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3460 (G > A)

General info

Mitimpact ID
MI.11080
Chr
chrM
Start
3460
Ref
G
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
154
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GCC/ACC
AA pos
52
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3460G>A
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
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Powered by MitoWheel

Conservation

PhyloP 100v
6.38 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.016 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
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 pathogenic Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Tolerated 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
Neutral 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
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
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
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
9722
Clinvar ALLELEID
24761
Clinvar CLNDISDB
.;

medgen:cn517202;

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

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
Mitochondrial complex i deficiency, mitochondrial type 3;

not provided;

mitochondrial disease;

leber optic atrophy;

leigh syndrome
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
3460G>A
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Cfrm [p]
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
0.0507%
MITOMAP General GenBank Seqs
31
MITOMAP General GenBank Curated refs
11579587 37733737 10520236 34122299 7853025 28994349 15466086 1928099 8931573 16083845 19800080 1550131 10545708 19098324 15720387 24508359 16120372 22079202 21067478 32220313 12023431 15629831 9852675 17479363 18806273 19525327 37988592 38346855 10939569 10976107 17886296 16972023 9012411 31932089 11741983 30053855 15629832 20301353 12205655 12711217 14748908 1734726 8680405 18647627 18216301 7611298 8270249 28040497 31817256 15060117 12638016 33706792 14750573 15033723 29444077 29587845 8571959 17122117 11124301 21457906 27071925 37587338 32219779 30369864 21694444 20053576 19370763 28716668 17292333 15282179 37737178 11329546 15282189 16532388 36361994 35383288 7629530 29980632 8195807 17652639 1732158 7710535 18402672 8600429 33552719 12518276 16523671 8556281 15638829 18235013 20454697 34573281 29253894 27847334 18562849 21788663 30081212 27177320 27746671 9302261 25909222 34168607 27787713 20491810 7599218 19268652 17003408 16738010 32704028 20471050 25192510 25053773 20064630 33911213 20809775 16083844 14671420 9150158 34673906 33159657 8496715 7924787 30591017 7735876 31584786 21397051 10426138 16829155 15883259 21859767 26404827 29189152 36827238 7603534 7977345 7901141 12446713 15342361 17406640 15972314 23847141 10608675 8213820 17942074 8401538 24369379 7635294 22410442 20943885 32991883 36565700 16380918 23297368 20232220 11074292 21253496 25338955 35778412 7770132 20123042 11001192 12409182 9412783 16564802 28991104 7821467 35623556 30304398 29387390 15728653 29983856 18320530 34670133 37878684 31040363 20599858 11523562 18674747 8742999 37038312 12807863 10426140 28481993 20628600 32887465 33477675 32105823 1674640 32991388 26605371 35858578 7760326 18214789 8941270 17434142 28314831 19255150 11906302 21887510 18070226 29426449 19319978 33584522 11331900 32504279 33095398 1444915 8071952 28392196 28233183 11853713 1959619 20211598 29991444 16050984 11937919 34915201 19710181 8024249 8659512 21810891 15126312 30572950 8755941 9561832 11339587
MITOMAP Variant Class
disease
Gnomad AN
56426
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
14
HelixMTdb AF het
7.14e-05
HelixMTdb mean ARF
0.29635
HelixMTdb max ARF
0.88333
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
COSM6716713
dbSNP 156
rs199476118

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
.

3460 (G > C)

General info

Mitimpact ID
MI.11079
Chr
chrM
Start
3460
Ref
G
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
154
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GCC/CCC
AA pos
52
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3460G>C
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
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Powered by MitoWheel

Conservation

PhyloP 100v
6.38 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.016 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
Pathogenic 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 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
Damaging 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-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
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
3460G>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
.

3460 (G > T)

