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8839 (G > A)

General info

Mitimpact ID
MI.665
Chr
chrM
Start
8839
Ref
G
Alt
A
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
313
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
GCC/ACC
AA pos
105
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8839G>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
6.527 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.801 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
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
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
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
692996
Clinvar ALLELEID
681532
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
8839G>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.1178%
MITOMAP General GenBank Seqs
72
MITOMAP General GenBank Curated refs
19370763 31152278 18269758 11938495 19026397 14760490 15791543 20304802
MITOMAP Variant Class
polymorphism
Gnomad AN
56420
Gnomad AC hom
58
Gnomad AF hom
0.001028
Gnomad AC het
8
Gnomad AF het
0.0001417
Gnomad filter
Pass
HelixMTdb AC hom
259
HelixMTdb AF hom
0.0013215
HelixMTdb AC het
18
HelixMTdb AF het
9.18e-05
HelixMTdb mean ARF
0.3923
HelixMTdb max ARF
0.89024
ToMMo JPN54K AC
11
ToMMo JPN54K AF
0.000203
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs1556423547

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
.

8839 (G > C)

General info

Mitimpact ID
MI.664
Chr
chrM
Start
8839
Ref
G
Alt
C
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
313
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
GCC/CCC
AA pos
105
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8839G>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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Powered by MitoWheel

Conservation

PhyloP 100v
6.527 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.801 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
Pathogenic Score and details of the meta-predictor
APOGEE2
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
155892
Clinvar ALLELEID
165641
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

mondo:mondo:0044970, medgen:c0751651, orphanet:68380
Clinvar CLNDN
Leigh syndrome;

mitochondrial disease
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
8839G>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
24118886 29467576 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
rs1556423547

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
.

8839 (G > T)

General info

Mitimpact ID
MI.663
Chr
chrM
Start
8839
Ref
G
Alt
T
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
313
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
GCC/TCC
AA pos
105
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8839G>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
6.527 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.801 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
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-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
8839G>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
56433
Gnomad AC hom
1
Gnomad AF hom
1.77e-05
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
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
.
~ 8839 (G/A) 8839 (G/C) 8839 (G/T)
~ 8839 (GCC/ACC) 8839 (GCC/CCC) 8839 (GCC/TCC)
MitImpact id MI.665 MI.664 MI.663
Chr chrM chrM chrM
Start 8839 8839 8839
Ref G G G
Alt A C 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 313 313 313
Gene start 8527 8527 8527
Gene end 9207 9207 9207
Gene strand + + +
Codon substitution GCC/ACC GCC/CCC GCC/TCC
AA position 105 105 105
AA ref A A A
AA alt T P S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516060 516060 516060
HGVS NC_012920.1:g.8839G>A NC_012920.1:g.8839G>C NC_012920.1:g.8839G>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 6.527 6.527 6.527
PhyloP 470Way 0.458 0.458 0.458
PhastCons 100V 1 1 1
PhastCons 470Way 0.801 0.801 0.801
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0 0.99
SIFT neutral deleterious neutral
SIFT score 0.09 0 0.31
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.0 0.001 0.015
VEST Neutral Neutral Neutral
VEST pvalue 0.31 0.13 0.27
VEST FDR 0.65 0.65 0.65
Mitoclass.1 damaging damaging neutral
SNPDryad Neutral Pathogenic Pathogenic
SNPDryad score 0.8 0.97 0.95
MutationTaster Disease automatic Disease automatic Disease
MutationTaster score 0.999018 0.999719 0.997734
MutationTaster converted rankscore 0.45878 0.48481 0.44143
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE A105T A105P A105S
fathmm Tolerated Tolerated Tolerated
fathmm score 3.09 3.06 3.36
fathmm converted rankscore 0.08371 0.08634 0.05918
AlphaMissense likely_pathogenic likely_pathogenic ambiguous
AlphaMissense score 0.7432 0.9544 0.3667
CADD Deleterious Deleterious Deleterious
CADD score 4.192014 3.75549 3.640292
CADD phred 23.8 23.3 23.2
PROVEAN Damaging Damaging Damaging
PROVEAN score -3.64 -4.63 -2.63
MutationAssessor high high medium
MutationAssessor score 4.525 4.87 2.9
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.582 0.414 0.524
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.502 0.396 0.48
MLC Neutral Neutral Neutral
MLC score 0.04973143 0.04973143 0.04973143
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Pathogenic Neutral
APOGEE1 score 0.31 0.57 0.37
APOGEE2 VUS- Pathogenic Likely-benign
APOGEE2 score 0.303226670189714 0.934394263639574 0.203254446757604
CAROL deleterious deleterious deleterious
CAROL score 1 1 0.99
Condel neutral neutral neutral
Condel score 0.05 0 0.16
COVEC WMV deleterious deleterious neutral
COVEC WMV score 2 6 -2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.87 0.9 0.78
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.224885 0.353369 0.12234
DEOGEN2 converted rankscore 0.58946 0.72067 0.44595
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.6 -3.6 -2.65
SIFT_transf medium impact low impact medium impact
SIFT transf score -0.28 -1.4 0.1
MutationAssessor transf high impact high impact medium impact
MutationAssessor transf score 2.01 2.3 0.36
CHASM Neutral Neutral Neutral
CHASM pvalue 0.76 0.58 0.71
CHASM FDR 0.9 0.9 0.9
ClinVar id 692996.0 155892.0 .
ClinVar Allele id 681532.0 165641.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380 .
ClinVar CLNDN Leigh_syndrome Leigh_syndrome|Mitochondrial_disease .
ClinVar CLNSIG Benign Pathogenic .
MITOMAP Disease Clinical info . NARP syndrome .
MITOMAP Disease Status . Reported .
MITOMAP Disease Hom/Het ./. -/+ ./.
MITOMAP General GenBank Freq 0.1178% 0.0% .
MITOMAP General GenBank Seqs 72 0 .
MITOMAP General Curated refs 19370763;31152278;18269758;11938495;19026397;14760490;15791543;20304802 24118886;29467576;30763462 .
MITOMAP Variant Class polymorphism disease .
gnomAD 3.1 AN 56420.0 56432.0 56433.0
gnomAD 3.1 AC Homo 58.0 0.0 1.0
gnomAD 3.1 AF Hom 0.001028 0.0 1.77201e-05
gnomAD 3.1 AC Het 8.0 0.0 0.0
gnomAD 3.1 AF Het 0.000141794 0.0 0.0
gnomAD 3.1 filter PASS npg PASS
HelixMTdb AC Hom 259.0 . .
HelixMTdb AF Hom 0.0013215432 . .
HelixMTdb AC Het 18.0 . .
HelixMTdb AF Het 9.1844704e-05 . .
HelixMTdb mean ARF 0.3923 . .
HelixMTdb max ARF 0.89024 . .
ToMMo 54KJPN AC 11 . .
ToMMo 54KJPN AF 0.000203 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs1556423547 rs1556423547 .
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