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11360 (A > G)

General info

Mitimpact ID
MI.17589
Chr
chrM
Start
11360
Ref
A
Alt
G
Gene symbol
MT-ND4 Extended gene annotation
Gene position
601
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
ATA/GTA
AA pos
201
AA ref
M
AA alt
V
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11360A>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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Conservation

PhyloP 100v
0.268 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.674 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging 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
.
fathmm
.
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
Deleterious 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
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
.
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
523304
Clinvar ALLELEID
514149
Clinvar CLNDISDB
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;

human phenotype ontology:hp:0001250, human phenotype ontology:hp:0001275, human phenotype ontology:hp:0001303, human phenotype ontology:hp:0002125, human phenotype ontology:hp:0002182, human phenotype ontology:hp:0002279, human phenotype ontology:hp:0002306, human phenotype ontology:hp:0002348, human phenotype ontology:hp:0002391, human phenotype ontology:hp:0002417, human phenotype ontology:hp:0002430, human phenotype ontology:hp:0002431, human phenotype ontology:hp:0002432, human phenotype ontology:hp:0002434, human phenotype ontology:hp:0002437, human phenotype ontology:hp:0002466, human phenotype ontology:hp:0002479, human phenotype ontology:hp:0002794, human phenotype ontology:hp:0006997, human phenotype ontology:hp:0010520, medgen:c0036572
Clinvar CLNDN
Leber optic atrophy;

leigh syndrome;

seizure
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
11360A>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0033%
MITOMAP General GenBank Seqs
2
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56434
Gnomad AC hom
4
Gnomad AF hom
7.08e-05
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
18
HelixMTdb AF hom
9.18e-05
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.4
HelixMTdb max ARF
0.4
ToMMo JPN54K AC
1
ToMMo JPN54K AF
1.8e-05
ToMMo JPN54K AN
54302
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
.

11360 (A > C)

General info

Mitimpact ID
MI.17587
Chr
chrM
Start
11360
Ref
A
Alt
C
Gene symbol
MT-ND4 Extended gene annotation
Gene position
601
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
ATA/CTA
AA pos
201
AA ref
M
AA alt
L
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11360A>C
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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Conservation

PhyloP 100v
0.268 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.674 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
.
fathmm
.
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
Deleterious 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
Deleterious Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
.

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
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
11360A>C
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
.

11360 (A > T)

General info

Mitimpact ID
MI.17588
Chr
chrM
Start
11360
Ref
A
Alt
T
Gene symbol
MT-ND4 Extended gene annotation
Gene position
601
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
ATA/TTA
AA pos
201
AA ref
M
AA alt
L
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11360A>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
0.268 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.674 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
.
fathmm
.
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
Deleterious 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
Deleterious Score and details of the meta-predictor
DEOGEN2
.
Meta SNP
.

