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9101 (T > G)

General info

Mitimpact ID
MI.1222
Chr
chrM
Start
9101
Ref
T
Alt
G
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
575
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ATC/AGC
AA pos
192
AA ref
I
AA alt
S
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.9101T>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
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Conservation

PhyloP 100v
3.196 Conservation Score
PhyloP 470way
-0.186 Conservation Score
PhastCons 100v
0.985 Conservation Score
PhastCons 470way
0.01 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
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
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
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic 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
693092
Clinvar ALLELEID
681628
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
9101T>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0294%
MITOMAP General GenBank Seqs
18
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56433
Gnomad AC hom
8
Gnomad AF hom
0.0001417
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
19
HelixMTdb AF hom
9.69e-05
HelixMTdb AC het
0
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
96
ToMMo JPN54K AF
0.001768
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs199476134

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
.

9101 (T > A)

General info

Mitimpact ID
MI.1223
Chr
chrM
Start
9101
Ref
T
Alt
A
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
575
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ATC/AAC
AA pos
192
AA ref
I
AA alt
N
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.9101T>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
3.196 Conservation Score
PhyloP 470way
-0.186 Conservation Score
PhastCons 100v
0.985 Conservation Score
PhastCons 470way
0.01 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
Ambiguous Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Tolerated 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
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-benign 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
9101T>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
.

9101 (T > C)

General info

Mitimpact ID
MI.1224
Chr
chrM
Start
9101
Ref
T
Alt
C
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
575
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ATC/ACC
AA pos
192
AA ref
I
AA alt
T
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.9101T>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
3.196 Conservation Score
PhyloP 470way
-0.186 Conservation Score
PhastCons 100v
0.985 Conservation Score
PhastCons 470way
0.01 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
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 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
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
Neutral Score and details of the predictor
PhD-SNP
Neutral Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-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
Neutral Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Medium impact Score and details of the cancer-specific predictor
SIFT transf
High impact Score and details of the cancer-specific predictor
MutationAssessor transf
Low 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
9643
Clinvar ALLELEID
24682
Clinvar CLNDISDB
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
Leigh syndrome;

leber optic atrophy
Clinvar CLNSIG
Benign
MITOMAP Allele
9101T>C
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.1014%
MITOMAP General GenBank Seqs
62
MITOMAP General GenBank Curated refs
16855009 35773337 7726182 16132471 18620007 17406640 12509511 20301353 30763462 21457906 27498855
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56427
Gnomad AC hom
59
Gnomad AF hom
0.0010456
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
193
HelixMTdb AF hom
0.0009847
HelixMTdb AC het
11
HelixMTdb AF het
5.61e-05
HelixMTdb mean ARF
0.41036
HelixMTdb max ARF
0.84603
ToMMo JPN54K AC
7
ToMMo JPN54K AF
0.000129
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs199476134

