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4136 (A > C)

General info

Mitimpact ID
MI.12486
Chr
chrM
Start
4136
Ref
A
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
830
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAC/TCC
AA pos
277
AA ref
Y
AA alt
S
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4136A>C
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
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Powered by MitoWheel

Conservation

PhyloP 100v
7.056 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.014 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
Neutral Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-pathogenic 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
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
4136A>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0033%
MITOMAP General GenBank Seqs
2
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56433
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
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.125
HelixMTdb max ARF
0.125
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
.

4136 (A > G)

General info

Mitimpact ID
MI.12485
Chr
chrM
Start
4136
Ref
A
Alt
G
Gene symbol
MT-ND1 Extended gene annotation
Gene position
830
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAC/TGC
AA pos
277
AA ref
Y
AA alt
C
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4136A>G
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.056 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.014 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
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
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
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
Neutral Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
Disease 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
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
Disease Score and details of the meta-predictor

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
9727
Clinvar ALLELEID
24766
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
4136A>G
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported - possibly synergistic
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.1161%
MITOMAP General GenBank Seqs
71
MITOMAP General GenBank Curated refs
7760326 22108605 19616643 7635294 2018041 8751850 7977345 9302261 35699829 9150158 15972314 7599217 21457906 29253894 18216301 22487888
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56415
Gnomad AC hom
35
Gnomad AF hom
0.0006204
Gnomad AC het
6
Gnomad AF het
0.0001063
Gnomad filter
Pass
HelixMTdb AC hom
140
HelixMTdb AF hom
0.0007143
HelixMTdb AC het
28
HelixMTdb AF het
0.0001428
HelixMTdb mean ARF
0.40005
HelixMTdb max ARF
0.90291
ToMMo JPN54K AC
45
ToMMo JPN54K AF
0.000829
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs199476121

Residue interaction

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

Compensated Pathogenic Deviations

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

4136 (A > T)

General info

Mitimpact ID
MI.12484
Chr
chrM
Start
4136
Ref
A
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
830
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAC/TTC
AA pos
277
AA ref
Y
AA alt
F
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4136A>T
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.056 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.014 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
Likely benign Score and details of the predictor
CADD
Deleterious 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
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

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
.

