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15812 (G > A)

General info

Mitimpact ID
MI.10598
Chr
chrM
Start
15812
Ref
G
Alt
A
Gene symbol
MT-CYB Extended gene annotation
Gene position
1066
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GTA/ATA
AA pos
356
AA ref
V
AA alt
M
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15812G>A
HGNC ID
7427
RC complex
III
Ensembl gene ID
ENSG00000198727
Ensembl protein ID
ENSP00000354554
Ensembl transcript ID
ENST00000361789
Uniprot ID
P00156
Uniprot name
CYB_HUMAN
Ncbi gene ID
4519
Ncbi protein ID
YP_003024038.1
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Powered by MitoWheel

Conservation

PhyloP 100v
-0.327 Conservation Score
PhyloP 470way
-0.139 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.498 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
.
fathmm
.
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
.
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
.
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
.
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
9675
Clinvar ALLELEID
24714
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
15812G>A
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported / secondary
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.8391%
MITOMAP General GenBank Seqs
513
MITOMAP General GenBank Curated refs
19370763 18668590 1634041 16532388 32887465 11349229 1463007 22561905 32094358 23304069 7977345 7901141 8899049 11938495 8600429 9561330 10377009 17406640 21067478 11571560 16901986 19527690 7635294 18931934 32943110 10894993 7770132 19427920 7599218 8680405 16050984 21041797 15060117 27217714 9150158 21457906 1764087 30369864
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56424
Gnomad AC hom
656
Gnomad AF hom
0.0116262
Gnomad AC het
4
Gnomad AF het
7.08e-05
Gnomad filter
Pass
HelixMTdb AC hom
1389
HelixMTdb AF hom
0.0070873
HelixMTdb AC het
24
HelixMTdb AF het
0.0001224
HelixMTdb mean ARF
0.47929
HelixMTdb max ARF
0.95858
ToMMo JPN54K AC
4
ToMMo JPN54K AF
7.4e-05
ToMMo JPN54K AN
54302
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
6.69 CPD variant frequency
AA ref
V
CPD AA alt
M
Aln pos
356
RefSeq protein ID
YP_214965 , YP_007024903 , YP_009024995 , YP_214952 , YP_007024916 , YP_659446 , YP_007024955 , YP_006460529 , YP_006460542 , YP_659511 , YP_008378955 , YP_004425136 , YP_006460490 , YP_006460503 , YP_006460516 , YP_659485 , YP_659459 , YP_007625639 , YP_009024930 , YP_009024878 , YP_009024891 , YP_001427434 , YP_009059471 , YP_238254 , YP_001427421 , YP_007316908 , NP_008470 , YP_007316895 , YP_007316934 , YP_007316921 , YP_007316947 , YP_008379072 , YP_008378929 , YP_009072462 , YP_002302312 , YP_009019991 , YP_002884238 , YP_026116 , YP_009072422 , NP_944684 , YP_007625535 , YP_161220 , YP_161272 , YP_001382284 , YP_007625392
Species name
Colobus guereza, Trachypithecus hatinhensis, Trachypithecus francoisi, Trachypithecus obscurus, Trachypithecus germaini, Semnopithecus entellus, Trachypithecus johnii, Pygathrix nigripes, Pygathrix cinerea 1 rl-2012, Pygathrix nemaeus, Cheirogaleus medius, Rhinopithecus bieti, Rhinopithecus bieti 1 rl-2012, Rhinopithecus strykeri, Rhinopithecus bieti 2 rl-2012, Rhinopithecus roxellana, Nasalis larvatus, Simias concolor, Allenopithecus nigroviridis, Cercopithecus mitis, Allochrocebus lhoesti, Chlorocebus pygerythrus, Chlorocebus cynosuros, Chlorocebus aethiops, Chlorocebus tantalus, Papio cynocephalus, Papio hamadryas, Papio anubis, Papio papio, Papio kindae, Papio ursinus, Lophocebus aterrimus, Cercocebus chrysogaster, Macaca silenus, Macaca thibetana, Macaca assamensis, Macaca fascicularis, Macaca mulatta, Macaca arctoides, Hyperoodon ampullatus, Ctenomys leucodon, Pseudocheirus peregrinus, Phascogale tapoatafa, Canis lupus lupus, Mephitis mephitis
Ncbi taxon ID
33548, 867383, 54180, 54181, 271260, 88029, 66063, 310352, 1194332, 54133, 9460, 61621, 1194334, 1194336, 1194335, 61622, 43780, 170207, 54135, 36225, 100224, 60710, 460675, 9534, 60712, 9556, 9557, 9555, 100937, 208091, 36229, 75566, 75569, 54601, 54602, 9551, 9541, 9544, 9540, 48744, 61871, 9333, 9293, 443256, 30548