General info

Mitimpact ID
MI.11078
Chr
chrM
Start
3460
Ref
G
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
154
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GCC/TCC
AA pos
52
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3460G>T
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
6.38 Conservation Score
PhyloP 470way
0.602 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.016 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
Polymorphism Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Ambiguous Score and details of the predictor
CADD
Deleterious 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
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
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
3460G>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
.
~ 3460 (G/A) 3460 (G/C) 3460 (G/T)
~ 3460 (GCC/ACC) 3460 (GCC/CCC) 3460 (GCC/TCC)
MitImpact id MI.11080 MI.11079 MI.11078
Chr chrM chrM chrM
Start 3460 3460 3460
Ref G G G
Alt A C T
Gene symbol MT-ND1 MT-ND1 MT-ND1
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1
Gene position 154 154 154
Gene start 3307 3307 3307
Gene end 4262 4262 4262
Gene strand + + +
Codon substitution GCC/ACC GCC/CCC GCC/TCC
AA position 52 52 52
AA ref A A A
AA alt T P S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516000 516000 516000
HGVS NC_012920.1:g.3460G>A NC_012920.1:g.3460G>C NC_012920.1:g.3460G>T
HGNC id 7455 7455 7455
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198888 ENSG00000198888 ENSG00000198888
Ensembl transcript id ENST00000361390 ENST00000361390 ENST00000361390
Ensembl protein id ENSP00000354687 ENSP00000354687 ENSP00000354687
Uniprot id P03886 P03886 P03886
Uniprot name NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN
Ncbi gene id 4535 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1 YP_003024026.1
PhyloP 100V 6.38 6.38 6.38
PhyloP 470Way 0.602 0.602 0.602
PhastCons 100V 1 1 1
PhastCons 470Way 0.016 0.016 0.016
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0 1.0
SIFT neutral neutral neutral
SIFT score 0.54 0.31 0.6
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.001 0.001 0.008
VEST Neutral Pathogenic Neutral
VEST pvalue 0.13 0.02 0.2
VEST FDR 0.4 0.35 0.45
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Pathogenic Pathogenic
SNPDryad score 0.7 0.96 0.93
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 4.23062e-11 1 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE A52T A52P A52S
fathmm Tolerated Tolerated Tolerated
fathmm score 2.62 2.56 2.64
fathmm converted rankscore 0.12988 0.13673 0.12780
AlphaMissense likely_pathogenic likely_pathogenic ambiguous
AlphaMissense score 0.624 0.9598 0.3716
CADD Deleterious Deleterious Deleterious
CADD score 4.240442 3.773263 3.601806
CADD phred 23.9 23.4 23.2
PROVEAN Tolerated Damaging Tolerated
PROVEAN score -2.36 -2.63 -0.79
MutationAssessor medium high high
MutationAssessor score 2.775 3.815 3.815
EFIN SP Damaging Damaging Neutral
EFIN SP score 0.294 0.522 0.75
EFIN HD Neutral Damaging Neutral
EFIN HD score 0.448 0.274 0.49
MLC Deleterious Deleterious Deleterious
MLC score 0.87500754 0.87500754 0.87500754
PANTHER score 0.262 . .
PhD-SNP score 0.592 . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.86 0.46 0.37
APOGEE2 Likely-pathogenic Likely-pathogenic VUS
APOGEE2 score 0.869393471058617 0.781113234821376 0.52821895292228
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 1.0
Condel neutral neutral neutral
Condel score 0.27 0.16 0.3
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 1 2 1
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.76 0.9 0.8
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.13119 0.228935 0.086155
DEOGEN2 converted rankscore 0.46053 0.59462 0.37661
Meta-SNP Disease . .
Meta-SNP score 0.624 . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.57 -3.57 -3.57
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.31 0.08 0.37
MutationAssessor transf medium impact high impact medium impact
MutationAssessor transf score 1.5 2.35 1.75
CHASM Neutral Neutral Neutral
CHASM pvalue 0.78 0.56 0.48
CHASM FDR 0.85 0.8 0.8
ClinVar id 9722.0 . .
ClinVar Allele id 24761.0 . .
ClinVar CLNDISDB .|MedGen:CN517202|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|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 MITOCHONDRIAL_COMPLEX_I_DEFICIENCY,_MITOCHONDRIAL_TYPE_3|not_provided|Mitochondrial_disease|Leber_optic_atrophy|Leigh_syndrome . .
ClinVar CLNSIG Pathogenic . .
MITOMAP Disease Clinical info LHON . .
MITOMAP Disease Status Cfrm [P] . .
MITOMAP Disease Hom/Het +/+ ./. ./.
MITOMAP General GenBank Freq 0.0507% . .
MITOMAP General GenBank Seqs 31 . .
MITOMAP General Curated refs 11579587;37733737;10520236;34122299;7853025;28994349;15466086;1928099;8931573;16083845;19800080;1550131;10545708;19098324;15720387;24508359;16120372;22079202;21067478;32220313;12023431;15629831;9852675;17479363;18806273;19525327;37988592;38346855;10939569;10976107;17886296;16972023;9012411;31932089;11741983;30053855;15629832;20301353;12205655;12711217;14748908;1734726;8680405;18647627;18216301;7611298;8270249;28040497;31817256;15060117;12638016;33706792;14750573;15033723;29444077;29587845;8571959;17122117;11124301;21457906;27071925;37587338;32219779;30369864;21694444;20053576;19370763;28716668;17292333;15282179;37737178;11329546;15282189;16532388;36361994;35383288;7629530;29980632;8195807;17652639;1732158;7710535;18402672;8600429;33552719;12518276;16523671;8556281;15638829;18235013;20454697;34573281;29253894;27847334;18562849;21788663;30081212;27177320;27746671;9302261;25909222;34168607;27787713;20491810;7599218;19268652;17003408;16738010;32704028;20471050;25192510;25053773;20064630;33911213;20809775;16083844;14671420;9150158;34673906;33159657;8496715;7924787;30591017;7735876;31584786;21397051;10426138;16829155;15883259;21859767;26404827;29189152;36827238;7603534;7977345;7901141;12446713;15342361;17406640;15972314;23847141;10608675;8213820;17942074;8401538;24369379;7635294;22410442;20943885;32991883;36565700;16380918;23297368;20232220;11074292;21253496;25338955;35778412;7770132;20123042;11001192;12409182;9412783;16564802;28991104;7821467;35623556;30304398;29387390;15728653;29983856;18320530;34670133;37878684;31040363;20599858;11523562;18674747;8742999;37038312;12807863;10426140;28481993;20628600;32887465;33477675;32105823;1674640;32991388;26605371;35858578;7760326;18214789;8941270;17434142;28314831;19255150;11906302;21887510;18070226;29426449;19319978;33584522;11331900;32504279;33095398;1444915;8071952;28392196;28233183;11853713;1959619;20211598;29991444;16050984;11937919;34915201;19710181;8024249;8659512;21810891;15126312;30572950;8755941;9561832;11339587 . .
MITOMAP Variant Class disease . .
gnomAD 3.1 AN 56426.0 . .
gnomAD 3.1 AC Homo 0.0 . .
gnomAD 3.1 AF Hom 0.0 . .
gnomAD 3.1 AC Het 1.0 . .
gnomAD 3.1 AF Het 1.77223e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 0.0 . .
HelixMTdb AF Hom 0.0 . .
HelixMTdb AC Het 14.0 . .
HelixMTdb AF Het 7.143477e-05 . .
HelixMTdb mean ARF 0.29635 . .
HelixMTdb max ARF 0.88333 . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 COSM6716713 . .
dbSNP 156 id rs199476118 . .
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