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9804 (G > T)

General info

Mitimpact ID
MI.7906
Chr
chrM
Start
9804
Ref
G
Alt
T
Gene symbol
MT-CO3 Extended gene annotation
Gene position
598
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GCC/TCC
AA pos
200
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9804G>T
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
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Powered by MitoWheel

Conservation

PhyloP 100v
4.009 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.995 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
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 benign 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
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
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
693230
Clinvar ALLELEID
681766
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
9804G>T
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
56433
Gnomad AC hom
4
Gnomad AF hom
7.08e-05
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
15
HelixMTdb AF hom
7.65e-05
HelixMTdb AC het
0
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
rs200613617

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
.

9804 (G > A)

General info

Mitimpact ID
MI.7905
Chr
chrM
Start
9804
Ref
G
Alt
A
Gene symbol
MT-CO3 Extended gene annotation
Gene position
598
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GCC/ACC
AA pos
200
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9804G>A
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
4.009 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.995 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
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
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
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
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
9652
Clinvar ALLELEID
24691
Clinvar CLNDISDB
Medgen:cn517202;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104;

.
Clinvar CLNDN
Not provided;

leigh syndrome;

leber optic atrophy;

see cases
Clinvar CLNSIG
Conflicting interpretations of pathogenicity
MITOMAP Allele
9804G>A
MITOMAP Disease Clinical info
Lhon / ms
MITOMAP Disease Status
Reported [vus]
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
0.2961%
MITOMAP General GenBank Seqs
181
MITOMAP General GenBank Curated refs
11579587 19370763 21978175 8240356 10520236 23735083 16132471 7710535 27119776 11938495 20301353 7599218 21457906 33507977 30831606 11339587
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56420
Gnomad AC hom
205
Gnomad AF hom
0.0036334
Gnomad AC het
15
Gnomad AF het
0.0002658
Gnomad filter
Pass
HelixMTdb AC hom
926
HelixMTdb AF hom
0.0047249
HelixMTdb AC het
30
HelixMTdb AF het
0.000153
HelixMTdb mean ARF
0.41575
HelixMTdb max ARF
0.925
ToMMo JPN54K AC
223
ToMMo JPN54K AF
0.004107
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs200613617

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
3.26 CPD variant frequency
AA ref
A
CPD AA alt
T
Aln pos
200
RefSeq protein ID
YP_008379066 , YP_009024898 , YP_008378975 , YP_009024872 , YP_009024924 , NP_114340 , YP_002302306 , YP_009019985 , YP_002884232 , YP_009072416 , YP_026110 , YP_009072456 , YP_009072469 , YP_001293625 , YP_626373 , YP_398760 , YP_004464991 , NP_009285 , YP_007626829 , NP_008231 , YP_423955 , YP_009022037
Species name
Lophocebus aterrimus, Cercopithecus diana, Erythrocebus patas, Cercopithecus mitis, Allenopithecus nigroviridis, Macaca sylvanus, Macaca thibetana, Macaca assamensis, Macaca fascicularis, Macaca arctoides, Macaca mulatta, Macaca silenus, Macaca tonkeana, Mammut americanum, Elephas maximus, Mammuthus primigenius, Mammuthus columbi, Loxodonta africana, Loxodonta cyclotis, Pongo pygmaeus, Lipotes vexillifer, Orcinus orca
Ncbi taxon ID
75566, 36224, 9538, 36225, 54135, 9546, 54602, 9551, 9541, 9540, 9544, 54601, 40843, 39053, 9783, 37349, 1027716, 9785, 99490, 9600, 118797, 9733

9804 (G > C)

General info

Mitimpact ID
MI.7904
Chr
chrM
Start
9804
Ref
G
Alt
C
Gene symbol
MT-CO3 Extended gene annotation
Gene position
598
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
GCC/CCC
AA pos
200
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9804G>C
HGNC ID
7422
RC complex
IV
Ensembl gene ID
ENSG00000198938
Ensembl protein ID
ENSP00000354982
Ensembl transcript ID
ENST00000362079
Uniprot ID
P00414
Uniprot name
COX3_HUMAN
Ncbi gene ID
4514
Ncbi protein ID
YP_003024032.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
4.009 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.995 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
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
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
693229
Clinvar ALLELEID
681765
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
9804G>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0033%
MITOMAP General GenBank Seqs
2
MITOMAP General GenBank Curated refs
23463613
MITOMAP Variant Class
polymorphism
Gnomad AN
56429
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Npg
HelixMTdb AC hom
3
HelixMTdb AF hom
1.53e-05
HelixMTdb AC het
0
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
2
ToMMo JPN54K AF
3.7e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs200613617

