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14831 (G > A)

General info

Mitimpact ID
MI.8503
Chr
chrM
Start
14831
Ref
G
Alt
A
Gene symbol
MT-CYB Extended gene annotation
Gene position
85
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GCA/ACA
AA pos
29
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.14831G>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
-1.78 Conservation Score
PhyloP 470way
-0.809 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.964 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
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
Deleterious 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
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
65517
Clinvar ALLELEID
76425
Clinvar CLNDISDB
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
Leigh syndrome;

leber optic atrophy
Clinvar CLNSIG
Benign
MITOMAP Allele
14831G>A
MITOMAP Disease Clinical info
Lhon
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.1881%
MITOMAP General GenBank Seqs
115
MITOMAP General GenBank Curated refs
19370763 19220304 12150954 17893651 20301353 11349229 16404693 20304802
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56375
Gnomad AC hom
162
Gnomad AF hom
0.0028736
Gnomad AC het
16
Gnomad AF het
0.0002838
Gnomad filter
Pass
HelixMTdb AC hom
571
HelixMTdb AF hom
0.0029135
HelixMTdb AC het
41
HelixMTdb AF het
0.0002092
HelixMTdb mean ARF
0.32594
HelixMTdb max ARF
0.7454499
ToMMo JPN54K AC
22
ToMMo JPN54K AF
0.000405
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
7.43 CPD variant frequency
AA ref
A
CPD AA alt
T
Aln pos
29
RefSeq protein ID
YP_637022 , YP_220679 , YP_003587317 , YP_003587291 , NP_008224 , YP_002120670 , NP_008211 , YP_659498 , YP_007625626 , YP_009025008 , YP_007024903 , YP_009024995 , YP_007024929 , YP_009047767 , YP_214952 , YP_007024916 , YP_007625639 , YP_009024878 , YP_626379 , NP_009291 , YP_398766 , YP_004464997 , NP_861488 , YP_001661380 , NP_659375 , YP_008080757 , YP_007625548 , YP_008578426 , YP_007626796 , YP_007626809 , YP_007626770 , YP_220692 , YP_424000 , YP_008578465 , YP_006576333 , NP_955691 , YP_007626783 , NP_008763 , YP_009034049 , YP_001382345 , YP_002120645 , YP_001742117 , YP_007625366 , YP_007625353 , NP_149460 , YP_007625392 , YP_001874852 , YP_778759 , NP_659362 , YP_001249296
Species name
Phascolarctos cinereus, Bradypus variegatus, Symphalangus syndactylus, Hylobates pileatus, Gorilla gorilla, Gorilla gorilla gorilla, Pan paniscus, Piliocolobus badius, Procolobus verus, Trachypithecus cristatus, Trachypithecus hatinhensis, Trachypithecus francoisi, Trachypithecus shortridgei, Trachypithecus pileatus, Trachypithecus obscurus, Trachypithecus germaini, Simias concolor, Cercopithecus mitis, Elephas maximus, Loxodonta africana, Mammuthus primigenius, Mammuthus columbi, Procavia capensis, Dendrohyrax dorsalis, Galeopterus variegatus, Chinchilla lanigera, Spalacopus cyanus, Desmodus rotundus, Spalax carmeli, Nannospalax golani, Nannospalax galili, Choloepus didactylus, Echymipera rufescens australis, Rhinophylla pumilio, Marmota himalayana, Nannospalax ehrenbergi, Nannospalax judaei, Cavia porcellus, Chrysocyon brachyurus, Ailurus fulgens styani, Ailurus fulgens, Spilogale putorius, Taxidea taxus, Arctonyx collaris, Ochotona collaris, Mephitis mephitis, Panthera pardus, Arctocephalus townsendi, Eumetopias jubatus, Ailuropoda melanoleuca
Ncbi taxon ID
38626, 9355, 9590, 9589, 9593, 9595, 9597, 164648, 373033, 122765, 867383, 54180, 1042121, 164651, 54181, 271260, 170207, 36225, 9783, 9785, 37349, 1027716, 9813, 42325, 482537, 34839, 61880, 9430, 164324, 191382, 1026970, 27675, 164528, 138707, 93163, 30637, 134510, 10141, 68728, 424585, 9649, 30552, 30554, 139309, 134600, 30548, 9691, 161921, 34886, 9646

14831 (G > C)

General info

Mitimpact ID
MI.8504
Chr
chrM
Start
14831
Ref
G
Alt
C
Gene symbol
MT-CYB Extended gene annotation
Gene position
85
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GCA/CCA
AA pos
29
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.14831G>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
-1.78 Conservation Score
PhyloP 470way
-0.809 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.964 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
Pathogenic 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
Tolerated 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
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Neutral 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
.

