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3395 (A > C)

General info

Mitimpact ID
MI.10944
Chr
chrM
Start
3395
Ref
A
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
89
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAT/TCT
AA pos
30
AA ref
Y
AA alt
S
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3395A>C
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
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Conservation

PhyloP 100v
6.937 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.04 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
.
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
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
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
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
692349
Clinvar ALLELEID
680885
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
3395A>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
23463613
MITOMAP Variant Class
polymorphism
Gnomad AN
56434
Gnomad AC hom
4
Gnomad AF hom
7.08e-05
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
31
HelixMTdb AF hom
0.0001581
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
rs1556422722

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
.

3395 (A > G)

General info

Mitimpact ID
MI.10945
Chr
chrM
Start
3395
Ref
A
Alt
G
Gene symbol
MT-ND1 Extended gene annotation
Gene position
89
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAT/TGT
AA pos
30
AA ref
Y
AA alt
C
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3395A>G
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
6.937 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.04 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
.
VEST
Pathogenic 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
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
Vus+ 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
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
692350
Clinvar ALLELEID
680886
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Likely benign
MITOMAP Allele
3395A>G
MITOMAP Disease Clinical info
Lhon / hcm with hearing loss
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
0.0474%
MITOMAP General GenBank Seqs
29
MITOMAP General GenBank Curated refs
16060290 32011699 36827238 15466285 23301511 36431069 24667788 23847141 28139165 15791543 21144833 20643099 32652755
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56432
Gnomad AC hom
20
Gnomad AF hom
0.0003544
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
73
HelixMTdb AF hom
0.0003724
HelixMTdb AC het
5
HelixMTdb AF het
2.55e-05
HelixMTdb mean ARF
0.3914599
HelixMTdb max ARF
0.66008
ToMMo JPN54K AC
17
ToMMo JPN54K AF
0.000313
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs1556422722

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
0.74 CPD variant frequency
AA ref
Y
CPD AA alt
C
Aln pos
31
RefSeq protein ID
YP_009072463 , YP_008378969 , YP_007183088 , YP_009024918 , YP_009024879
Species name
Macaca tonkeana, Erythrocebus patas, Theropithecus gelada, Allenopithecus nigroviridis, Allochrocebus lhoesti
Ncbi taxon ID
40843, 9538, 9565, 54135, 100224

3395 (A > T)

