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4216 (T > C)

General info

Mitimpact ID
MI.12652
Chr
chrM
Start
4216
Ref
T
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
910
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAT/CAT
AA pos
304
AA ref
Y
AA alt
H
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4216T>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
0.217 Conservation Score
PhyloP 470way
-0.507 Conservation Score
PhastCons 100v
0.977 Conservation Score
PhastCons 470way
0.012 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
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral 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
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
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
9724
Clinvar ALLELEID
24763
Clinvar CLNDISDB
Medgen:cn517202;

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
Not provided;

leber optic atrophy;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
4216T>C
MITOMAP Disease Clinical info
Lhon / insulin resistance /possible adaptive high altitude variant / miscarriage
MITOMAP Disease Status
Conflicting reports
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
10.4786%
MITOMAP General GenBank Seqs
6406
MITOMAP General GenBank Curated refs
15470367 1634041 21741027 19005266 16044424 10545708 15465027 8899049 21067478 16901986 18806273 18308428 18269758 19076426 1900003 8680405 18216301 15060117 10803467 29444077 11526508 24002810 11179019 21457906 30369864 19370763 9027481 31478599 16532388 11349229 11935318 23464625 20197120 18495510 18402672 15338331 7599217 16523671 11339587 15638829 12406974 15827561 34573281 17454741 9719386 12888043 9302261 19930207 7599218 16172508 17003408 36701026 28267784 29996615 29486301 12150954 7763260 31798871 9150158 7942855 31797714 20067846 15108120 19050702 11062027 15382008 8593537 20728388 22561905 32094358 7814218 7977345 19026397 17406640 15972314 22927010 11571560 19062322 9915963 16404693 31152278 15286228 7635294 23288206 16773565 18931934 10737123 7770132 19427920 10424809 9832034 29387390 18668590 16132471 30876822 11820805 15786469 18691441 32887465 1463007 19130794 27498855 12112086 8741876 15591266 23304069 16120329 28696810 11938495 16759180 30831606 16714301 11133798 8071952 16996290 10680807 10894993 11853713 24069186 15975594 10234520 16050984 18682780 17684475 29987491 10936107 8755941 18590963 30446962 22487888
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
55886
Gnomad AC hom
6570
Gnomad AF hom
0.117561
Gnomad AC het
3
Gnomad AF het
5.36e-05
Gnomad filter
Pass
HelixMTdb AC hom
33421
HelixMTdb AF hom
0.1705301
HelixMTdb AC het
129
HelixMTdb AF het
0.0006582
HelixMTdb mean ARF
0.80523
HelixMTdb max ARF
0.94444
ToMMo JPN54K AC
509
ToMMo JPN54K AF
0.009374
ToMMo JPN54K AN
54302
COSMIC 90
COSM1138371
dbSNP 156
rs1599988

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
.

4216 (T > A)

General info

Mitimpact ID
MI.12653
Chr
chrM
Start
4216
Ref
T
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
910
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAT/AAT
AA pos
304
AA ref
Y
AA alt
N
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4216T>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.217 Conservation Score
PhyloP 470way
-0.507 Conservation Score
PhastCons 100v
0.977 Conservation Score
PhastCons 470way
0.012 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
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic 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
4216T>A
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
56433
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
.

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
.

4216 (T > G)

General info

Mitimpact ID
MI.12654
Chr
chrM
Start
4216
Ref
T
Alt
G
Gene symbol
MT-ND1 Extended gene annotation
Gene position
910
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
TAT/GAT
AA pos
304
AA ref
Y
AA alt
D
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4216T>G
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
0.217 Conservation Score
PhyloP 470way
-0.507 Conservation Score
PhastCons 100v
0.977 Conservation Score
PhastCons 470way
0.012 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
Disease Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Ambiguous Score and details of the predictor
CADD
Neutral 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
Neutral Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

