Logo MitImpact
Home Description Output legend Molecular Dynamics How to cite License

8803 (A > T)

General info

Mitimpact ID
MI.589
Chr
chrM
Start
8803
Ref
A
Alt
T
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
277
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ACA/TCA
AA pos
93
AA ref
T
AA alt
S
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8803A>T
HGNC ID
7414
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot ID
P00846
Uniprot name
ATP6_HUMAN
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.089 Conservation Score
PhyloP 470way
0.929 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.77 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
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
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
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
235370
Clinvar ALLELEID
237056
Clinvar CLNDISDB
Medgen:cn517202;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

mondo:mondo:0044970, medgen:c0751651, orphanet:68380
Clinvar CLNDN
Not provided;

leigh syndrome;

mitochondrial disease
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
8803A>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0131%
MITOMAP General GenBank Seqs
8
MITOMAP General GenBank Curated refs
15465027 11938495 20700462
MITOMAP Variant Class
polymorphism
Gnomad AN
56434
Gnomad AC hom
22
Gnomad AF hom
0.0003898
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
159
HelixMTdb AF hom
0.0008112
HelixMTdb AC het
5
HelixMTdb AF het
2.55e-05
HelixMTdb mean ARF
0.88274
HelixMTdb max ARF
0.92308
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs878853020

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
.

8803 (A > C)

General info

Mitimpact ID
MI.590
Chr
chrM
Start
8803
Ref
A
Alt
C
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
277
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ACA/CCA
AA pos
93
AA ref
T
AA alt
P
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8803A>C
HGNC ID
7414
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot ID
P00846
Uniprot name
ATP6_HUMAN
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.089 Conservation Score
PhyloP 470way
0.929 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.77 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 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
High 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
.

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
8803A>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
.

8803 (A > G)

General info

Mitimpact ID
MI.591
Chr
chrM
Start
8803
Ref
A
Alt
G
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
277
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ACA/GCA
AA pos
93
AA ref
T
AA alt
A
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8803A>G
HGNC ID
7414
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot ID
P00846
Uniprot name
ATP6_HUMAN
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.089 Conservation Score
PhyloP 470way
0.929 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.77 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
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
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
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
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
692989
Clinvar ALLELEID
681525
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Likely benign
MITOMAP Allele
8803A>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0147%
MITOMAP General GenBank Seqs
9
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56433
Gnomad AC hom
26
Gnomad AF hom
0.0004607
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
69
HelixMTdb AF hom
0.000352
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.85714
HelixMTdb max ARF
0.85714
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs878853020