General info

Mitimpact ID
MI.10946
Chr
chrM
Start
3395
Ref
A
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
89
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAT/TTT
AA pos
30
AA ref
Y
AA alt
F
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3395A>T
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
6.937 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.04 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging Score and details of the predictor
SIFT
Neutral Score and details of the predictor
SIFT4G
.
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
Neutral 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
Pathogenic 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
3395A>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
56434
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
1
Gnomad AF het
1.77e-05
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
.
~ 3395 (A/C) 3395 (A/G) 3395 (A/T)
~ 3395 (TAT/TCT) 3395 (TAT/TGT) 3395 (TAT/TTT)
MitImpact id MI.10944 MI.10945 MI.10946
Chr chrM chrM chrM
Start 3395 3395 3395
Ref A A A
Alt C G T
Gene symbol MT-ND1 MT-ND1 MT-ND1
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1
Gene position 89 89 89
Gene start 3307 3307 3307
Gene end 4262 4262 4262
Gene strand + + +
Codon substitution TAT/TCT TAT/TGT TAT/TTT
AA position 30 30 30
AA ref Y Y Y
AA alt S C F
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516000 516000 516000
HGVS NC_012920.1:g.3395A>C NC_012920.1:g.3395A>G NC_012920.1:g.3395A>T
HGNC id 7455 7455 7455
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198888 ENSG00000198888 ENSG00000198888
Ensembl transcript id ENST00000361390 ENST00000361390 ENST00000361390
Ensembl protein id ENSP00000354687 ENSP00000354687 ENSP00000354687
Uniprot id P03886 P03886 P03886
Uniprot name NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN
Ncbi gene id 4535 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1 YP_003024026.1
PhyloP 100V 6.937 6.937 6.937
PhyloP 470Way 0.58 0.58 0.58
PhastCons 100V 1 1 1
PhastCons 470Way 0.04 0.04 0.04
PolyPhen2 possibly_damaging benign possibly_damaging
PolyPhen2 score 0.81 0.17 0.77
SIFT neutral neutral neutral
SIFT score 0.65 0.18 0.7
SIFT4G . . .
SIFT4G score 0.0 0.0 0.0
VEST Neutral Pathogenic Neutral
VEST pvalue 0.06 0.04 0.2
VEST FDR 0.35 0.35 0.45
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Pathogenic Neutral
SNPDryad score 0.85 0.92 0.6
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 0.999972 0.999797 0.997569
MutationTaster converted rankscore 0.18612 0.20333 0.22606
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE Y30S Y30C Y30F
fathmm Tolerated Tolerated Tolerated
fathmm score 2.81 2.69 2.73
fathmm converted rankscore 0.10975 0.12268 0.11839
AlphaMissense ambiguous likely_benign likely_benign
AlphaMissense score 0.3406 0.2972 0.2043
CADD Neutral Deleterious Neutral
CADD score 1.951402 3.336995 1.643244
CADD phred 15.91 22.9 14.09
PROVEAN Damaging Damaging Damaging
PROVEAN score -7.95 -7.95 -3.53
MutationAssessor low medium medium
MutationAssessor score 1.92 3.39 2.425
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.606 0.636 0.624
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.55 0.374 0.424
MLC Neutral Neutral Neutral
MLC score 0.11841391 0.11841391 0.11841391
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Pathogenic Pathogenic
APOGEE1 score 0.48 0.62 0.53
APOGEE2 VUS+ VUS+ VUS+
APOGEE2 score 0.58116423595287 0.709381895931522 0.656767897734645
CAROL neutral neutral neutral
CAROL score 0.78 0.79 0.73
Condel neutral deleterious neutral
Condel score 0.42 0.51 0.47
COVEC WMV . neutral .
COVEC WMV score 0 -2 0
MtoolBox deleterious neutral deleterious
MtoolBox DS 0.82 0.35 0.74
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.140833 0.365967 0.11641
DEOGEN2 converted rankscore 0.47557 0.73130 0.43573
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact medium impact low impact
PolyPhen2 transf score -1.34 -0.1 -1.24
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.43 -0.09 0.48
MutationAssessor transf medium impact high impact medium impact
MutationAssessor transf score 0.79 2.26 1.11
CHASM Neutral Neutral Neutral
CHASM pvalue 0.16 0.04 0.38
CHASM FDR 0.8 0.8 0.8
ClinVar id 692349.0 692350.0 .
ClinVar Allele id 680885.0 680886.0 .
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 Uncertain_significance Likely_benign .
MITOMAP Disease Clinical info . LHON / HCM with hearing loss .
MITOMAP Disease Status . Reported .
MITOMAP Disease Hom/Het ./. +/+ ./.
MITOMAP General GenBank Freq 0.0016% 0.0474% .
MITOMAP General GenBank Seqs 1 29 .
MITOMAP General Curated refs 23463613 16060290;32011699;36827238;15466285;23301511;36431069;24667788;23847141;28139165;15791543;21144833;20643099;32652755 .
MITOMAP Variant Class polymorphism polymorphism;disease .
gnomAD 3.1 AN 56434.0 56432.0 56434.0
gnomAD 3.1 AC Homo 4.0 20.0 0.0
gnomAD 3.1 AF Hom 7.08793e-05 0.000354409 0.0
gnomAD 3.1 AC Het 0.0 0.0 1.0
gnomAD 3.1 AF Het 0.0 0.0 1.77198e-05
gnomAD 3.1 filter PASS PASS PASS
HelixMTdb AC Hom 31.0 73.0 .
HelixMTdb AF Hom 0.00015817699 0.0003724813 .
HelixMTdb AC Het 0.0 5.0 .
HelixMTdb AF Het 0.0 2.5512418e-05 .
HelixMTdb mean ARF . 0.39146 .
HelixMTdb max ARF . 0.66008 .
ToMMo 54KJPN AC . 17 .
ToMMo 54KJPN AF . 0.000313 .
ToMMo 54KJPN AN . 54302 .
COSMIC 90 . . .
dbSNP 156 id rs1556422722 rs1556422722 .
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