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11696 (G > A)

General info

Mitimpact ID
MI.18291
Chr
chrM
Start
11696
Ref
G
Alt
A
Gene symbol
MT-ND4 Extended gene annotation
Gene position
937
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
GTC/ATC
AA pos
313
AA ref
V
AA alt
I
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11696G>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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Conservation

PhyloP 100v
1.117 Conservation Score
PhyloP 470way
-0.26 Conservation Score
PhastCons 100v
0.005 Conservation Score
PhastCons 470way
0.004 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
Deleterious 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
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
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
Medium 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
9710
Clinvar ALLELEID
24749
Clinvar CLNDISDB
Mondo:mondo:0010772, medgen:c1839040, omim:500001, orphanet:99718;

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
Leber optic atrophy and dystonia;

leber optic atrophy;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
11696G>A
MITOMAP Disease Clinical info
Lhon / ldyt / deaf / hypertension helper mut.
MITOMAP Disease Status
Reported / possibly synergistic
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
0.597%
MITOMAP General GenBank Seqs
365
MITOMAP General GenBank Curated refs
21978175 18676632 17723226 18223312 21482521 19818876 35104579 24467713 8644732 27159682 15972314 29253894 16714301 24062162 35801081 20301353 17922426 17300996 18639500 29387390 24002810 29987491 17123466 16364244 21457906 22487888
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56427
Gnomad AC hom
56
Gnomad AF hom
0.0009924
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
264
HelixMTdb AF hom
0.001347
HelixMTdb AC het
8
HelixMTdb AF het
4.08e-05
HelixMTdb mean ARF
0.35087
HelixMTdb max ARF
0.65169
ToMMo JPN54K AC
553
ToMMo JPN54K AF
0.010184
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs200873900

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
.

11696 (G > C)

General info

Mitimpact ID
MI.18292
Chr
chrM
Start
11696
Ref
G
Alt
C
Gene symbol
MT-ND4 Extended gene annotation
Gene position
937
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
GTC/CTC
AA pos
313
AA ref
V
AA alt
L
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11696G>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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Powered by MitoWheel

Conservation

PhyloP 100v
1.117 Conservation Score
PhyloP 470way
-0.26 Conservation Score
PhastCons 100v
0.005 Conservation Score
PhastCons 470way
0.004 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
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
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
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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
11696G>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
.

11696 (G > T)

General info

Mitimpact ID
MI.18293
Chr
chrM
Start
11696
Ref
G
Alt
T
Gene symbol
MT-ND4 Extended gene annotation
Gene position
937
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
GTC/TTC
AA pos
313
AA ref
V
AA alt
F
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11696G>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
1.117 Conservation Score
PhyloP 470way
-0.26 Conservation Score
PhastCons 100v
0.005 Conservation Score
PhastCons 470way
0.004 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
Pathogenic 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
Deleterious 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
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
11696G>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
.
~ 11696 (G/A) 11696 (G/C) 11696 (G/T)
~ 11696 (GTC/ATC) 11696 (GTC/CTC) 11696 (GTC/TTC)
MitImpact id MI.18291 MI.18292 MI.18293
Chr chrM chrM chrM
Start 11696 11696 11696
Ref G G G
Alt A 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 937 937 937
Gene start 10760 10760 10760
Gene end 12137 12137 12137
Gene strand + + +
Codon substitution GTC/ATC GTC/CTC GTC/TTC
AA position 313 313 313
AA ref V V V
AA alt I L F
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516003 516003 516003
HGVS NC_012920.1:g.11696G>A NC_012920.1:g.11696G>C NC_012920.1:g.11696G>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 1.117 1.117 1.117
PhyloP 470Way -0.26 -0.26 -0.26
PhastCons 100V 0.005 0.005 0.005
PhastCons 470Way 0.004 0.004 0.004
PolyPhen2 benign benign benign
PolyPhen2 score 0.01 0.05 0.38
SIFT neutral neutral neutral
SIFT score 0.7 1.0 0.11
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 1.0 0.937 0.107
VEST Neutral Neutral Pathogenic
VEST pvalue 0.28 0.15 0.04
VEST FDR 0.45 0.4 0.35
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.78 0.5 0.38
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 4.98847e-06 0.999993 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE V313I V313L V313F
fathmm Tolerated Tolerated Tolerated
fathmm score 4.76 4.75 4.66
fathmm converted rankscore 0.01576 0.01589 0.01756
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.0757 0.1458 0.2637
CADD Neutral Neutral Neutral
CADD score -0.960482 -0.814922 0.959151
CADD phred 0.019 0.04 10.43
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score -0.32 -0.54 -1.91
MutationAssessor neutral neutral neutral
MutationAssessor score -1.085 -1.485 0.8
EFIN SP Damaging Neutral Neutral
EFIN SP score 0.284 0.702 0.73
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.338 0.912 0.592
MLC Deleterious Deleterious Deleterious
MLC score 0.79349991 0.79349991 0.79349991
PANTHER score 0.333 . .
PhD-SNP score 0.039 . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.82 0.33 0.44
APOGEE2 VUS- Likely-benign VUS-
APOGEE2 score 0.338351889297234 0.0712247635222073 0.289499771404907
CAROL neutral neutral neutral
CAROL score 0.29 0.05 0.87
Condel deleterious deleterious neutral
Condel score 0.85 0.98 0.37
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -6
MtoolBox neutral neutral neutral
MtoolBox DS 0.12 0.15 0.29
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.013156 0.014771 0.031141
DEOGEN2 converted rankscore 0.11431 0.12515 0.21906
Meta-SNP Neutral . .
Meta-SNP score 0.054 . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score 1.16 0.48 -0.52
SIFT_transf medium impact high impact medium impact
SIFT transf score 0.41 1.88 -0.31
MutationAssessor transf low impact low impact medium impact
MutationAssessor transf score -1.7 -1.56 -1
CHASM Neutral Neutral Neutral
CHASM pvalue 0.83 0.53 0.28
CHASM FDR 0.9 0.8 0.8
ClinVar id 9710.0 . .
ClinVar Allele id 24749.0 . .
ClinVar CLNDISDB MONDO:MONDO:0010772,MedGen:C1839040,OMIM:500001,Orphanet:99718|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 Leber_optic_atrophy_and_dystonia|Leber_optic_atrophy|Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info LHON / LDYT / DEAF / hypertension helper mut. . .
MITOMAP Disease Status Reported / possibly synergistic . .
MITOMAP Disease Hom/Het +/+ ./. ./.
MITOMAP General GenBank Freq 0.597% . .
MITOMAP General GenBank Seqs 365 . .
MITOMAP General Curated refs 21978175;18676632;17723226;18223312;21482521;19818876;35104579;24467713;8644732;27159682;15972314;29253894;16714301;24062162;35801081;20301353;17922426;17300996;18639500;29387390;24002810;29987491;17123466;16364244;21457906;22487888 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56427.0 . .
gnomAD 3.1 AC Homo 56.0 . .
gnomAD 3.1 AF Hom 0.000992433 . .
gnomAD 3.1 AC Het 0.0 . .
gnomAD 3.1 AF Het 0.0 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 264.0 . .
HelixMTdb AF Hom 0.0013470557 . .
HelixMTdb AC Het 8.0 . .
HelixMTdb AF Het 4.081987e-05 . .
HelixMTdb mean ARF 0.35087 . .
HelixMTdb max ARF 0.65169 . .
ToMMo 54KJPN AC 553 . .
ToMMo 54KJPN AF 0.010184 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs200873900 . .
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