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12018 (C > G)

General info

Mitimpact ID
MI.18959
Chr
chrM
Start
12018
Ref
C
Alt
G
Gene symbol
MT-ND4 Extended gene annotation
Gene position
1259
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
ACC/AGC
AA pos
420
AA ref
T
AA alt
S
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.12018C>G
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
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Powered by MitoWheel

Conservation

PhyloP 100v
2.323 Conservation Score
PhyloP 470way
0.353 Conservation Score
PhastCons 100v
0.007 Conservation Score
PhastCons 470way
0.108 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
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
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
370057
Clinvar ALLELEID
354287
Clinvar CLNDISDB
Human phenotype ontology:hp:0000252, human phenotype ontology:hp:0001366, human phenotype ontology:hp:0005485, human phenotype ontology:hp:0005489, human phenotype ontology:hp:0005497, mondo:mondo:0001149, medgen:c4551563;

medgen:c0424605;

medgen:c1391997;

human phenotype ontology:hp:0000365, human phenotype ontology:hp:0000404, human phenotype ontology:hp:0001728, human phenotype ontology:hp:0001729, human phenotype ontology:hp:0001754, human phenotype ontology:hp:0008560, human phenotype ontology:hp:0008563, mondo:mondo:0005365, medgen:c1384666;

human phenotype ontology:hp:0000256, human phenotype ontology:hp:0005491, human phenotype ontology:hp:0005496, human phenotype ontology:hp:0200135, medgen:c2243051;

mondo:mondo:0005027, mesh:d004827, medgen:c0014544;

human phenotype ontology:hp:0001298, medgen:c0085584;

human phenotype ontology:hp:0000726, human phenotype ontology:hp:0002274, human phenotype ontology:hp:0007122, human phenotype ontology:hp:0007150, human phenotype ontology:hp:0007283, mondo:mondo:0001627, medgen:c0497327;

medgen:cn239811;

human phenotype ontology:hp:0001252, medgen:c0026827;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Microcephaly;

developmental delay;

congenital cardiomyopathy;

hearing impairment;

macrocephaly;

epilepsy;

encephalopathy;

dementia;

calcification of extrapyramidal basal ganglia;

hypotonia;

leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
12018C>G
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
28027978
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
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
rs1057516068

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
.

12018 (C > A)

General info

Mitimpact ID
MI.18961
Chr
chrM
Start
12018
Ref
C
Alt
A
Gene symbol
MT-ND4 Extended gene annotation
Gene position
1259
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
ACC/AAC
AA pos
420
AA ref
T
AA alt
N
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.12018C>A
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
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Powered by MitoWheel

Conservation

PhyloP 100v
2.323 Conservation Score
PhyloP 470way
0.353 Conservation Score
PhastCons 100v
0.007 Conservation Score
PhastCons 470way
0.108 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
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
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
.

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
12018C>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
56434
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
.

12018 (C > T)

