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13637 (A > G)

General info

Mitimpact ID
MI.22028
Chr
chrM
Start
13637
Ref
A
Alt
G
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1301
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
CAA/CGA
AA pos
434
AA ref
Q
AA alt
R
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.13637A>G
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
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Conservation

PhyloP 100v
0.242 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.01 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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 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
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
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
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
65511
Clinvar ALLELEID
76419
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104
Clinvar CLNDN
Leigh syndrome;

leber optic atrophy
Clinvar CLNSIG
Benign
MITOMAP Allele
13637A>G
MITOMAP Disease Clinical info
Possible lhon factor
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.9733%
MITOMAP General GenBank Seqs
595
MITOMAP General GenBank Curated refs
11406419 19370763 19005266 11349229 29208909 32094358 7901141 11938495 17406640 31152278 16901986 29253894 15286228 18269758 17620140 24319328 20301353 7599218 20939899 20053576
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56431
Gnomad AC hom
643
Gnomad AF hom
0.0113944
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
3615
HelixMTdb AF hom
0.0184454
HelixMTdb AC het
36
HelixMTdb AF het
0.0001836
HelixMTdb mean ARF
0.91422
HelixMTdb max ARF
0.97175
ToMMo JPN54K AC
1
ToMMo JPN54K AF
1.8e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs200855215

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
.

13637 (A > C)

General info

Mitimpact ID
MI.22029
Chr
chrM
Start
13637
Ref
A
Alt
C
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1301
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
CAA/CCA
AA pos
434
AA ref
Q
AA alt
P
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.13637A>C
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
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Powered by MitoWheel

Conservation

PhyloP 100v
0.242 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.01 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
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
Damaging 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
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
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
.

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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
13637A>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
.

13637 (A > T)

General info

Mitimpact ID
MI.22030
Chr
chrM
Start
13637
Ref
A
Alt
T
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1301
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
CAA/CTA
AA pos
434
AA ref
Q
AA alt
L
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.13637A>T
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.242 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.01 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
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
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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
13637A>T
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
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.10667
HelixMTdb max ARF
0.10667
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
.
~ 13637 (A/G) 13637 (A/C) 13637 (A/T)
~ 13637 (CAA/CGA) 13637 (CAA/CCA) 13637 (CAA/CTA)
MitImpact id MI.22028 MI.22029 MI.22030
Chr chrM chrM chrM
Start 13637 13637 13637
Ref A A A
Alt G C T
Gene symbol MT-ND5 MT-ND5 MT-ND5
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5
Gene position 1301 1301 1301
Gene start 12337 12337 12337
Gene end 14148 14148 14148
Gene strand + + +
Codon substitution CAA/CGA CAA/CCA CAA/CTA
AA position 434 434 434
AA ref Q Q Q
AA alt R P L
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516005 516005 516005
HGVS NC_012920.1:g.13637A>G NC_012920.1:g.13637A>C NC_012920.1:g.13637A>T
HGNC id 7461 7461 7461
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198786 ENSG00000198786 ENSG00000198786
Ensembl transcript id ENST00000361567 ENST00000361567 ENST00000361567
Ensembl protein id ENSP00000354813 ENSP00000354813 ENSP00000354813
Uniprot id P03915 P03915 P03915
Uniprot name NU5M_HUMAN NU5M_HUMAN NU5M_HUMAN
Ncbi gene id 4540 4540 4540
Ncbi protein id YP_003024036.1 YP_003024036.1 YP_003024036.1
PhyloP 100V 0.242 0.242 0.242
PhyloP 470Way 0.819 0.819 0.819
PhastCons 100V 0 0 0
PhastCons 470Way 0.01 0.01 0.01
PolyPhen2 benign benign benign
PolyPhen2 score 0.01 0.01 0.18
SIFT neutral neutral neutral
SIFT score 0.36 0.23 0.69
SIFT4G Tolerated Damaging Tolerated
SIFT4G score 0.077 0.046 0.068
VEST Neutral Neutral Neutral
VEST pvalue 0.63 0.24 0.42
VEST FDR 0.7 0.45 0.5
Mitoclass.1 damaging neutral damaging
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.34 0.82 0.74
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 7.49937e-14 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE Q434R Q434P Q434L
fathmm Tolerated Tolerated Tolerated
fathmm score 1.53 1.53 1.52
fathmm converted rankscore 0.30401 0.30401 0.30669
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.1492 0.1239 0.1836
CADD Neutral Neutral Neutral
CADD score 0.579848 2.111156 2.232526
CADD phred 8.015 16.93 17.72
PROVEAN Tolerated Damaging Damaging
PROVEAN score -2.38 -4.15 -4.89
MutationAssessor low low medium
MutationAssessor score 1.835 1.755 2.575
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.816 0.846 0.798
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.646 0.586 0.568
MLC Neutral Neutral Neutral
MLC score 0.34335204 0.34335204 0.34335204
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.37 0.32 0.24
APOGEE2 Benign Likely-benign Likely-benign
APOGEE2 score 0.0553716493981075 0.21473901303539 0.162676058273109
CAROL neutral neutral neutral
CAROL score 0.63 0.77 0.19
Condel deleterious deleterious deleterious
Condel score 0.68 0.61 0.76
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -3
MtoolBox neutral deleterious neutral
MtoolBox DS 0.19 0.65 0.42
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.064807 0.079101 0.083965
DEOGEN2 converted rankscore 0.32529 0.36047 0.37173
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score 1.15 1.15 -0.12
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.1 -0.06 0.42
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 0.16 0.16 0.71
CHASM Neutral Neutral Neutral
CHASM pvalue 0.44 0.4 0.32
CHASM FDR 0.8 0.8 0.8
ClinVar id 65511.0 . .
ClinVar Allele id 76419.0 . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 . .
ClinVar CLNDN Leigh_syndrome|Leber_optic_atrophy . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info Possible LHON factor . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.9733% . 0.0%
MITOMAP General GenBank Seqs 595 . 0
MITOMAP General Curated refs 11406419;19370763;19005266;11349229;29208909;32094358;7901141;11938495;17406640;31152278;16901986;29253894;15286228;18269758;17620140;24319328;20301353;7599218;20939899;20053576 . .
MITOMAP Variant Class polymorphism;disease . polymorphism
gnomAD 3.1 AN 56431.0 . .
gnomAD 3.1 AC Homo 643.0 . .
gnomAD 3.1 AF Hom 0.0113944 . .
gnomAD 3.1 AC Het 0.0 . .
gnomAD 3.1 AF Het 0.0 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 3615.0 . 0.0
HelixMTdb AF Hom 0.018445477 . 0.0
HelixMTdb AC Het 36.0 . 1.0
HelixMTdb AF Het 0.00018368941 . 5.1024836e-06
HelixMTdb mean ARF 0.91422 . 0.10667
HelixMTdb max ARF 0.97175 . 0.10667
ToMMo 54KJPN AC 1 . .
ToMMo 54KJPN AF 1.8e-05 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs200855215 . .
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