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
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
4216T>G
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
.
~ 4216 (T/C) 4216 (T/A) 4216 (T/G)
~ 4216 (TAT/CAT) 4216 (TAT/AAT) 4216 (TAT/GAT)
MitImpact id MI.12652 MI.12653 MI.12654
Chr chrM chrM chrM
Start 4216 4216 4216
Ref T T T
Alt C A G
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 910 910 910
Gene start 3307 3307 3307
Gene end 4262 4262 4262
Gene strand + + +
Codon substitution TAT/CAT TAT/AAT TAT/GAT
AA position 304 304 304
AA ref Y Y Y
AA alt H N D
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516000 516000 516000
HGVS NC_012920.1:g.4216T>C NC_012920.1:g.4216T>A NC_012920.1:g.4216T>G
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 0.217 0.217 0.217
PhyloP 470Way -0.507 -0.507 -0.507
PhastCons 100V 0.977 0.977 0.977
PhastCons 470Way 0.012 0.012 0.012
PolyPhen2 benign benign benign
PolyPhen2 score 0.01 0.02 0.36
SIFT neutral neutral neutral
SIFT score 0.37 0.15 0.08
SIFT4G Tolerated Tolerated Damaging
SIFT4G score 1.0 0.061 0.001
VEST Neutral Neutral Neutral
VEST pvalue 0.15 0.15 0.08
VEST FDR 0.4 0.4 0.35
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.03 0.47 0.68
MutationTaster Polymorphism Polymorphism Disease
MutationTaster score 0.999999 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.81001
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE Y304H Y304N Y304D
fathmm Tolerated Tolerated Tolerated
fathmm score 2.8 2.77 2.76
fathmm converted rankscore 0.11082 0.11407 0.11515
AlphaMissense likely_benign likely_benign ambiguous
AlphaMissense score 0.1252 0.1397 0.414
CADD Neutral Neutral Neutral
CADD score -0.954968 2.220539 2.274909
CADD phred 0.02 17.64 18.0
PROVEAN Tolerated Tolerated Damaging
PROVEAN score 3.51 -1.66 -3.26
MutationAssessor neutral low medium
MutationAssessor score 0.01 1.07 2.63
EFIN SP Damaging Neutral Neutral
EFIN SP score 0.326 0.794 0.736
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.968 0.862 0.41
MLC Neutral Neutral Neutral
MLC score 0.24865713 0.24865713 0.24865713
PANTHER score 0.111 . .
PhD-SNP score 0.274 . .
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.73 0.52 0.51
APOGEE2 Likely-benign Likely-benign VUS+
APOGEE2 score 0.192594329647387 0.170665337831623 0.569041925615149
CAROL neutral neutral neutral
CAROL score 0.62 0.85 0.91
Condel deleterious deleterious neutral
Condel score 0.68 0.57 0.36
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -3
MtoolBox neutral neutral neutral
MtoolBox DS 0.11 0.17 0.3
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.010696 0.040712 0.115708
DEOGEN2 converted rankscore 0.09633 0.25618 0.43450
Meta-SNP Neutral . .
Meta-SNP score 0.133 . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score 1.12 0.84 -0.52
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.15 -0.15 -0.32
MutationAssessor transf low impact medium impact medium impact
MutationAssessor transf score -2.23 -0.52 0.74
CHASM Neutral Neutral Neutral
CHASM pvalue 0.3 0.28 0.26
CHASM FDR 0.8 0.8 0.8
ClinVar id 9724.0 . .
ClinVar Allele id 24763.0 . .
ClinVar CLNDISDB MedGen:CN517202|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 not_provided|Leber_optic_atrophy|Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info LHON / Insulin Resistance /possible adaptive high altitude variant / miscarriage . .
MITOMAP Disease Status Conflicting reports . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 10.4786% . .
MITOMAP General GenBank Seqs 6406 . .
MITOMAP General Curated refs 15470367;1634041;21741027;19005266;16044424;10545708;15465027;8899049;21067478;16901986;18806273;18308428;18269758;19076426;1900003;8680405;18216301;15060117;10803467;29444077;11526508;24002810;11179019;21457906;30369864;19370763;9027481;31478599;16532388;11349229;11935318;23464625;20197120;18495510;18402672;15338331;7599217;16523671;11339587;15638829;12406974;15827561;34573281;17454741;9719386;12888043;9302261;19930207;7599218;16172508;17003408;36701026;28267784;29996615;29486301;12150954;7763260;31798871;9150158;7942855;31797714;20067846;15108120;19050702;11062027;15382008;8593537;20728388;22561905;32094358;7814218;7977345;19026397;17406640;15972314;22927010;11571560;19062322;9915963;16404693;31152278;15286228;7635294;23288206;16773565;18931934;10737123;7770132;19427920;10424809;9832034;29387390;18668590;16132471;30876822;11820805;15786469;18691441;32887465;1463007;19130794;27498855;12112086;8741876;15591266;23304069;16120329;28696810;11938495;16759180;30831606;16714301;11133798;8071952;16996290;10680807;10894993;11853713;24069186;15975594;10234520;16050984;18682780;17684475;29987491;10936107;8755941;18590963;30446962;22487888 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 55886.0 56433.0 .
gnomAD 3.1 AC Homo 6570.0 0.0 .
gnomAD 3.1 AF Hom 0.117561 0.0 .
gnomAD 3.1 AC Het 3.0 0.0 .
gnomAD 3.1 AF Het 5.36807e-05 0.0 .
gnomAD 3.1 filter PASS npg .
HelixMTdb AC Hom 33421.0 . .
HelixMTdb AF Hom 0.1705301 . .
HelixMTdb AC Het 129.0 . .
HelixMTdb AF Het 0.0006582204 . .
HelixMTdb mean ARF 0.80523 . .
HelixMTdb max ARF 0.94444 . .
ToMMo 54KJPN AC 509 . .
ToMMo 54KJPN AF 0.009374 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 COSM1138371 . .
dbSNP 156 id rs1599988 . .
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