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
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
11360A>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
.
~ 11360 (A/G) 11360 (A/C) 11360 (A/T)
~ 11360 (ATA/GTA) 11360 (ATA/CTA) 11360 (ATA/TTA)
MitImpact id MI.17589 MI.17587 MI.17588
Chr chrM chrM chrM
Start 11360 11360 11360
Ref A A A
Alt G C 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 601 601 601
Gene start 10760 10760 10760
Gene end 12137 12137 12137
Gene strand + + +
Codon substitution ATA/GTA ATA/CTA ATA/TTA
AA position 201 201 201
AA ref M M M
AA alt V L L
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516003 516003 516003
HGVS NC_012920.1:g.11360A>G NC_012920.1:g.11360A>C NC_012920.1:g.11360A>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 0.268 0.268 0.268
PhyloP 470Way 0.819 0.819 0.819
PhastCons 100V 0 0 0
PhastCons 470Way 0.674 0.674 0.674
PolyPhen2 possibly_damaging benign benign
PolyPhen2 score 0.54 0.03 0.03
SIFT neutral neutral neutral
SIFT score 0.17 1.0 1.0
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 0.102 0.899 0.899
VEST Neutral Neutral Neutral
VEST pvalue 0.23 0.23 0.23
VEST FDR 0.45 0.45 0.45
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.86 0.74 0.74
MutationTaster . . .
MutationTaster score . . .
MutationTaster converted rankscore . . .
MutationTaster model . . .
MutationTaster AAE . . .
fathmm . . .
fathmm score . . .
fathmm converted rankscore . . .
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.1087 0.1359 0.1359
CADD Neutral Neutral Neutral
CADD score 1.46454 1.173033 1.358301
CADD phred 13.13 11.61 12.57
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score -1.83 -1.08 -1.08
MutationAssessor neutral neutral neutral
MutationAssessor score 0.51 -0.575 -0.575
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.762 0.682 0.682
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.682 0.906 0.906
MLC Deleterious Deleterious Deleterious
MLC score 0.63114853 0.63114853 0.63114853
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.38 0.37 0.38
APOGEE2 Likely-benign Likely-benign Likely-benign
APOGEE2 score 0.218313249686207 0.0769896756240004 0.0769896756240004
CAROL neutral neutral neutral
CAROL score 0.82 0.03 0.03
Condel neutral deleterious deleterious
Condel score 0.32 0.99 0.99
COVEC WMV neutral neutral neutral
COVEC WMV score -3 -6 -6
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.6 0.51 0.51
DEOGEN2 . . .
DEOGEN2 score . . .
DEOGEN2 converted rankscore . . .
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score -0.78 0.7 0.7
SIFT_transf medium impact high impact high impact
SIFT transf score -0.18 1.88 1.88
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 0.51 -0.57 -0.57
CHASM Neutral Neutral Neutral
CHASM pvalue 0.15 0.17 0.17
CHASM FDR 0.8 0.8 0.8
ClinVar id 523304.0 . .
ClinVar Allele id 514149.0 . .
ClinVar CLNDISDB 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|Human_Phenotype_Ontology:HP:0001250,Human_Phenotype_Ontology:HP:0001275,Human_Phenotype_Ontology:HP:0001303,Human_Phenotype_Ontology:HP:0002125,Human_Phenotype_Ontology:HP:0002182,Human_Phenotype_Ontology:HP:0002279,Human_Phenotype_Ontology:HP:0002306,Human_Phenotype_Ontology:HP:0002348,Human_Phenotype_Ontology:HP:0002391,Human_Phenotype_Ontology:HP:0002417,Human_Phenotype_Ontology:HP:0002430,Human_Phenotype_Ontology:HP:0002431,Human_Phenotype_Ontology:HP:0002432,Human_Phenotype_Ontology:HP:0002434,Human_Phenotype_Ontology:HP:0002437,Human_Phenotype_Ontology:HP:0002466,Human_Phenotype_Ontology:HP:0002479,Human_Phenotype_Ontology:HP:0002794,Human_Phenotype_Ontology:HP:0006997,Human_Phenotype_Ontology:HP:0010520,MedGen:C0036572 . .
ClinVar CLNDN Leber_optic_atrophy|Leigh_syndrome|Seizure . .
ClinVar CLNSIG Uncertain_significance . .
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 0.0033% . .
MITOMAP General GenBank Seqs 2 . .
MITOMAP General Curated refs . . .
MITOMAP Variant Class polymorphism . .
gnomAD 3.1 AN 56434.0 . .
gnomAD 3.1 AC Homo 4.0 . .
gnomAD 3.1 AF Hom 7.08793e-05 . .
gnomAD 3.1 AC Het 1.0 . .
gnomAD 3.1 AF Het 1.77198e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 18.0 . .
HelixMTdb AF Hom 9.1844704e-05 . .
HelixMTdb AC Het 1.0 . .
HelixMTdb AF Het 5.1024836e-06 . .
HelixMTdb mean ARF 0.4 . .
HelixMTdb max ARF 0.4 . .
ToMMo 54KJPN AC 1 . .
ToMMo 54KJPN AF 1.8e-05 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id . . .
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