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3394 (T > C)

General info

Mitimpact ID
MI.10941
Chr
chrM
Start
3394
Ref
T
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
88
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAT/CAT
AA pos
30
AA ref
Y
AA alt
H
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3394T>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
3.149 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
0.999 Conservation Score
PhastCons 470way
0.042 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
Disease automatic 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
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
Disease Score and details of the predictor

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
Disease Score and details of the meta-predictor

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
9725
Clinvar ALLELEID
24764
Clinvar CLNDISDB
Medgen:cn517202;

human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Not provided;

leber optic atrophy;

leigh syndrome
Clinvar CLNSIG
Conflicting interpretations of pathogenicity
MITOMAP Allele
3394T>C
MITOMAP Disease Clinical info
Lhon / diabetes / cptdeficiency / high altitude adaptation
MITOMAP Disease Status
hg m9 marker;reported [vus] -population dependent
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
1.3135%
MITOMAP General GenBank Seqs
803
MITOMAP General GenBank Curated refs
21978175 10520236 1634041 30597069 29997041 8645285 19199242 20728388 32887465 11349229 18545700 33420243 8728705 22233893 16168441 1417830 22561905 27498855 32094358 21385625 7603534 27465874 11938495 34724985 17406640 15972314 15338331 7599217 15638829 16404693 18679013 33840063 16714301 7635294 22517755 27177320 23350576 16773565 9302261 20211276 17320116 33763872 16414144 35801081 24667788 1442494 11853713 8680405 23091534 19043581 20304802 22312186 21041797 29996615 23563965 10704697 12439205 18639500 19324017 18428021 29387390 29444077 24002810 29987491 21457906 20003445 16331560 20067846 21694444
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56420
Gnomad AC hom
514
Gnomad AF hom
0.0091102
Gnomad AC het
12
Gnomad AF het
0.0002126
Gnomad filter
Pass
HelixMTdb AC hom
2127
HelixMTdb AF hom
0.0108529
HelixMTdb AC het
16
HelixMTdb AF het
8.16e-05
HelixMTdb mean ARF
0.39657
HelixMTdb max ARF
0.86364
ToMMo JPN54K AC
1228
ToMMo JPN54K AF
0.022614
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs41460449

Residue interaction

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

Compensated Pathogenic Deviations

Frequency
0.89 CPD variant frequency
AA ref
.
CPD AA alt
.
Aln pos
.
RefSeq protein ID
.
Species name
.
Ncbi taxon ID
.

3394 (T > A)

General info

Mitimpact ID
MI.10943
Chr
chrM
Start
3394
Ref
T
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
88
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAT/AAT
AA pos
30
AA ref
Y
AA alt
N
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3394T>A
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
3.149 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
0.999 Conservation Score
PhastCons 470way
0.042 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
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
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-pathogenic 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
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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
3394T>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
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
.

3394 (T > G)