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
4136A>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
.
~ 4136 (A/C) 4136 (A/G) 4136 (A/T)
~ 4136 (TAC/TCC) 4136 (TAC/TGC) 4136 (TAC/TTC)
MitImpact id MI.12486 MI.12485 MI.12484
Chr chrM chrM chrM
Start 4136 4136 4136
Ref A A A
Alt C G T
Gene symbol MT-ND1 MT-ND1 MT-ND1
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1
Gene position 830 830 830
Gene start 3307 3307 3307
Gene end 4262 4262 4262
Gene strand + + +
Codon substitution TAC/TCC TAC/TGC TAC/TTC
AA position 277 277 277
AA ref Y Y Y
AA alt S C F
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516000 516000 516000
HGVS NC_012920.1:g.4136A>C NC_012920.1:g.4136A>G NC_012920.1:g.4136A>T
HGNC id 7455 7455 7455
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198888 ENSG00000198888 ENSG00000198888
Ensembl transcript id ENST00000361390 ENST00000361390 ENST00000361390
Ensembl protein id ENSP00000354687 ENSP00000354687 ENSP00000354687
Uniprot id P03886 P03886 P03886
Uniprot name NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN
Ncbi gene id 4535 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1 YP_003024026.1
PhyloP 100V 7.056 7.056 7.056
PhyloP 470Way 0.58 0.58 0.58
PhastCons 100V 1 1 1
PhastCons 470Way 0.014 0.014 0.014
PolyPhen2 probably_damaging probably_damaging possibly_damaging
PolyPhen2 score 0.94 0.98 0.74
SIFT neutral neutral neutral
SIFT score 0.4 0.14 0.78
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.004 0.004 0.004
VEST Neutral Pathogenic Neutral
VEST pvalue 0.06 0.05 0.21
VEST FDR 0.35 0.35 0.45
Mitoclass.1 damaging damaging neutral
SNPDryad Pathogenic Pathogenic Neutral
SNPDryad score 1.0 1.0 0.8
MutationTaster Polymorphism Disease automatic Polymorphism
MutationTaster score 0.999998 1.19993e-05 0.999856
MutationTaster converted rankscore 0.08975 0.18198 0.20048
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE Y277S Y277C Y277F
fathmm Tolerated Tolerated Tolerated
fathmm score 2.65 2.61 2.71
fathmm converted rankscore 0.12676 0.13095 0.12055
AlphaMissense likely_pathogenic ambiguous likely_benign
AlphaMissense score 0.5842 0.454 0.1468
CADD Deleterious Deleterious Deleterious
CADD score 3.742591 3.573686 3.448066
CADD phred 23.3 23.2 23.0
PROVEAN Damaging Damaging Damaging
PROVEAN score -8.05 -8.05 -3.56
MutationAssessor high high low
MutationAssessor score 4.075 4.075 0.94
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.696 0.828 0.654
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.5 0.37 0.448
MLC Deleterious Deleterious Deleterious
MLC score 0.64566359 0.64566359 0.64566359
PANTHER score . 0.637 .
PhD-SNP score . 0.775 .
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.66 0.71 0.55
APOGEE2 Likely-pathogenic Likely-pathogenic VUS
APOGEE2 score 0.730580261898728 0.747408192173243 0.507959907109622
CAROL neutral deleterious neutral
CAROL score 0.94 0.99 0.69
Condel neutral neutral deleterious
Condel score 0.23 0.08 0.52
COVEC WMV deleterious deleterious neutral
COVEC WMV score 2 2 -3
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.77 0.76 0.62
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.123855 0.147178 0.102646
DEOGEN2 converted rankscore 0.44850 0.48514 0.41057
Meta-SNP . Disease .
Meta-SNP score . 0.871 .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -1.87 -2.34 -1.18
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.18 -0.17 0.58
MutationAssessor transf high impact high impact medium impact
MutationAssessor transf score 2.04 2.34 0.2
CHASM Neutral Neutral Neutral
CHASM pvalue 0.19 0.03 0.33
CHASM FDR 0.8 0.8 0.8
ClinVar id . 9727.0 .
ClinVar Allele id . 24766.0 .
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 .
MITOMAP Disease Status . Reported - possibly synergistic .
MITOMAP Disease Hom/Het ./. +/- ./.
MITOMAP General GenBank Freq 0.0033% 0.1161% .
MITOMAP General GenBank Seqs 2 71 .
MITOMAP General Curated refs . 7760326;22108605;19616643;7635294;2018041;8751850;7977345;9302261;35699829;9150158;15972314;7599217;21457906;29253894;18216301;22487888 .
MITOMAP Variant Class polymorphism polymorphism;disease .
gnomAD 3.1 AN 56433.0 56415.0 .
gnomAD 3.1 AC Homo 0.0 35.0 .
gnomAD 3.1 AF Hom 0.0 0.0006204019999999999 .
gnomAD 3.1 AC Het 0.0 6.0 .
gnomAD 3.1 AF Het 0.0 0.000106355 .
gnomAD 3.1 filter npg PASS .
HelixMTdb AC Hom 0.0 140.0 .
HelixMTdb AF Hom 0.0 0.0007143477 .
HelixMTdb AC Het 1.0 28.0 .
HelixMTdb AF Het 5.1024836e-06 0.00014286954 .
HelixMTdb mean ARF 0.125 0.40005 .
HelixMTdb max ARF 0.125 0.90291 .
ToMMo 54KJPN AC . 45 .
ToMMo 54KJPN AF . 0.000829 .
ToMMo 54KJPN AN . 54302 .
COSMIC 90 . . .
dbSNP 156 id . rs199476121 .
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