15812 (G > C)

General info

Mitimpact ID
MI.10597
Chr
chrM
Start
15812
Ref
G
Alt
C
Gene symbol
MT-CYB Extended gene annotation
Gene position
1066
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GTA/CTA
AA pos
356
AA ref
V
AA alt
L
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15812G>C
HGNC ID
7427
RC complex
III
Ensembl gene ID
ENSG00000198727
Ensembl protein ID
ENSP00000354554
Ensembl transcript ID
ENST00000361789
Uniprot ID
P00156
Uniprot name
CYB_HUMAN
Ncbi gene ID
4519
Ncbi protein ID
YP_003024038.1
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Powered by MitoWheel

Conservation

PhyloP 100v
-0.327 Conservation Score
PhyloP 470way
-0.139 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.498 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
.
fathmm
.
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
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
Neutral Score and details of the meta-predictor
APOGEE2
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
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
High impact Score and details of the cancer-specific predictor
SIFT transf
High 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
15812G>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
2
HelixMTdb AF hom
1.02e-05
HelixMTdb AC het
2
HelixMTdb AF het
1.02e-05
HelixMTdb mean ARF
0.16468
HelixMTdb max ARF
0.21978
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
.

15812 (G > T)

General info

Mitimpact ID
MI.10596
Chr
chrM
Start
15812
Ref
G
Alt
T
Gene symbol
MT-CYB Extended gene annotation
Gene position
1066
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GTA/TTA
AA pos
356
AA ref
V
AA alt
L
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15812G>T
HGNC ID
7427
RC complex
III
Ensembl gene ID
ENSG00000198727
Ensembl protein ID
ENSP00000354554
Ensembl transcript ID
ENST00000361789
Uniprot ID
P00156
Uniprot name
CYB_HUMAN
Ncbi gene ID
4519
Ncbi protein ID
YP_003024038.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.327 Conservation Score
PhyloP 470way
-0.139 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.498 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
.
fathmm
.
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
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
Neutral Score and details of the meta-predictor
APOGEE2
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
.
Meta SNP
.