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
.
~ 8803 (A/T) 8803 (A/C) 8803 (A/G)
~ 8803 (ACA/TCA) 8803 (ACA/CCA) 8803 (ACA/GCA)
MitImpact id MI.589 MI.590 MI.591
Chr chrM chrM chrM
Start 8803 8803 8803
Ref A A A
Alt T C G
Gene symbol MT-ATP6 MT-ATP6 MT-ATP6
Extended annotation mitochondrially encoded ATP synthase membrane subunit 6 mitochondrially encoded ATP synthase membrane subunit 6 mitochondrially encoded ATP synthase membrane subunit 6
Gene position 277 277 277
Gene start 8527 8527 8527
Gene end 9207 9207 9207
Gene strand + + +
Codon substitution ACA/TCA ACA/CCA ACA/GCA
AA position 93 93 93
AA ref T T T
AA alt S P A
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516060 516060 516060
HGVS NC_012920.1:g.8803A>T NC_012920.1:g.8803A>C NC_012920.1:g.8803A>G
HGNC id 7414 7414 7414
Respiratory Chain complex V V V
Ensembl gene id ENSG00000198899 ENSG00000198899 ENSG00000198899
Ensembl transcript id ENST00000361899 ENST00000361899 ENST00000361899
Ensembl protein id ENSP00000354632 ENSP00000354632 ENSP00000354632
Uniprot id P00846 P00846 P00846
Uniprot name ATP6_HUMAN ATP6_HUMAN ATP6_HUMAN
Ncbi gene id 4508 4508 4508
Ncbi protein id YP_003024031.1 YP_003024031.1 YP_003024031.1
PhyloP 100V 7.089 7.089 7.089
PhyloP 470Way 0.929 0.929 0.929
PhastCons 100V 1 1 1
PhastCons 470Way 0.77 0.77 0.77
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 0.99 1.0 0.99
SIFT neutral neutral deleterious
SIFT score 0.17 0.05 0.03
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.001 0.0 0.012
VEST Neutral Neutral Neutral
VEST pvalue 0.46 0.18 0.48
VEST FDR 0.65 0.65 0.65
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Pathogenic Neutral
SNPDryad score 0.88 0.99 0.63
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 0.951047 0.562649 0.867998
MutationTaster converted rankscore 0.26484 0.31244 0.28252
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE T93S T93P T93A
fathmm Tolerated Tolerated Tolerated
fathmm score 4.22 4.2 4.3
fathmm converted rankscore 0.02640 0.02689 0.02437
AlphaMissense ambiguous likely_benign likely_benign
AlphaMissense score 0.3414 0.2438 0.2729
CADD Deleterious Deleterious Deleterious
CADD score 3.168962 3.465532 3.415409
CADD phred 22.7 23.0 23.0
PROVEAN Damaging Damaging Damaging
PROVEAN score -3.46 -5.37 -4.24
MutationAssessor medium high high
MutationAssessor score 3.28 4.3 3.95
EFIN SP Neutral Damaging Neutral
EFIN SP score 0.602 0.532 0.806
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.538 0.41 0.578
MLC Neutral Neutral Neutral
MLC score 0.12939827 0.12939827 0.12939827
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.37 0.35 0.4
APOGEE2 Likely-benign VUS- Likely-benign
APOGEE2 score 0.138094870474602 0.330019454834901 0.0958420322413996
CAROL deleterious deleterious deleterious
CAROL score 0.99 1 1
Condel neutral neutral neutral
Condel score 0.09 0.03 0.02
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 1 1 5
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.71 0.78 0.68
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.113189 0.123138 0.118071
DEOGEN2 converted rankscore 0.43004 0.44729 0.43861
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -2.65 -3.6 -2.65
SIFT_transf medium impact medium impact medium impact
SIFT transf score -0.1 -0.43 -0.56
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 0.69 1.66 0.99
CHASM Neutral Neutral Neutral
CHASM pvalue 0.57 0.5 0.5
CHASM FDR 0.9 0.9 0.9
ClinVar id 235370.0 . 692989.0
ClinVar Allele id 237056.0 . 681525.0
ClinVar CLNDISDB MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380 . MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506
ClinVar CLNDN not_provided|Leigh_syndrome|Mitochondrial_disease . Leigh_syndrome
ClinVar CLNSIG Uncertain_significance . Likely_benign
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 0.0131% . 0.0147%
MITOMAP General GenBank Seqs 8 . 9
MITOMAP General Curated refs 15465027;11938495;20700462 . .
MITOMAP Variant Class polymorphism . polymorphism
gnomAD 3.1 AN 56434.0 . 56433.0
gnomAD 3.1 AC Homo 22.0 . 26.0
gnomAD 3.1 AF Hom 0.000389836 . 0.000460723
gnomAD 3.1 AC Het 0.0 . 0.0
gnomAD 3.1 AF Het 0.0 . 0.0
gnomAD 3.1 filter PASS . PASS
HelixMTdb AC Hom 159.0 . 69.0
HelixMTdb AF Hom 0.0008112949 . 0.00035207137
HelixMTdb AC Het 5.0 . 1.0
HelixMTdb AF Het 2.5512418e-05 . 5.1024836e-06
HelixMTdb mean ARF 0.88274 . 0.85714
HelixMTdb max ARF 0.92308 . 0.85714
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs878853020 . rs878853020
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