General info

Mitimpact ID
MI.10942
Chr
chrM
Start
3394
Ref
T
Alt
G
Gene symbol
MT-ND1 Extended gene annotation
Gene position
88
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAT/GAT
AA pos
30
AA ref
Y
AA alt
D
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3394T>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
3.149 Conservation Score
PhyloP 470way
0.458 Conservation Score
PhastCons 100v
0.999 Conservation Score
PhastCons 470way
0.042 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
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
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-pathogenic 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
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
3394T>G
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
.
~ 3394 (T/C) 3394 (T/A) 3394 (T/G)
~ 3394 (TAT/CAT) 3394 (TAT/AAT) 3394 (TAT/GAT)
MitImpact id MI.10941 MI.10943 MI.10942
Chr chrM chrM chrM
Start 3394 3394 3394
Ref T T T
Alt C A G
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 88 88 88
Gene start 3307 3307 3307
Gene end 4262 4262 4262
Gene strand + + +
Codon substitution TAT/CAT TAT/AAT TAT/GAT
AA position 30 30 30
AA ref Y Y Y
AA alt H N D
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516000 516000 516000
HGVS NC_012920.1:g.3394T>C NC_012920.1:g.3394T>A NC_012920.1:g.3394T>G
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 3.149 3.149 3.149
PhyloP 470Way 0.458 0.458 0.458
PhastCons 100V 0.999 0.999 0.999
PhastCons 470Way 0.042 0.042 0.042
PolyPhen2 benign possibly_damaging probably_damaging
PolyPhen2 score 0.11 0.87 0.93
SIFT neutral neutral neutral
SIFT score 0.55 0.46 0.41
SIFT4G . . .
SIFT4G score 0.04 0.0 0.001
VEST Neutral Neutral Pathogenic
VEST pvalue 0.14 0.08 0.04
VEST FDR 0.4 0.35 0.35
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Neutral Pathogenic
SNPDryad score 0.22 0.85 0.93
MutationTaster Disease automatic Polymorphism Disease
MutationTaster score 8.74485e-05 0.999992 1
MutationTaster converted rankscore 0.19599 0.08975 0.81001
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE Y30H Y30N Y30D
fathmm Tolerated Tolerated Tolerated
fathmm score 2.7 2.72 2.71
fathmm converted rankscore 0.12162 0.11947 0.12055
AlphaMissense ambiguous ambiguous likely_pathogenic
AlphaMissense score 0.4241 0.3654 0.5766
CADD Neutral Neutral Deleterious
CADD score 1.51611 2.219026 3.513566
CADD phred 13.4 17.63 23.1
PROVEAN Damaging Damaging Damaging
PROVEAN score -4.4 -7.96 -8.85
MutationAssessor medium high high
MutationAssessor score 1.975 4.435 3.885
EFIN SP Damaging Neutral Neutral
EFIN SP score 0.316 0.678 0.704
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.48 0.464 0.41
MLC Neutral Neutral Neutral
MLC score 0.11871567 0.11871567 0.11871567
PANTHER score . . .
PhD-SNP score 0.677 . .
APOGEE1 Pathogenic Pathogenic Neutral
APOGEE1 score 0.76 0.56 0.45
APOGEE2 VUS+ Likely-pathogenic Likely-pathogenic
APOGEE2 score 0.582179289643209 0.782942956077328 0.769613884148873
CAROL neutral neutral neutral
CAROL score 0.36 0.86 0.93
Condel deleterious neutral neutral
Condel score 0.72 0.3 0.24
COVEC WMV neutral deleterious deleterious
COVEC WMV score -3 1 1
MtoolBox neutral deleterious deleterious
MtoolBox DS 0.34 0.78 0.85
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.139993 0.365967 0.172961
DEOGEN2 converted rankscore 0.47430 0.73130 0.52165
Meta-SNP Disease . .
Meta-SNP score 0.631 . .
PolyPhen2 transf medium impact low impact low impact
PolyPhen2 transf score 0.1 -1.53 -1.81
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.32 0.24 0.19
MutationAssessor transf medium impact high impact medium impact
MutationAssessor transf score 0.71 2.74 1.83
CHASM Neutral Neutral Neutral
CHASM pvalue 0.11 0.11 0.08
CHASM FDR 0.8 0.8 0.8
ClinVar id 9725.0 . .
ClinVar Allele id 24764.0 . .
ClinVar CLNDISDB MedGen:CN517202|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN not_provided|Leber_optic_atrophy|Leigh_syndrome . .
ClinVar CLNSIG Conflicting_interpretations_of_pathogenicity . .
MITOMAP Disease Clinical info LHON / Diabetes / CPTdeficiency / high altitude adaptation . .
MITOMAP Disease Status hg M9 marker;Reported [VUS] -population dependent . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 1.3135% . .
MITOMAP General GenBank Seqs 803 . .
MITOMAP General Curated refs 21978175;10520236;1634041;30597069;29997041;8645285;19199242;20728388;32887465;11349229;18545700;33420243;8728705;22233893;16168441;1417830;22561905;27498855;32094358;21385625;7603534;27465874;11938495;34724985;17406640;15972314;15338331;7599217;15638829;16404693;18679013;33840063;16714301;7635294;22517755;27177320;23350576;16773565;9302261;20211276;17320116;33763872;16414144;35801081;24667788;1442494;11853713;8680405;23091534;19043581;20304802;22312186;21041797;29996615;23563965;10704697;12439205;18639500;19324017;18428021;29387390;29444077;24002810;29987491;21457906;20003445;16331560;20067846;21694444 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56420.0 56433.0 .
gnomAD 3.1 AC Homo 514.0 1.0 .
gnomAD 3.1 AF Hom 0.00911024 1.77201e-05 .
gnomAD 3.1 AC Het 12.0 0.0 .
gnomAD 3.1 AF Het 0.000212691 0.0 .
gnomAD 3.1 filter PASS PASS .
HelixMTdb AC Hom 2127.0 . .
HelixMTdb AF Hom 0.010852982 . .
HelixMTdb AC Het 16.0 . .
HelixMTdb AF Het 8.163974e-05 . .
HelixMTdb mean ARF 0.39657 . .
HelixMTdb max ARF 0.86364 . .
ToMMo 54KJPN AC 1228 . .
ToMMo 54KJPN AF 0.022614 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs41460449 . .
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