Cancer-specific predictors

PolyPhen2 transf
High impact Score and details of the cancer-specific predictor
SIFT transf
High 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
15812G>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
.
~ 15812 (G/A) 15812 (G/C) 15812 (G/T)
~ 15812 (GTA/ATA) 15812 (GTA/CTA) 15812 (GTA/TTA)
MitImpact id MI.10598 MI.10597 MI.10596
Chr chrM chrM chrM
Start 15812 15812 15812
Ref G G G
Alt A C T
Gene symbol MT-CYB MT-CYB MT-CYB
Extended annotation mitochondrially encoded cytochrome b mitochondrially encoded cytochrome b mitochondrially encoded cytochrome b
Gene position 1066 1066 1066
Gene start 14747 14747 14747
Gene end 15887 15887 15887
Gene strand + + +
Codon substitution GTA/ATA GTA/CTA GTA/TTA
AA position 356 356 356
AA ref V V V
AA alt M L L
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516020 516020 516020
HGVS NC_012920.1:g.15812G>A NC_012920.1:g.15812G>C NC_012920.1:g.15812G>T
HGNC id 7427 7427 7427
Respiratory Chain complex III III III
Ensembl gene id ENSG00000198727 ENSG00000198727 ENSG00000198727
Ensembl transcript id ENST00000361789 ENST00000361789 ENST00000361789
Ensembl protein id ENSP00000354554 ENSP00000354554 ENSP00000354554
Uniprot id P00156 P00156 P00156
Uniprot name CYB_HUMAN CYB_HUMAN CYB_HUMAN
Ncbi gene id 4519 4519 4519
Ncbi protein id YP_003024038.1 YP_003024038.1 YP_003024038.1
PhyloP 100V -0.327 -0.327 -0.327
PhyloP 470Way -0.139 -0.139 -0.139
PhastCons 100V 0 0 0
PhastCons 470Way 0.498 0.498 0.498
PolyPhen2 benign benign benign
PolyPhen2 score 0.03 0 0
SIFT neutral neutral neutral
SIFT score 0.24 1.0 1.0
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 0.078 0.123 0.123
VEST Neutral Neutral Neutral
VEST pvalue 0.21 0.19 0.19
VEST FDR 0.45 0.45 0.45
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.04 0.36 0.36
MutationTaster . . .
MutationTaster score . . .
MutationTaster converted rankscore . . .
MutationTaster model . . .
MutationTaster AAE . . .
fathmm . . .
fathmm score . . .
fathmm converted rankscore . . .
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.0949 0.1009 0.1009
CADD Neutral Neutral Neutral
CADD score 1.070891 0.880654 0.989883
CADD phred 11.06 9.952 10.6
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score -0.73 -0.52 -0.52
MutationAssessor . neutral neutral
MutationAssessor score . 0.16 0.16
EFIN SP Damaging Neutral Neutral
EFIN SP score 0.506 0.856 0.856
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.862 0.708 0.708
MLC Neutral Neutral Neutral
MLC score 0.19811093 0.19811093 0.19811093
PANTHER score . . .
PhD-SNP score 0.305 . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.55 0.22 0.23
APOGEE2 Likely-benign Benign Benign
APOGEE2 score 0.0980768556384623 0.0254184496059961 0.0254177174965784
CAROL neutral neutral neutral
CAROL score 0.75 0.0 0.0
Condel deleterious deleterious deleterious
Condel score 0.61 1.0 1.0
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -6
MtoolBox neutral neutral neutral
MtoolBox DS 0.14 0.14 0.14
DEOGEN2 . . .
DEOGEN2 score . . .
DEOGEN2 converted rankscore . . .
Meta-SNP Neutral . .
Meta-SNP score 0.318 . .
PolyPhen2 transf medium impact high impact high impact
PolyPhen2 transf score 0.68 2.07 2.07
SIFT_transf medium impact high impact high impact
SIFT transf score -0.05 1.85 1.85
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 0.23 -0.9 -0.9
CHASM Neutral Neutral Neutral
CHASM pvalue 0.7 0.67 0.67
CHASM FDR 0.85 0.85 0.85
ClinVar id 9675.0 . .
ClinVar Allele id 24714.0 . .
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 . .
MITOMAP Disease Status Reported / Secondary . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.8391% 0.0016% .
MITOMAP General GenBank Seqs 513 1 .
MITOMAP General Curated refs 19370763;18668590;1634041;16532388;32887465;11349229;1463007;22561905;32094358;23304069;7977345;7901141;8899049;11938495;8600429;9561330;10377009;17406640;21067478;11571560;16901986;19527690;7635294;18931934;32943110;10894993;7770132;19427920;7599218;8680405;16050984;21041797;15060117;27217714;9150158;21457906;1764087;30369864 . .
MITOMAP Variant Class polymorphism;disease polymorphism .
gnomAD 3.1 AN 56424.0 . .
gnomAD 3.1 AC Homo 656.0 . .
gnomAD 3.1 AF Hom 0.0116263 . .
gnomAD 3.1 AC Het 4.0 . .
gnomAD 3.1 AF Het 7.08918e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 1389.0 2.0 .
HelixMTdb AF Hom 0.0070873494 1.0204967e-05 .
HelixMTdb AC Het 24.0 2.0 .
HelixMTdb AF Het 0.0001224596 1.0204967e-05 .
HelixMTdb mean ARF 0.47929 0.16468 .
HelixMTdb max ARF 0.95858 0.21978 .
ToMMo 54KJPN AC 4 . .
ToMMo 54KJPN AF 7.4e-05 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id . . .
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