General info

Mitimpact ID
MI.18960
Chr
chrM
Start
12018
Ref
C
Alt
T
Gene symbol
MT-ND4 Extended gene annotation
Gene position
1259
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
ACC/ATC
AA pos
420
AA ref
T
AA alt
I
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.12018C>T
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
2.323 Conservation Score
PhyloP 470way
0.353 Conservation Score
PhastCons 100v
0.007 Conservation Score
PhastCons 470way
0.108 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
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
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
Deleterious 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
12018C>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
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
.
~ 12018 (C/G) 12018 (C/A) 12018 (C/T)
~ 12018 (ACC/AGC) 12018 (ACC/AAC) 12018 (ACC/ATC)
MitImpact id MI.18959 MI.18961 MI.18960
Chr chrM chrM chrM
Start 12018 12018 12018
Ref C C C
Alt G A T
Gene symbol MT-ND4 MT-ND4 MT-ND4
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4
Gene position 1259 1259 1259
Gene start 10760 10760 10760
Gene end 12137 12137 12137
Gene strand + + +
Codon substitution ACC/AGC ACC/AAC ACC/ATC
AA position 420 420 420
AA ref T T T
AA alt S N I
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516003 516003 516003
HGVS NC_012920.1:g.12018C>G NC_012920.1:g.12018C>A NC_012920.1:g.12018C>T
HGNC id 7459 7459 7459
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198886 ENSG00000198886 ENSG00000198886
Ensembl transcript id ENST00000361381 ENST00000361381 ENST00000361381
Ensembl protein id ENSP00000354961 ENSP00000354961 ENSP00000354961
Uniprot id P03905 P03905 P03905
Uniprot name NU4M_HUMAN NU4M_HUMAN NU4M_HUMAN
Ncbi gene id 4538 4538 4538
Ncbi protein id YP_003024035.1 YP_003024035.1 YP_003024035.1
PhyloP 100V 2.323 2.323 2.323
PhyloP 470Way 0.353 0.353 0.353
PhastCons 100V 0.007 0.007 0.007
PhastCons 470Way 0.108 0.108 0.108
PolyPhen2 benign benign benign
PolyPhen2 score 0.02 0.32 0.32
SIFT neutral neutral neutral
SIFT score 0.47 0.3 0.37
SIFT4G Tolerated Damaging Damaging
SIFT4G score 0.165 0.014 0.002
VEST Neutral Neutral Neutral
VEST pvalue 0.71 0.64 0.31
VEST FDR 0.75 0.7 0.45
Mitoclass.1 neutral neutral damaging
SNPDryad Neutral Neutral Pathogenic
SNPDryad score 0.36 0.76 0.91
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1.0 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE T420S T420N T420I
fathmm Tolerated Tolerated Tolerated
fathmm score 2.61 2.57 2.5
fathmm converted rankscore 0.13095 0.13552 0.14408
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.1102 0.1313 0.2917
CADD Neutral Neutral Neutral
CADD score 0.458832 1.882611 2.402333
CADD phred 7.108 15.48 18.84
PROVEAN Tolerated Tolerated Damaging
PROVEAN score -1.28 -2.21 -3.59
MutationAssessor low low medium
MutationAssessor score 1.075 1.7 2.05
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.73 0.758 0.718
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.956 0.706 0.532
MLC Neutral Neutral Neutral
MLC score 0.15866981 0.15866981 0.15866981
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.44 0.37 0.34
APOGEE2 Benign Likely-benign VUS-
APOGEE2 score 0.0237896289078951 0.161877591273765 0.35108639500598
CAROL neutral neutral neutral
CAROL score 0.51 0.64 0.56
Condel deleterious deleterious deleterious
Condel score 0.73 0.49 0.53
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -3 -3
MtoolBox neutral neutral deleterious
MtoolBox DS 0.17 0.36 0.56
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.02069 0.025333 0.069324
DEOGEN2 converted rankscore 0.16245 0.18966 0.33681
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score 0.87 -0.41 -0.41
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.17 0 0.07
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 0.26 1.41 1.53
CHASM Neutral Neutral Neutral
CHASM pvalue 0.55 0.55 0.36
CHASM FDR 0.8 0.8 0.8
ClinVar id 370057.0 . .
ClinVar Allele id 354287.0 . .
ClinVar CLNDISDB Human_Phenotype_Ontology:HP:0000252,Human_Phenotype_Ontology:HP:0001366,Human_Phenotype_Ontology:HP:0005485,Human_Phenotype_Ontology:HP:0005489,Human_Phenotype_Ontology:HP:0005497,MONDO:MONDO:0001149,MedGen:C4551563|MedGen:C0424605|MedGen:C1391997|Human_Phenotype_Ontology:HP:0000365,Human_Phenotype_Ontology:HP:0000404,Human_Phenotype_Ontology:HP:0001728,Human_Phenotype_Ontology:HP:0001729,Human_Phenotype_Ontology:HP:0001754,Human_Phenotype_Ontology:HP:0008560,Human_Phenotype_Ontology:HP:0008563,MONDO:MONDO:0005365,MedGen:C1384666|Human_Phenotype_Ontology:HP:0000256,Human_Phenotype_Ontology:HP:0005491,Human_Phenotype_Ontology:HP:0005496,Human_Phenotype_Ontology:HP:0200135,MedGen:C2243051|MONDO:MONDO:0005027,MeSH:D004827,MedGen:C0014544|Human_Phenotype_Ontology:HP:0001298,MedGen:C0085584|Human_Phenotype_Ontology:HP:0000726,Human_Phenotype_Ontology:HP:0002274,Human_Phenotype_Ontology:HP:0007122,Human_Phenotype_Ontology:HP:0007150,Human_Phenotype_Ontology:HP:0007283,MONDO:MONDO:0001627,MedGen:C0497327|MedGen:CN239811|Human_Phenotype_Ontology:HP:0001252,MedGen:C0026827|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN Microcephaly|Developmental_delay|Congenital_cardiomyopathy|Hearing_impairment|Macrocephaly|Epilepsy|Encephalopathy|Dementia|Calcification_of_extrapyramidal_basal_ganglia|Hypotonia|Leigh_syndrome . .
ClinVar CLNSIG Uncertain_significance . .
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 0.0% . .
MITOMAP General GenBank Seqs 0 . .
MITOMAP General Curated refs 28027978 . .
MITOMAP Variant Class polymorphism . .
gnomAD 3.1 AN . 56434.0 .
gnomAD 3.1 AC Homo . 1.0 .
gnomAD 3.1 AF Hom . 1.77198e-05 .
gnomAD 3.1 AC Het . 0.0 .
gnomAD 3.1 AF Het . 0.0 .
gnomAD 3.1 filter . PASS .
HelixMTdb AC Hom . . .
HelixMTdb AF Hom . . .
HelixMTdb AC Het . . .
HelixMTdb AF Het . . .
HelixMTdb mean ARF . . .
HelixMTdb max ARF . . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs1057516068 . .
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