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13513 (G > C)

General info

Mitimpact ID
MI.21769
Chr
chrM
Start
13513
Ref
G
Alt
C
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1177
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
GAC/CAC
AA pos
393
AA ref
D
AA alt
H
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.13513G>C
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
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Powered by MitoWheel

Conservation

PhyloP 100v
9.29 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.845 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
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
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
Deleterious 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
Deleterious 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
13513G>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
.
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
3
ToMMo JPN54K AF
5.5e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs267606897

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
.

13513 (G > A)

General info

Mitimpact ID
MI.21768
Chr
chrM
Start
13513
Ref
G
Alt
A
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1177
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
GAC/AAC
AA pos
393
AA ref
D
AA alt
N
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.13513G>A
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
9.29 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.845 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
Disease automatic 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
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
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Pathogenic Score and details of the meta-predictor
CAROL
Deleterious 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
Disease Score and details of the meta-predictor

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
9702
Clinvar ALLELEID
24741
Clinvar CLNDISDB
Medgen:c1838951;

mondo:mondo:0010789, medgen:c0162671, omim:540000, orphanet:550;

medgen:cn517202;

mondo:mondo:0044970, medgen:c0751651, orphanet:68380;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome due to mitochondrial complex i deficiency;

juvenile myopathy, encephalopathy, lactic acidosis and stroke;

not provided;

mitochondrial disease;

leigh syndrome
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
13513G>A
MITOMAP Disease Clinical info
Leigh disease / melas / lhon-melas overlap syndrome / negative association w carotid atherosclerosis
MITOMAP Disease Status
Cfrm [p]
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
19370763 30095618 23010433 31996177 18674747 29670672 37038312 15382008 28429146 37737178 30461153 19617458 27450679 30128709 10589546 18495510 36975485 10908920 34146515 14520659 27919073 18402672 18977334 28951770 32220313 15972314 34298071 33746872 23847141 24931247 30950033 33717984 16483543 24667782 17400793 24642831 12624137 29428506 29228836 34670906 21174521 26741492 19054921 35778412 18332249 19268652 20408961 21850008 9299505 25192510 31669237 11198278 15576045 20064630 38465286 23874496 21364701 14730434 21457906 20972245
MITOMAP Variant Class
disease
Gnomad AN
56431
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Npg
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
rs267606897

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
.

13513 (G > T)