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
.
~ 9101 (T/G) 9101 (T/A) 9101 (T/C)
~ 9101 (ATC/AGC) 9101 (ATC/AAC) 9101 (ATC/ACC)
MitImpact id MI.1222 MI.1223 MI.1224
Chr chrM chrM chrM
Start 9101 9101 9101
Ref T T T
Alt G A C
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 575 575 575
Gene start 8527 8527 8527
Gene end 9207 9207 9207
Gene strand + + +
Codon substitution ATC/AGC ATC/AAC ATC/ACC
AA position 192 192 192
AA ref I I I
AA alt S N T
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516060 516060 516060
HGVS NC_012920.1:g.9101T>G NC_012920.1:g.9101T>A NC_012920.1:g.9101T>C
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 3.196 3.196 3.196
PhyloP 470Way -0.186 -0.186 -0.186
PhastCons 100V 0.985 0.985 0.985
PhastCons 470Way 0.01 0.01 0.01
PolyPhen2 benign possibly_damaging benign
PolyPhen2 score 0.16 0.44 0.01
SIFT neutral neutral neutral
SIFT score 0.34 0.25 1
SIFT4G Tolerated Damaging Tolerated
SIFT4G score 0.053 0.003 1.0
VEST Neutral Neutral Neutral
VEST pvalue 0.34 0.28 0.46
VEST FDR 0.65 0.65 0.65
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.21 0.22 0.67
MutationTaster Polymorphism Polymorphism Disease automatic
MutationTaster score 1.0 1.0 1.3394e-09
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE I192S I192N I192T
fathmm Tolerated Tolerated Tolerated
fathmm score 4.43 4.36 4.45
fathmm converted rankscore 0.02158 0.02298 0.02121
AlphaMissense likely_benign ambiguous likely_benign
AlphaMissense score 0.2797 0.4595 0.1778
CADD Neutral Deleterious Neutral
CADD score 2.500048 2.85859 -1.174692
CADD phred 19.47 21.7 0.007
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score 0.8 -0.33 3.43
MutationAssessor neutral medium neutral
MutationAssessor score 0.55 2.435 -1.645
EFIN SP Neutral Neutral Damaging
EFIN SP score 0.914 0.874 0.336
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.892 0.488 0.37
MLC Neutral Neutral Neutral
MLC score 0.00838916 0.00838916 0.00838916
PANTHER score . . 0.317
PhD-SNP score . . 0.054
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.52 0.52 0.8
APOGEE2 Benign Likely-benign Likely-benign
APOGEE2 score 0.0523992298108639 0.142852143871903 0.17466378736353
CAROL neutral neutral neutral
CAROL score 0.6 0.71 0.01
Condel deleterious neutral deleterious
Condel score 0.59 0.41 1
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -3 -6
MtoolBox neutral deleterious neutral
MtoolBox DS 0.29 0.56 0.11
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.014431 0.023565 0.015045
DEOGEN2 converted rankscore 0.12290 0.17967 0.12694
Meta-SNP . . Neutral
Meta-SNP score . . 0.095
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score -0.07 -0.66 1.14
SIFT_transf medium impact medium impact high impact
SIFT transf score 0.13 0.02 1.98
MutationAssessor transf medium impact medium impact low impact
MutationAssessor transf score -0.53 0.09 -2.03
CHASM Neutral Neutral Neutral
CHASM pvalue 0.66 0.69 0.71
CHASM FDR 0.9 0.9 0.9
ClinVar id 693092.0 . 9643.0
ClinVar Allele id 681628.0 . 24682.0
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . 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 Leigh_syndrome . Leigh_syndrome|Leber_optic_atrophy
ClinVar CLNSIG Benign . Benign
MITOMAP Disease Clinical info . . LHON
MITOMAP Disease Status . . Reported
MITOMAP Disease Hom/Het ./. ./. +/-
MITOMAP General GenBank Freq 0.0294% . 0.1014%
MITOMAP General GenBank Seqs 18 . 62
MITOMAP General Curated refs . . 16855009;35773337;7726182;16132471;18620007;17406640;12509511;20301353;30763462;21457906;27498855
MITOMAP Variant Class polymorphism . polymorphism;disease
gnomAD 3.1 AN 56433.0 . 56427.0
gnomAD 3.1 AC Homo 8.0 . 59.0
gnomAD 3.1 AF Hom 0.000141761 . 0.0010456
gnomAD 3.1 AC Het 0.0 . 1.0
gnomAD 3.1 AF Het 0.0 . 1.7722e-05
gnomAD 3.1 filter PASS . PASS
HelixMTdb AC Hom 19.0 . 193.0
HelixMTdb AF Hom 9.694719e-05 . 0.0009847793
HelixMTdb AC Het 0.0 . 11.0
HelixMTdb AF Het 0.0 . 5.6127315e-05
HelixMTdb mean ARF . . 0.41036
HelixMTdb max ARF . . 0.84603
ToMMo 54KJPN AC 96 . 7
ToMMo 54KJPN AF 0.001768 . 0.000129
ToMMo 54KJPN AN 54302 . 54302
COSMIC 90 . . .
dbSNP 156 id rs199476134 . rs199476134
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