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13708 (G > A)

General info

Mitimpact ID
MI.22186
Chr
chrM
Start
13708
Ref
G
Alt
A
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1372
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
GCA/ACA
AA pos
458
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.13708G>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
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Powered by MitoWheel

Conservation

PhyloP 100v
0.633 Conservation Score
PhyloP 470way
-0.807 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.002 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
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
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
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
9696
Clinvar ALLELEID
24735
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
Clinvar CLNDN
Leber optic atrophy;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
13708G>A
MITOMAP Disease Clinical info
Lhon / increased ms risk / higher freq in pd-ads
MITOMAP Disease Status
Conflicting reports
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
7.459%
MITOMAP General GenBank Seqs
4560
MITOMAP General GenBank Curated refs
15470367 18619472 10520236 1634041 19220304 27119776 19005266 16044424 1550131 18545700 10545708 1417830 17603766 21067478 18205894 18590963 8163275 16901986 18806273 18712405 18308428 18270557 15234467 21288980 1900003 8680405 15060117 24002810 20691156 11179019 21457906 30369864 21694444 19370763 16313983 9027481 15625560 16532388 11349229 11935318 21878127 1732158 7710535 8600429 9561330 10216058 34573281 19527690 12888043 9302261 19223931 8053461 7599218 17003408 20304802 29486301 36322731 12150954 7763260 31798871 9150158 7942855 31797714 20067846 21978175 18477584 15382008 22561905 32094358 7814218 7977345 7901141 19026397 17406640 15972314 19151382 11571560 17660050 9915963 8213820 16404693 18775412 19062322 31152278 15286228 7635294 18286226 16773565 18931934 19489744 10737123 7770132 19427920 21724059 10424809 28341142 12618962 16960846 8978068 25313049 18668590 18322915 18853457 11820805 18691441 32887465 1463007 19130794 19818876 27498855 8741876 15591266 23304069 11938495 16714301 8071952 10680807 12802679 24069186 15932126 15975594 10234520 16050984 19500771 18386806 21041797 19340307 8024249 12937995 18810306 29987491 10936107 8755941 1764087 11339587
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56361
Gnomad AC hom
4263
Gnomad AF hom
0.0756373
Gnomad AC het
21
Gnomad AF het
0.0003725
Gnomad filter
Pass
HelixMTdb AC hom
19999
HelixMTdb AF hom
0.1020445
HelixMTdb AC het
86
HelixMTdb AF het
0.0004388
HelixMTdb mean ARF
0.51484
HelixMTdb max ARF
0.96842
ToMMo JPN54K AC
1215
ToMMo JPN54K AF
0.022375
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs28359178

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
.

13708 (G > C)

General info

Mitimpact ID
MI.22187
Chr
chrM
Start
13708
Ref
G
Alt
C
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1372
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
GCA/CCA
AA pos
458
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.13708G>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.633 Conservation Score
PhyloP 470way
-0.807 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.002 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly 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
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 pathogenic 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
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
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
Deleterious 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
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
13708G>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
.

13708 (G > T)

