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15497 (G > A)

General info

Mitimpact ID
MI.9927
Chr
chrM
Start
15497
Ref
G
Alt
A
Gene symbol
MT-CYB Extended gene annotation
Gene position
751
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GGC/AGC
AA pos
251
AA ref
G
AA alt
S
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15497G>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
5.323 Conservation Score
PhyloP 470way
0.641 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.83 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
Deleterious Score and details of the predictor
PROVEAN
Damaging 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
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
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
9687
Clinvar ALLELEID
24726
Clinvar CLNDISDB
Medgen:cn517202;

human phenotype ontology:hp:0001513, mondo:mondo:0011122, mesh:d009765, medgen:c0028754, orphanet:71529;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Not provided;

obesity;

leigh syndrome
Clinvar CLNSIG
Benign/likely benign
MITOMAP Allele
15497G>A
MITOMAP Disease Clinical info
Exit / obesity
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.5529%
MITOMAP General GenBank Seqs
338
MITOMAP General GenBank Curated refs
11406419 19091329 18477584 17015183 15382008 17033820 11349229 18545700 15126279 11811990 15052619 21099167 15466285 11938495 19026397 15638829 12949126 16714301 16895436 24667788 12905068 12870132 12509511 17259400 24002810 11404057 14760490 21457906 17257906 20067846
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56417
Gnomad AC hom
218
Gnomad AF hom
0.003864
Gnomad AC het
5
Gnomad AF het
8.86e-05
Gnomad filter
Pass
HelixMTdb AC hom
687
HelixMTdb AF hom
0.0035054
HelixMTdb AC het
27
HelixMTdb AF het
0.0001377
HelixMTdb mean ARF
0.32919
HelixMTdb max ARF
0.80745
ToMMo JPN54K AC
2505
ToMMo JPN54K AF
0.046131
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
4.75 CPD variant frequency
AA ref
G
CPD AA alt
S
Aln pos
251
RefSeq protein ID
YP_637022 , NP_008237 , NP_007847 , YP_214965 , YP_659498 , YP_007625626 , YP_659472 , YP_009025008 , YP_007024903 , YP_009024995 , YP_007024929 , YP_009047767 , YP_214952 , YP_007024916 , YP_659446 , YP_004425136 , YP_006460490 , YP_006460503 , YP_006460516 , YP_659485 , YP_004425123 , YP_006460477 , YP_009024904 , YP_009024891 , YP_007183100 , YP_008379072 , YP_008378929 , YP_008379098 , YP_009024917 , NP_114346 , NP_149943
Species name
Phascolarctos cinereus, Pongo pygmaeus, Pongo abelii, Colobus guereza, Piliocolobus badius, Procolobus verus, Presbytis melalophos, Trachypithecus cristatus, Trachypithecus hatinhensis, Trachypithecus francoisi, Trachypithecus shortridgei, Trachypithecus pileatus, Trachypithecus obscurus, Trachypithecus germaini, Semnopithecus entellus, Rhinopithecus bieti, Rhinopithecus bieti 1 rl-2012, Rhinopithecus strykeri, Rhinopithecus bieti 2 rl-2012, Rhinopithecus roxellana, Rhinopithecus avunculus, Rhinopithecus brelichi, Cercopithecus diana, Allochrocebus lhoesti, Theropithecus gelada, Lophocebus aterrimus, Cercocebus chrysogaster, Mandrillus sphinx, Cercocebus torquatus, Macaca sylvanus, Trichosurus vulpecula
Ncbi taxon ID
38626, 9600, 9601, 33548, 164648, 373033, 78451, 122765, 867383, 54180, 1042121, 164651, 54181, 271260, 88029, 61621, 1194334, 1194336, 1194335, 61622, 66062, 224329, 36224, 100224, 9565, 75566, 75569, 9561, 9530, 9546, 9337

15497 (G > C)

General info

Mitimpact ID
MI.9926
Chr
chrM
Start
15497
Ref
G
Alt
C
Gene symbol
MT-CYB Extended gene annotation
Gene position
751
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GGC/CGC
AA pos
251
AA ref
G
AA alt
R
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15497G>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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Conservation

PhyloP 100v
5.323 Conservation Score
PhyloP 470way
0.641 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.83 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
.
fathmm
.
AlphaMissense
Ambiguous 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
Neutral Score and details of the predictor
EFIN HD
Damaging 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
Deleterious Score and details of the meta-predictor
MtoolBox
Deleterious Score and details of the meta-predictor
DEOGEN2
.
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
15497G>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
.

15497 (G > T)

General info

Mitimpact ID
MI.9928
Chr
chrM
Start
15497
Ref
G
Alt
T
Gene symbol
MT-CYB Extended gene annotation
Gene position
751
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GGC/TGC
AA pos
251
AA ref
G
AA alt
C
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.15497G>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
5.323 Conservation Score
PhyloP 470way
0.641 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.83 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
.
fathmm
.
AlphaMissense
Likely benign Score and details of the predictor
CADD
Deleterious 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
Damaging 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
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
.
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
15497G>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
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
1
HelixMTdb AF hom
5.1e-06
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
.