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
.
~ 9804 (G/T) 9804 (G/A) 9804 (G/C)
~ 9804 (GCC/TCC) 9804 (GCC/ACC) 9804 (GCC/CCC)
MitImpact id MI.7906 MI.7905 MI.7904
Chr chrM chrM chrM
Start 9804 9804 9804
Ref G G G
Alt T A C
Gene symbol MT-CO3 MT-CO3 MT-CO3
Extended annotation mitochondrially encoded cytochrome c oxidase III mitochondrially encoded cytochrome c oxidase III mitochondrially encoded cytochrome c oxidase III
Gene position 598 598 598
Gene start 9207 9207 9207
Gene end 9990 9990 9990
Gene strand + + +
Codon substitution GCC/TCC GCC/ACC GCC/CCC
AA position 200 200 200
AA ref A A A
AA alt S T P
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516050 516050 516050
HGVS NC_012920.1:g.9804G>T NC_012920.1:g.9804G>A NC_012920.1:g.9804G>C
HGNC id 7422 7422 7422
Respiratory Chain complex IV IV IV
Ensembl gene id ENSG00000198938 ENSG00000198938 ENSG00000198938
Ensembl transcript id ENST00000362079 ENST00000362079 ENST00000362079
Ensembl protein id ENSP00000354982 ENSP00000354982 ENSP00000354982
Uniprot id P00414 P00414 P00414
Uniprot name COX3_HUMAN COX3_HUMAN COX3_HUMAN
Ncbi gene id 4514 4514 4514
Ncbi protein id YP_003024032.1 YP_003024032.1 YP_003024032.1
PhyloP 100V 4.009 4.009 4.009
PhyloP 470Way 0.848 0.848 0.848
PhastCons 100V 1 1 1
PhastCons 470Way 0.995 0.995 0.995
PolyPhen2 benign benign probably_damaging
PolyPhen2 score 0.24 0.01 0.93
SIFT neutral neutral neutral
SIFT score 0.41 0.47 0.2
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.021 0.031 0.001
VEST Neutral Neutral Pathogenic
VEST pvalue 0.2 0.16 0.02
VEST FDR 0.45 0.45 0.35
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Neutral Pathogenic
SNPDryad score 0.49 0.85 0.94
MutationTaster Polymorphism Disease automatic Polymorphism
MutationTaster score 0.999998 8.45389e-08 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE A200S A200T A200P
fathmm Tolerated Tolerated Tolerated
fathmm score 2.47 2.54 2.44
fathmm converted rankscore 0.14783 0.13916 0.15145
AlphaMissense likely_benign ambiguous likely_pathogenic
AlphaMissense score 0.3238 0.4109 0.9858
CADD Neutral Neutral Deleterious
CADD score 2.18512 2.332071 3.887761
CADD phred 17.41 18.38 23.5
PROVEAN Damaging Damaging Damaging
PROVEAN score -2.53 -3.26 -4.49
MutationAssessor medium medium high
MutationAssessor score 2.655 2.565 4.965
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.462 0.19 0.582
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.576 0.306 0.356
MLC Deleterious Deleterious Deleterious
MLC score 0.53180639 0.53180639 0.53180639
PANTHER score . 0.203 .
PhD-SNP score . 0.848 .
APOGEE1 Neutral Pathogenic Neutral
APOGEE1 score 0.45 0.86 0.49
APOGEE2 VUS- VUS VUS
APOGEE2 score 0.302585961080542 0.396250309034834 0.459619904469772
CAROL neutral neutral neutral
CAROL score 0.5 0.52 0.96
Condel deleterious deleterious neutral
Condel score 0.59 0.73 0.14
COVEC WMV neutral neutral deleterious
COVEC WMV score -3 -3 2
MtoolBox neutral neutral deleterious
MtoolBox DS 0.3 0.25 0.84
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.082401 0.084082 0.174375
DEOGEN2 converted rankscore 0.36820 0.37199 0.52358
Meta-SNP . Neutral .
Meta-SNP score . 0.343 .
PolyPhen2 transf medium impact medium impact low impact
PolyPhen2 transf score -0.38 1.07 -1.96
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.1 0.16 -0.15
MutationAssessor transf medium impact medium impact high impact
MutationAssessor transf score 1.06 0.7 2.66
CHASM Neutral Neutral Neutral
CHASM pvalue 0.44 0.71 0.59
CHASM FDR 0.8 0.85 0.8
ClinVar id 693230.0 9652.0 693229.0
ClinVar Allele id 681766.0 24691.0 681765.0
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|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 Leigh_syndrome not_provided|Leigh_syndrome|Leber_optic_atrophy|See_cases Leigh_syndrome
ClinVar CLNSIG Uncertain_significance Conflicting_interpretations_of_pathogenicity Uncertain_significance
MITOMAP Disease Clinical info . LHON / MS .
MITOMAP Disease Status . Reported [VUS] .
MITOMAP Disease Hom/Het ./. +/+ ./.
MITOMAP General GenBank Freq 0.0016% 0.2961% 0.0033%
MITOMAP General GenBank Seqs 1 181 2
MITOMAP General Curated refs . 11579587;19370763;21978175;8240356;10520236;23735083;16132471;7710535;27119776;11938495;20301353;7599218;21457906;33507977;30831606;11339587 23463613
MITOMAP Variant Class polymorphism polymorphism;disease polymorphism
gnomAD 3.1 AN 56433.0 56420.0 56429.0
gnomAD 3.1 AC Homo 4.0 205.0 0.0
gnomAD 3.1 AF Hom 7.088050000000001e-05 0.00363346 0.0
gnomAD 3.1 AC Het 0.0 15.0 0.0
gnomAD 3.1 AF Het 0.0 0.000265863 0.0
gnomAD 3.1 filter PASS PASS npg
HelixMTdb AC Hom 15.0 926.0 3.0
HelixMTdb AF Hom 7.653725e-05 0.0047249 1.530745e-05
HelixMTdb AC Het 0.0 30.0 0.0
HelixMTdb AF Het 0.0 0.0001530745 0.0
HelixMTdb mean ARF . 0.41575 .
HelixMTdb max ARF . 0.925 .
ToMMo 54KJPN AC . 223 2
ToMMo 54KJPN AF . 0.004107 3.7e-05
ToMMo 54KJPN AN . 54302 54302
COSMIC 90 . . .
dbSNP 156 id rs200613617 rs200613617 rs200613617
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