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12811 (T > C)

General info

Mitimpact ID
MI.20263
Chr
chrM
Start
12811
Ref
T
Alt
C
Gene symbol
MT-ND5 Extended gene annotation
Gene position
475
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
TAC/CAC
AA pos
159
AA ref
Y
AA alt
H
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.12811T>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
-1.369 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.785 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
Neutral 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
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
Neutral 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
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
65510
Clinvar ALLELEID
76418
Clinvar CLNDISDB
Medgen:cn517202;

mondo:mondo:0044970, medgen:c0751651, orphanet:68380;

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
Not provided;

mitochondrial disease;

leigh syndrome;

leber optic atrophy
Clinvar CLNSIG
Benign
MITOMAP Allele
12811T>C
MITOMAP Disease Clinical info
Possible lhon factor
MITOMAP Disease Status
Reported [b]
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
1.1139%
MITOMAP General GenBank Seqs
681
MITOMAP General GenBank Curated refs
21978175 21281460 31478599 22110754 19022198 18545700 19818876 32094358 17434142 21099167 17072496 23304069 7901141 8600429 11938495 19026397 17406640 15638829 16404693 19527690 29253894 16714301 16895436 20301353 24667788 19167085 7599218 12436196 33493461 29387390 17259400 29987491 31797714 17257906 20067846 30446962
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56431
Gnomad AC hom
328
Gnomad AF hom
0.0058124
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
1274
HelixMTdb AF hom
0.0065005
HelixMTdb AC het
14
HelixMTdb AF het
7.14e-05
HelixMTdb mean ARF
0.7633299
HelixMTdb max ARF
0.91667
ToMMo JPN54K AC
2645
ToMMo JPN54K AF
0.048709
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs199974018

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
.

12811 (T > A)

General info

Mitimpact ID
MI.20262
Chr
chrM
Start
12811
Ref
T
Alt
A
Gene symbol
MT-ND5 Extended gene annotation
Gene position
475
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
TAC/AAC
AA pos
159
AA ref
Y
AA alt
N
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.12811T>A
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
-1.369 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.785 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
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 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
Deleterious 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
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
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
12811T>A
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
.

12811 (T > G)

General info

Mitimpact ID
MI.20261
Chr
chrM
Start
12811
Ref
T
Alt
G
Gene symbol
MT-ND5 Extended gene annotation
Gene position
475
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
TAC/GAC
AA pos
159
AA ref
Y
AA alt
D
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.12811T>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-1.369 Conservation Score
PhyloP 470way
0.666 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.785 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
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
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
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
Deleterious 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
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
12811T>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
.
~ 12811 (T/C) 12811 (T/A) 12811 (T/G)
~ 12811 (TAC/CAC) 12811 (TAC/AAC) 12811 (TAC/GAC)
MitImpact id MI.20263 MI.20262 MI.20261
Chr chrM chrM chrM
Start 12811 12811 12811
Ref T T T
Alt C A G
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 475 475 475
Gene start 12337 12337 12337
Gene end 14148 14148 14148
Gene strand + + +
Codon substitution TAC/CAC TAC/AAC TAC/GAC
AA position 159 159 159
AA ref Y Y Y
AA alt H N D
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516005 516005 516005
HGVS NC_012920.1:g.12811T>C NC_012920.1:g.12811T>A NC_012920.1:g.12811T>G
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 -1.369 -1.369 -1.369
PhyloP 470Way 0.666 0.666 0.666
PhastCons 100V 0 0 0
PhastCons 470Way 0.785 0.785 0.785
PolyPhen2 benign possibly_damaging possibly_damaging
PolyPhen2 score 0.01 0.48 0.75
SIFT neutral neutral neutral
SIFT score 0.52 0.31 0.22
SIFT4G Tolerated Damaging Damaging
SIFT4G score 0.349 0.005 0.001
VEST Neutral Neutral Neutral
VEST pvalue 0.62 0.46 0.41
VEST FDR 0.65 0.55 0.5
Mitoclass.1 neutral damaging damaging
SNPDryad Pathogenic Pathogenic Pathogenic
SNPDryad score 0.98 0.99 0.96
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 0.000140357 0.998428 0.998863
MutationTaster converted rankscore 0.20048 0.22162 0.21844
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE Y159H Y159N Y159D
fathmm Tolerated Tolerated Tolerated
fathmm score 4.62 4.7 4.66
fathmm converted rankscore 0.01834 0.01673 0.01756
AlphaMissense likely_benign likely_benign ambiguous
AlphaMissense score 0.123 0.1595 0.3605
CADD Neutral Neutral Deleterious
CADD score 0.043467 2.254487 3.535134
CADD phred 3.016 17.87 23.1
PROVEAN Tolerated Damaging Damaging
PROVEAN score -1.81 -6.07 -7.26
MutationAssessor neutral low medium
MutationAssessor score 0.68 1.27 2.165
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.828 0.788 0.75
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.97 0.686 0.368
MLC Deleterious Deleterious Deleterious
MLC score 0.63974893 0.63974893 0.63974893
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.32 0.28 0.36
APOGEE2 Benign VUS- VUS+
APOGEE2 score 0.011745441687242 0.321958989354946 0.571234760296309
CAROL neutral neutral neutral
CAROL score 0.46 0.66 0.85
Condel deleterious neutral neutral
Condel score 0.76 0.42 0.24
COVEC WMV neutral neutral .
COVEC WMV score -6 -3 0
MtoolBox neutral deleterious deleterious
MtoolBox DS 0.17 0.43 0.56
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.029089 0.091686 0.09079
DEOGEN2 converted rankscore 0.20925 0.38848 0.38659
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact medium impact low impact
PolyPhen2 transf score 1.15 -0.71 -1.2
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.25 0.04 -0.07
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score -0.36 0.48 1.96
CHASM Neutral Neutral Neutral
CHASM pvalue 0.4 0.35 0.37
CHASM FDR 0.8 0.8 0.8
ClinVar id 65510.0 . .
ClinVar Allele id 76418.0 . .
ClinVar CLNDISDB MedGen:CN517202|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|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 not_provided|Mitochondrial_disease|Leigh_syndrome|Leber_optic_atrophy . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info Possible LHON factor . .
MITOMAP Disease Status Reported [B] . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 1.1139% . .
MITOMAP General GenBank Seqs 681 . .
MITOMAP General Curated refs 21978175;21281460;31478599;22110754;19022198;18545700;19818876;32094358;17434142;21099167;17072496;23304069;7901141;8600429;11938495;19026397;17406640;15638829;16404693;19527690;29253894;16714301;16895436;20301353;24667788;19167085;7599218;12436196;33493461;29387390;17259400;29987491;31797714;17257906;20067846;30446962 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56431.0 . .
gnomAD 3.1 AC Homo 328.0 . .
gnomAD 3.1 AF Hom 0.00581241 . .
gnomAD 3.1 AC Het 1.0 . .
gnomAD 3.1 AF Het 1.77208e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 1274.0 . .
HelixMTdb AF Hom 0.006500564 . .
HelixMTdb AC Het 14.0 . .
HelixMTdb AF Het 7.143477e-05 . .
HelixMTdb mean ARF 0.76333 . .
HelixMTdb max ARF 0.91667 . .
ToMMo 54KJPN AC 2645 . .
ToMMo 54KJPN AF 0.048709 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs199974018 . .
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