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
.
~ 15497 (G/A) 15497 (G/C) 15497 (G/T)
~ 15497 (GGC/AGC) 15497 (GGC/CGC) 15497 (GGC/TGC)
MitImpact id MI.9927 MI.9926 MI.9928
Chr chrM chrM chrM
Start 15497 15497 15497
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 751 751 751
Gene start 14747 14747 14747
Gene end 15887 15887 15887
Gene strand + + +
Codon substitution GGC/AGC GGC/CGC GGC/TGC
AA position 251 251 251
AA ref G G G
AA alt S R C
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516020 516020 516020
HGVS NC_012920.1:g.15497G>A NC_012920.1:g.15497G>C NC_012920.1:g.15497G>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 5.323 5.323 5.323
PhyloP 470Way 0.641 0.641 0.641
PhastCons 100V 1 1 1
PhastCons 470Way 0.83 0.83 0.83
PolyPhen2 benign probably_damaging probably_damaging
PolyPhen2 score 0.13 0.94 0.96
SIFT neutral neutral neutral
SIFT score 0.51 0.42 0.18
SIFT4G Tolerated Damaging Damaging
SIFT4G score 0.056 0.0 0.0
VEST Neutral Neutral Neutral
VEST pvalue 0.18 0.07 0.06
VEST FDR 0.45 0.35 0.35
Mitoclass.1 neutral damaging damaging
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.09 0.84 0.72
MutationTaster . . .
MutationTaster score . . .
MutationTaster converted rankscore . . .
MutationTaster model . . .
MutationTaster AAE . . .
fathmm . . .
fathmm score . . .
fathmm converted rankscore . . .
AlphaMissense likely_benign ambiguous likely_benign
AlphaMissense score 0.1039 0.5139 0.2552
CADD Deleterious Deleterious Deleterious
CADD score 4.073119 3.902953 4.152156
CADD phred 23.7 23.5 23.8
PROVEAN Damaging Damaging Damaging
PROVEAN score -3.62 -5.28 -6.01
MutationAssessor low high medium
MutationAssessor score 1.685 3.875 3.385
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.892 0.79 0.792
EFIN HD Neutral Damaging Damaging
EFIN HD score 0.564 0.216 0.206
MLC Neutral Neutral Neutral
MLC score 0.10459291 0.10459291 0.10459291
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Pathogenic Neutral
APOGEE1 score 0.47 0.53 0.38
APOGEE2 Benign VUS VUS+
APOGEE2 score 0.0528521838042733 0.532850201760996 0.59829479879663
CAROL neutral neutral neutral
CAROL score 0.4 0.94 0.98
Condel deleterious neutral neutral
Condel score 0.69 0.24 0.11
COVEC WMV neutral deleterious deleterious
COVEC WMV score -6 2 2
MtoolBox neutral deleterious deleterious
MtoolBox DS 0.22 0.77 0.81
DEOGEN2 . . .
DEOGEN2 score . . .
DEOGEN2 converted rankscore . . .
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact low impact low impact
PolyPhen2 transf score 0.04 -1.85 -2.02
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.23 0.15 -0.14
MutationAssessor transf medium impact high impact high impact
MutationAssessor transf score 0.3 2.93 2.44
CHASM Neutral Neutral Neutral
CHASM pvalue 0.65 0.65 0.12
CHASM FDR 0.8 0.8 0.8
ClinVar id 9687.0 . .
ClinVar Allele id 24726.0 . .
ClinVar CLNDISDB MedGen:CN517202|Human_Phenotype_Ontology:HP:0001513,MONDO:MONDO:0011122,MeSH:D009765,MedGen:C0028754,Orphanet:71529|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN not_provided|Obesity|Leigh_syndrome . .
ClinVar CLNSIG Benign/Likely_benign . .
MITOMAP Disease Clinical info EXIT / Obesity . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.5529% . 0.0%
MITOMAP General GenBank Seqs 338 . 0
MITOMAP General Curated refs 11406419;19091329;18477584;17015183;15382008;17033820;11349229;18545700;15126279;11811990;15052619;21099167;15466285;11938495;19026397;15638829;12949126;16714301;16895436;24667788;12905068;12870132;12509511;17259400;24002810;11404057;14760490;21457906;17257906;20067846 . .
MITOMAP Variant Class polymorphism;disease . polymorphism
gnomAD 3.1 AN 56417.0 . .
gnomAD 3.1 AC Homo 218.0 . .
gnomAD 3.1 AF Hom 0.00386408 . .
gnomAD 3.1 AC Het 5.0 . .
gnomAD 3.1 AF Het 8.86258e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 687.0 . 1.0
HelixMTdb AF Hom 0.003505406 . 5.1024836e-06
HelixMTdb AC Het 27.0 . 0.0
HelixMTdb AF Het 0.00013776706 . 0.0
HelixMTdb mean ARF 0.32919 . .
HelixMTdb max ARF 0.80745 . .
ToMMo 54KJPN AC 2505 . .
ToMMo 54KJPN AF 0.046131 . .
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