General info

Mitimpact ID
MI.21767
Chr
chrM
Start
13513
Ref
G
Alt
T
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1177
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
GAC/TAC
AA pos
393
AA ref
D
AA alt
Y
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.13513G>T
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
9.29 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.845 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
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
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
Deleterious 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
Deleterious Score and details of the meta-predictor
Condel
Deleterious 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
High 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
13513G>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
.
~ 13513 (G/C) 13513 (G/A) 13513 (G/T)
~ 13513 (GAC/CAC) 13513 (GAC/AAC) 13513 (GAC/TAC)
MitImpact id MI.21769 MI.21768 MI.21767
Chr chrM chrM chrM
Start 13513 13513 13513
Ref G G G
Alt C A T
Gene symbol MT-ND5 MT-ND5 MT-ND5
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5
Gene position 1177 1177 1177
Gene start 12337 12337 12337
Gene end 14148 14148 14148
Gene strand + + +
Codon substitution GAC/CAC GAC/AAC GAC/TAC
AA position 393 393 393
AA ref D D D
AA alt H N Y
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516005 516005 516005
HGVS NC_012920.1:g.13513G>C NC_012920.1:g.13513G>A NC_012920.1:g.13513G>T
HGNC id 7461 7461 7461
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198786 ENSG00000198786 ENSG00000198786
Ensembl transcript id ENST00000361567 ENST00000361567 ENST00000361567
Ensembl protein id ENSP00000354813 ENSP00000354813 ENSP00000354813
Uniprot id P03915 P03915 P03915
Uniprot name NU5M_HUMAN NU5M_HUMAN NU5M_HUMAN
Ncbi gene id 4540 4540 4540
Ncbi protein id YP_003024036.1 YP_003024036.1 YP_003024036.1
PhyloP 100V 9.29 9.29 9.29
PhyloP 470Way 0.848 0.848 0.848
PhastCons 100V 1 1 1
PhastCons 470Way 0.845 0.845 0.845
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1 1 1
SIFT neutral neutral neutral
SIFT score 0.53 0.32 1.0
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.0 0.0 0.0
VEST Neutral Neutral Neutral
VEST pvalue 0.28 0.45 0.25
VEST FDR 0.45 0.55 0.45
Mitoclass.1 damaging damaging damaging
SNPDryad Pathogenic Pathogenic Pathogenic
SNPDryad score 0.99 0.98 0.99
MutationTaster Disease Disease automatic Disease
MutationTaster score 0.999981 0.999904 0.999991
MutationTaster converted rankscore 0.54805 0.50806 0.58761
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE D393H D393N D393Y
fathmm Tolerated Tolerated Tolerated
fathmm score 4.51 4.5 4.56
fathmm converted rankscore 0.02015 0.02032 0.01933
AlphaMissense likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.9844 0.9241 0.9474
CADD Deleterious Deleterious Deleterious
CADD score 3.69017 4.364119 3.995895
CADD phred 23.3 24.1 23.6
PROVEAN Damaging Damaging Damaging
PROVEAN score -6.3 -4.5 -8.09
MutationAssessor medium high medium
MutationAssessor score 2.98 4.265 3.29
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.252 0.034 0.236
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.306 0.438 0.32
MLC Deleterious Deleterious Deleterious
MLC score 0.63624842 0.63624842 0.63624842
PANTHER score . 0.823 .
PhD-SNP score . 0.891 .
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.89 0.97 0.82
APOGEE2 Likely-pathogenic Pathogenic Likely-pathogenic
APOGEE2 score 0.834280803179125 0.917725267895409 0.844457955738889
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 1.0
Condel neutral neutral deleterious
Condel score 0.27 0.16 0.5
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 1 2 2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.89 0.87 0.91
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.239301 0.4076 0.215918
DEOGEN2 converted rankscore 0.60739 0.76317 0.57793
Meta-SNP . Disease .
Meta-SNP score . 0.893 .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.6 -3.6 -3.6
SIFT_transf medium impact medium impact high impact
SIFT transf score 0.26 0.05 1.89
MutationAssessor transf medium impact high impact high impact
MutationAssessor transf score 1.92 3.09 3.09
CHASM Neutral Neutral Neutral
CHASM pvalue 0.44 0.8 0.33
CHASM FDR 0.8 0.85 0.8
ClinVar id . 9702.0 .
ClinVar Allele id . 24741.0 .
ClinVar CLNDISDB . MedGen:C1838951|MONDO:MONDO:0010789,MedGen:C0162671,OMIM:540000,Orphanet:550|MedGen:CN517202|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN . Leigh_syndrome_due_to_mitochondrial_complex_I_deficiency|Juvenile_myopathy,_encephalopathy,_lactic_acidosis_AND_stroke|not_provided|Mitochondrial_disease|Leigh_syndrome .
ClinVar CLNSIG . Pathogenic .
MITOMAP Disease Clinical info . Leigh Disease / MELAS / LHON-MELAS Overlap Syndrome / negative association w Carotid Atherosclerosis .
MITOMAP Disease Status . Cfrm [P] .
MITOMAP Disease Hom/Het ./. -/+ ./.
MITOMAP General GenBank Freq 0.0016% 0.0016% .
MITOMAP General GenBank Seqs 1 1 .
MITOMAP General Curated refs . 19370763;30095618;23010433;31996177;18674747;29670672;37038312;15382008;28429146;37737178;30461153;19617458;27450679;30128709;10589546;18495510;36975485;10908920;34146515;14520659;27919073;18402672;18977334;28951770;32220313;15972314;34298071;33746872;23847141;24931247;30950033;33717984;16483543;24667782;17400793;24642831;12624137;29428506;29228836;34670906;21174521;26741492;19054921;35778412;18332249;19268652;20408961;21850008;9299505;25192510;31669237;11198278;15576045;20064630;38465286;23874496;21364701;14730434;21457906;20972245 .
MITOMAP Variant Class polymorphism disease .
gnomAD 3.1 AN . 56431.0 .
gnomAD 3.1 AC Homo . 0.0 .
gnomAD 3.1 AF Hom . 0.0 .
gnomAD 3.1 AC Het . 0.0 .
gnomAD 3.1 AF Het . 0.0 .
gnomAD 3.1 filter . npg .
HelixMTdb AC Hom . . .
HelixMTdb AF Hom . . .
HelixMTdb AC Het . . .
HelixMTdb AF Het . . .
HelixMTdb mean ARF . . .
HelixMTdb max ARF . . .
ToMMo 54KJPN AC 3 . .
ToMMo 54KJPN AF 5.5e-05 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs267606897 rs267606897 .
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