General info

Mitimpact ID
MI.22185
Chr
chrM
Start
13708
Ref
G
Alt
T
Gene symbol
MT-ND5 Extended gene annotation
Gene position
1372
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
GCA/TCA
AA pos
458
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.13708G>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
0.633 Conservation Score
PhyloP 470way
-0.807 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.002 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
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
.
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
13708G>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
.
~ 13708 (G/A) 13708 (G/C) 13708 (G/T)
~ 13708 (GCA/ACA) 13708 (GCA/CCA) 13708 (GCA/TCA)
MitImpact id MI.22186 MI.22187 MI.22185
Chr chrM chrM chrM
Start 13708 13708 13708
Ref G G G
Alt A C 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 1372 1372 1372
Gene start 12337 12337 12337
Gene end 14148 14148 14148
Gene strand + + +
Codon substitution GCA/ACA GCA/CCA GCA/TCA
AA position 458 458 458
AA ref A A A
AA alt T P S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516005 516005 516005
HGVS NC_012920.1:g.13708G>A NC_012920.1:g.13708G>C NC_012920.1:g.13708G>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 0.633 0.633 0.633
PhyloP 470Way -0.807 -0.807 -0.807
PhastCons 100V 0 0 0
PhastCons 470Way 0.002 0.002 0.002
PolyPhen2 benign possibly_damaging benign
PolyPhen2 score 0.02 0.86 0.4
SIFT neutral neutral neutral
SIFT score 0.48 0.26 0.5
SIFT4G Tolerated Damaging Damaging
SIFT4G score 0.078 0.003 0.004
VEST Neutral Neutral Neutral
VEST pvalue 0.37 0.11 0.37
VEST FDR 0.5 0.4 0.5
Mitoclass.1 neutral damaging neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.01 0.62 0.56
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1.0 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE A458T A458P A458S
fathmm Tolerated Tolerated Tolerated
fathmm score 1.25 1.21 1.32
fathmm converted rankscore 0.36512 0.37230 0.35219
AlphaMissense likely_benign likely_pathogenic likely_benign
AlphaMissense score 0.1315 0.9753 0.2215
CADD Neutral Neutral Neutral
CADD score 1.254751 2.050274 1.87414
CADD phred 12.03 16.53 15.43
PROVEAN Tolerated Damaging Tolerated
PROVEAN score -1.5 -2.87 -1.51
MutationAssessor low high high
MutationAssessor score 1.6 4.175 3.83
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.29 0.536 0.538
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.736 0.396 0.704
MLC Deleterious Deleterious Deleterious
MLC score 0.6244191 0.6244191 0.6244191
PANTHER score 0.627 . .
PhD-SNP score 0.783 . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.76 0.33 0.34
APOGEE2 VUS- VUS+ Likely-benign
APOGEE2 score 0.307025749980826 0.696841096401621 0.260757785070776
CAROL neutral neutral neutral
CAROL score 0.5 0.89 0.44
Condel deleterious neutral deleterious
Condel score 0.73 0.2 0.55
COVEC WMV neutral deleterious neutral
COVEC WMV score -6 1 -3
MtoolBox neutral neutral neutral
MtoolBox DS 0.21 0.38 0.26
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.03024 0.343481 0.028973
DEOGEN2 converted rankscore 0.21483 0.71212 0.20865
Meta-SNP Neutral . .
Meta-SNP score 0.4 . .
PolyPhen2 transf medium impact low impact medium impact
PolyPhen2 transf score 0.86 -1.5 -0.58
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.21 -0.02 0.23
MutationAssessor transf medium impact high impact medium impact
MutationAssessor transf score 0.15 2.13 1.5
CHASM Neutral Neutral Neutral
CHASM pvalue 0.68 0.74 0.72
CHASM FDR 0.85 0.85 0.85
ClinVar id 9696.0 . .
ClinVar Allele id 24735.0 . .
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 . .
ClinVar CLNDN Leber_optic_atrophy|Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info LHON / Increased MS risk / higher freq in PD-ADS . .
MITOMAP Disease Status Conflicting reports . .
MITOMAP Disease Hom/Het +/+ ./. ./.
MITOMAP General GenBank Freq 7.459% . .
MITOMAP General GenBank Seqs 4560 . .
MITOMAP General Curated refs 15470367;18619472;10520236;1634041;19220304;27119776;19005266;16044424;1550131;18545700;10545708;1417830;17603766;21067478;18205894;18590963;8163275;16901986;18806273;18712405;18308428;18270557;15234467;21288980;1900003;8680405;15060117;24002810;20691156;11179019;21457906;30369864;21694444;19370763;16313983;9027481;15625560;16532388;11349229;11935318;21878127;1732158;7710535;8600429;9561330;10216058;34573281;19527690;12888043;9302261;19223931;8053461;7599218;17003408;20304802;29486301;36322731;12150954;7763260;31798871;9150158;7942855;31797714;20067846;21978175;18477584;15382008;22561905;32094358;7814218;7977345;7901141;19026397;17406640;15972314;19151382;11571560;17660050;9915963;8213820;16404693;18775412;19062322;31152278;15286228;7635294;18286226;16773565;18931934;19489744;10737123;7770132;19427920;21724059;10424809;28341142;12618962;16960846;8978068;25313049;18668590;18322915;18853457;11820805;18691441;32887465;1463007;19130794;19818876;27498855;8741876;15591266;23304069;11938495;16714301;8071952;10680807;12802679;24069186;15932126;15975594;10234520;16050984;19500771;18386806;21041797;19340307;8024249;12937995;18810306;29987491;10936107;8755941;1764087;11339587 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56361.0 . .
gnomAD 3.1 AC Homo 4263.0 . .
gnomAD 3.1 AF Hom 0.0756374 . .
gnomAD 3.1 AC Het 21.0 . .
gnomAD 3.1 AF Het 0.000372598 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 19999.0 . .
HelixMTdb AF Hom 0.10204457 . .
HelixMTdb AC Het 86.0 . .
HelixMTdb AF Het 0.00043881356 . .
HelixMTdb mean ARF 0.51484 . .
HelixMTdb max ARF 0.96842 . .
ToMMo 54KJPN AC 1215 . .
ToMMo 54KJPN AF 0.022375 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs28359178 . .
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