutationTaster score 1 5.41935e-08 0.999999
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE T109P T109A T109S
fathmm Tolerated Tolerated Tolerated
fathmm score 1.08 1.3 1.17
fathmm converted rankscore 0.39401 0.35590 0.37910
AlphaMissense likely_pathogenic likely_benign ambiguous
AlphaMissense score 0.875 0.1896 0.4212
CADD Deleterious Neutral Deleterious
CADD score 3.350782 0.621844 3.120626
CADD phred 22.9 8.306 22.6
PROVEAN Damaging Tolerated Tolerated
PROVEAN score -3.22 -1.32 -1.67
MutationAssessor medium low medium
MutationAssessor score 3.43 1.145 2.625
EFIN SP Neutral Damaging Neutral
EFIN SP score 0.84 0.274 0.722
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.362 0.756 0.608
MLC Neutral Neutral Neutral
MLC score 0.39830406 0.39830406 0.39830406
PANTHER score . . .
PhD-SNP score . 0.312 .
APOGEE1 Neutral Pathogenic Neutral
APOGEE1 score 0.39 0.94 0.49
APOGEE2 VUS+ VUS- Likely-benign
APOGEE2 score 0.65107812042749 0.298052633383873 0.21646614175768
CAROL deleterious neutral neutral
CAROL score 1.0 0.81 0.92
Condel neutral deleterious neutral
Condel score 0.03 0.6 0.19
COVEC WMV deleterious neutral .
COVEC WMV score 5 -3 0
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.84 0.66 0.76
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.338599 0.026581 0.031592
DEOGEN2 converted rankscore 0.70784 0.19643 0.22111
Meta-SNP . Neutral .
Meta-SNP score . 0.262 .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -2.31 -1.31 -1.57
SIFT_transf medium impact high impact medium impact
SIFT transf score -0.57 1.88 -0.04
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 1.98 -0.04 1.63
CHASM Neutral Neutral Neutral
CHASM pvalue 0.4 0.28 0.65
CHASM FDR 0.8 0.8 0.8
ClinVar id . 9709.0 .
ClinVar Allele id . 24748.0 .
ClinVar CLNDISDB . MONDO:MONDO:0010789,MedGen:C0162671,OMIM:540000,Orphanet:550|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN . Juvenile_myopathy,_encephalopathy,_lactic_acidosis_AND_stroke|Leigh_syndrome .
ClinVar CLNSIG . Benign .
MITOMAP Disease Clinical info . AD, PD MELAS .
MITOMAP Disease Status . Conflicting reports .
MITOMAP Disease Hom/Het ./. +/+ ./.
MITOMAP General GenBank Freq 0.0% 0.3664% .
MITOMAP General GenBank Seqs 0 224 .
MITOMAP General Curated refs 1757091 11843871;23563965;21099167;2043137;8213827;16895436;15505787;15533721;18468491;18691441;15972314;24667788;20067846;29987491;18545700;21457906;1323207;16714301 .
MITOMAP Variant Class polymorphism polymorphism;disease .
gnomAD 3.1 AN . 56432.0 .
gnomAD 3.1 AC Homo . 94.0 .
gnomAD 3.1 AF Hom . 0.00166572 .
gnomAD 3.1 AC Het . 1.0 .
gnomAD 3.1 AF Het . 1.77204e-05 .
gnomAD 3.1 filter . PASS .
HelixMTdb AC Hom . 471.0 .
HelixMTdb AF Hom . 0.0024032698 .
HelixMTdb AC Het . 2.0 .
HelixMTdb AF Het . 1.0204967e-05 .
HelixMTdb mean ARF . 0.64334 .
HelixMTdb max ARF . 0.85714 .
ToMMo 54KJPN AC . 3515 .
ToMMo 54KJPN AF . 0.064731 .
ToMMo 54KJPN AN . 54302 .
COSMIC 90 . . .
dbSNP 156 id . rs199476113 .
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