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8989 (G > C)

General info

Mitimpact ID
MI.989
Chr
chrM
Start
8989
Ref
G
Alt
C
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
463
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
GCC/CCC
AA pos
155
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8989G>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
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Conservation

PhyloP 100v
7.779 Conservation Score
PhyloP 470way
0.965 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.086 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
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 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
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
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
.

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Low 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
155893
Clinvar ALLELEID
165642
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Not provided
MITOMAP Allele
8989G>C
MITOMAP Disease Clinical info
NArp syndrome
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
23266623 30763462
MITOMAP Variant Class
disease
Gnomad AN
56432
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
.
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
rs587776444

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
A
CPD AA alt
P
Aln pos
156
RefSeq protein ID
YP_002261370
Species name
Rhinolophus formosae
Ncbi taxon ID
472238

8989 (G > A)

General info

Mitimpact ID
MI.987
Chr
chrM
Start
8989
Ref
G
Alt
A
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
463
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
GCC/ACC
AA pos
155
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8989G>A
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
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Conservation

PhyloP 100v
7.779 Conservation Score
PhyloP 470way
0.965 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.086 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
Neutral Score and details of the predictor
SNPDryad
Neutral Score and details of the predictor
MutationTaster
Disease 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
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
Neutral Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor

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
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
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
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
693046
Clinvar ALLELEID
681582
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Likely benign
MITOMAP Allele
8989G>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0573%
MITOMAP General GenBank Seqs
35
MITOMAP General GenBank Curated refs
9461455
MITOMAP Variant Class
polymorphism
Gnomad AN
56415
Gnomad AC hom
13
Gnomad AF hom
0.0002304
Gnomad AC het
6
Gnomad AF het
0.0001063
Gnomad filter
Pass
HelixMTdb AC hom
68
HelixMTdb AF hom
0.0003469
HelixMTdb AC het
31
HelixMTdb AF het
0.0001581
HelixMTdb mean ARF
0.30079
HelixMTdb max ARF
0.88406
ToMMo JPN54K AC
23
ToMMo JPN54K AF
0.000424
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs587776444

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
.

8989 (G > T)

General info

Mitimpact ID
MI.988
Chr
chrM
Start
8989
Ref
G
Alt
T
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
463
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
GCC/TCC
AA pos
155
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8989G>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
7.779 Conservation Score
PhyloP 470way
0.965 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.086 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
Neutral Score and details of the predictor
SNPDryad
Pathogenic Score and details of the predictor
MutationTaster
Disease 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
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
8989G>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
1
HelixMTdb AF hom
5.1e-06
HelixMTdb AC het
0
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
.
~ 8989 (G/C) 8989 (G/A) 8989 (G/T)
~ 8989 (GCC/CCC) 8989 (GCC/ACC) 8989 (GCC/TCC)
MitImpact id MI.989 MI.987 MI.988
Chr chrM chrM chrM
Start 8989 8989 8989
Ref G G G
Alt C A T
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 463 463 463
Gene start 8527 8527 8527
Gene end 9207 9207 9207
Gene strand + + +
Codon substitution GCC/CCC GCC/ACC GCC/TCC
AA position 155 155 155
AA ref A A A
AA alt P T S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516060 516060 516060
HGVS NC_012920.1:g.8989G>C NC_012920.1:g.8989G>A NC_012920.1:g.8989G>T
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 7.779 7.779 7.779
PhyloP 470Way 0.965 0.965 0.965
PhastCons 100V 1 1 1
PhastCons 470Way 0.086 0.086 0.086
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0 0.99
SIFT deleterious neutral neutral
SIFT score 0 0.79 0.29
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.015 0.018 0.001
VEST Neutral Neutral Neutral
VEST pvalue 0.15 0.36 0.34
VEST FDR 0.65 0.65 0.65
Mitoclass.1 damaging neutral neutral
SNPDryad Pathogenic Neutral Pathogenic
SNPDryad score 0.97 0.8 0.95
MutationTaster Disease automatic Disease Disease
MutationTaster score 0.999445 0.99806 0.995532
MutationTaster converted rankscore 0.4708 0.4447 0.42735
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE A155P A155T A155S
fathmm Tolerated Tolerated Tolerated
fathmm score 3.82 4.31 4.43
fathmm converted rankscore 0.03728 0.02412 0.02158
AlphaMissense likely_pathogenic likely_pathogenic ambiguous
AlphaMissense score 0.9255 0.6292 0.3458
CADD Deleterious Deleterious Deleterious
CADD score 3.858663 4.295187 3.743465
CADD phred 23.5 24.0 23.3
PROVEAN Damaging Damaging Damaging
PROVEAN score -4.39 -3.22 -2.51
MutationAssessor high low medium
MutationAssessor score 4.34 1.935 2.99
EFIN SP Damaging Neutral Neutral
EFIN SP score 0.588 0.822 0.664
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.436 0.468 0.514
MLC Neutral Neutral Neutral
MLC score 0.06524232 0.06524232 0.06524232
PANTHER score . 0.472 .
PhD-SNP score . 0.708 .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.37 0.21 0.35
APOGEE2 Likely-pathogenic Likely-benign Likely-benign
APOGEE2 score 0.895475608124623 0.101801569016326 0.218675747790464
CAROL deleterious deleterious deleterious
CAROL score 1 1 0.99
Condel neutral neutral neutral
Condel score 0 0.4 0.15
COVEC WMV deleterious neutral neutral
COVEC WMV score 6 -2 -2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.91 0.74 0.73
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.299028 0.07066 0.072529
DEOGEN2 converted rankscore 0.67157 0.34015 0.34477
Meta-SNP . Disease .
Meta-SNP score . 0.51 .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.6 -3.6 -2.65
SIFT_transf low impact medium impact medium impact
SIFT transf score -1.4 0.62 0.07
MutationAssessor transf high impact medium impact medium impact
MutationAssessor transf score 2.28 -0.01 0.05
CHASM Neutral Neutral Neutral
CHASM pvalue 0.76 0.75 0.86
CHASM FDR 0.9 0.9 0.9
ClinVar id 155893.0 693046.0 .
ClinVar Allele id 165642.0 681582.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN Leigh_syndrome Leigh_syndrome .
ClinVar CLNSIG not_provided Likely_benign .
MITOMAP Disease Clinical info NARP syndrome . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het -/+ ./. ./.
MITOMAP General GenBank Freq 0.0% 0.0573% 0.0%
MITOMAP General GenBank Seqs 0 35 0
MITOMAP General Curated refs 23266623;30763462 9461455 .
MITOMAP Variant Class disease polymorphism polymorphism
gnomAD 3.1 AN 56432.0 56415.0 .
gnomAD 3.1 AC Homo 0.0 13.0 .
gnomAD 3.1 AF Hom 0.0 0.000230435 .
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 . 68.0 1.0
HelixMTdb AF Hom . 0.00034696888 5.1024836e-06
HelixMTdb AC Het . 31.0 0.0
HelixMTdb AF Het . 0.00015817699 0.0
HelixMTdb mean ARF . 0.30079 .
HelixMTdb max ARF . 0.88406 .
ToMMo 54KJPN AC . 23 .
ToMMo 54KJPN AF . 0.000424 .
ToMMo 54KJPN AN . 54302 .
COSMIC 90 . . .
dbSNP 156 id rs587776444 rs587776444 .
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