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
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
693773
Clinvar ALLELEID
680663
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
14831G>C
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
23463613
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
6
HelixMTdb AF hom
3.06e-05
HelixMTdb AC het
1
HelixMTdb AF het
5.1e-06
HelixMTdb mean ARF
0.11377
HelixMTdb max ARF
0.11377
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
.

14831 (G > T)

General info

Mitimpact ID
MI.8502
Chr
chrM
Start
14831
Ref
G
Alt
T
Gene symbol
MT-CYB Extended gene annotation
Gene position
85
Gene start
14747
Gene end
15887
Gene strand
+
Codon substitution
GCA/TCA
AA pos
29
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516020
HGVS
NC_012920.1:g.14831G>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
-1.78 Conservation Score
PhyloP 470way
-0.809 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.964 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
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic 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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
14831G>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
.
~ 14831 (G/A) 14831 (G/C) 14831 (G/T)
~ 14831 (GCA/ACA) 14831 (GCA/CCA) 14831 (GCA/TCA)
MitImpact id MI.8503 MI.8504 MI.8502
Chr chrM chrM chrM
Start 14831 14831 14831
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 85 85 85
Gene start 14747 14747 14747
Gene end 15887 15887 15887
Gene strand + + +
Codon substitution GCA/ACA GCA/CCA GCA/TCA
AA position 29 29 29
AA ref A A A
AA alt T P S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516020 516020 516020
HGVS NC_012920.1:g.14831G>A NC_012920.1:g.14831G>C NC_012920.1:g.14831G>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 -1.78 -1.78 -1.78
PhyloP 470Way -0.809 -0.809 -0.809
PhastCons 100V 0 0 0
PhastCons 470Way 0.964 0.964 0.964
PolyPhen2 benign benign benign
PolyPhen2 score 0 0.08 0.03
SIFT neutral neutral neutral
SIFT score 0.39 0.21 0.47
SIFT4G Tolerated Damaging Tolerated
SIFT4G score 0.143 0.003 0.913
VEST Neutral Pathogenic Neutral
VEST pvalue 0.12 0.04 0.15
VEST FDR 0.4 0.35 0.45
Mitoclass.1 neutral damaging neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.04 0.77 0.01
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 0.0823 0.266 0.0935
CADD Neutral Deleterious Neutral
CADD score 1.05195 3.393583 -0.794863
CADD phred 10.95 23.0 0.044
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score -0.89 -2.11 -0.77
MutationAssessor low medium neutral
MutationAssessor score 0.845 3.12 0.505
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.986 0.98 0.98
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.914 0.36 0.954
MLC Deleterious Deleterious Deleterious
MLC score 0.53669503 0.53669503 0.53669503
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Pathogenic
APOGEE1 score 0.46 0.39 0.51
APOGEE2 Benign Likely-benign Benign
APOGEE2 score 0.0132235428191455 0.221121093329446 0.0118493751797299
CAROL neutral neutral neutral
CAROL score 0.61 0.77 0.5
Condel deleterious deleterious deleterious
Condel score 0.7 0.57 0.72
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -2 -6
MtoolBox neutral neutral neutral
MtoolBox DS 0.12 0.29 0.11
DEOGEN2 . . .
DEOGEN2 score . . .
DEOGEN2 converted rankscore . . .
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf high impact medium impact medium impact
PolyPhen2 transf score 2.07 0.26 0.68
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.12 -0.09 0.19
MutationAssessor transf medium impact high impact medium impact
MutationAssessor transf score -0.04 2.12 -0.66
CHASM Neutral Neutral Neutral
CHASM pvalue 0.65 0.43 0.42
CHASM FDR 0.8 0.8 0.8
ClinVar id 65517.0 693773.0 .
ClinVar Allele id 76425.0 680663.0 .
ClinVar CLNDISDB 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|Leber_optic_atrophy Leigh_syndrome .
ClinVar CLNSIG Benign Uncertain_significance .
MITOMAP Disease Clinical info LHON . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.1881% 0.0% .
MITOMAP General GenBank Seqs 115 0 .
MITOMAP General Curated refs 19370763;19220304;12150954;17893651;20301353;11349229;16404693;20304802 23463613 .
MITOMAP Variant Class polymorphism;disease polymorphism .
gnomAD 3.1 AN 56375.0 . .
gnomAD 3.1 AC Homo 162.0 . .
gnomAD 3.1 AF Hom 0.00287361 . .
gnomAD 3.1 AC Het 16.0 . .
gnomAD 3.1 AF Het 0.000283814 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 571.0 6.0 .
HelixMTdb AF Hom 0.002913518 3.06149e-05 .
HelixMTdb AC Het 41.0 1.0 .
HelixMTdb AF Het 0.00020920183 5.1024836e-06 .
HelixMTdb mean ARF 0.32594 0.11377 .
HelixMTdb max ARF 0.74545 0.11377 .
ToMMo 54KJPN AC 22 . .
ToMMo 54KJPN AF 0.000405 . .
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