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9355 (A > T)

General info

Mitimpact ID
MI.6952
Chr
chrM
Start
9355
Ref
A
Alt
T
Gene symbol
MT-CO3 Extended gene annotation
Gene position
149
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
AAC/ATC
AA pos
50
AA ref
N
AA alt
I
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9355A>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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Conservation

PhyloP 100v
0.212 Conservation Score
PhyloP 470way
-0.43 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.026 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
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 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
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
High 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
523307
Clinvar ALLELEID
514152
Clinvar CLNDISDB
Human phenotype ontology:hp:0001251, human phenotype ontology:hp:0001253, human phenotype ontology:hp:0002513, human phenotype ontology:hp:0007050, human phenotype ontology:hp:0007157, mondo:mondo:0000437, medgen:c0007758, orphanet:102002;

human phenotype ontology:hp:0002355, human phenotype ontology:hp:0007101, human phenotype ontology:hp:0009030, medgen:c0311394;

human phenotype ontology:hp:0001509, human phenotype ontology:hp:0003501, human phenotype ontology:hp:0003507, human phenotype ontology:hp:0003512, human phenotype ontology:hp:0003518, human phenotype ontology:hp:0003519, human phenotype ontology:hp:0004322, human phenotype ontology:hp:0008871, human phenotype ontology:hp:0008882, human phenotype ontology:hp:0008888, human phenotype ontology:hp:0008913, medgen:c0349588;

human phenotype ontology:hp:0000365, human phenotype ontology:hp:0000404, human phenotype ontology:hp:0001728, human phenotype ontology:hp:0001729, human phenotype ontology:hp:0001754, human phenotype ontology:hp:0008560, human phenotype ontology:hp:0008563, mondo:mondo:0005365, medgen:c1384666;

human phenotype ontology:hp:0001494, human phenotype ontology:hp:0012048, mondo:mondo:0019771, medgen:c2242577, orphanet:93958;

human phenotype ontology:hp:0008316, medgen:c4021546;

human phenotype ontology:hp:0003546, medgen:c0424551;

human phenotype ontology:hp:0010535, mondo:mondo:0005296, medgen:c0037315;

human phenotype ontology:hp:0001031, medgen:c1403035;

human phenotype ontology:hp:0008504, medgen:c4024664;

human phenotype ontology:hp:0006554, human phenotype ontology:hp:0006556, mondo:mondo:0019542, mesh:d017114, medgen:c0162557, orphanet:90062;

human phenotype ontology:hp:0012432, medgen:c0518656;

human phenotype ontology:hp:0000102, human phenotype ontology:hp:0000787, mondo:mondo:0008171, medgen:c0392525
Clinvar CLNDN
Cerebellar ataxia;

difficulty walking;

short stature;

hearing impairment;

oromandibular dystonia;

abnormal mitochondria in muscle tissue;

exercise intolerance;

sleep apnea;

subcutaneous lipoma;

moderate sensorineural hearing impairment;

acute hepatic failure;

chronic fatigue;

nephrolithiasis
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
9355A>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
6
HelixMTdb AF hom
3.06e-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
rs1556423663

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
.

9355 (A > C)

General info

Mitimpact ID
MI.6953
Chr
chrM
Start
9355
Ref
A
Alt
C
Gene symbol
MT-CO3 Extended gene annotation
Gene position
149
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
AAC/ACC
AA pos
50
AA ref
N
AA alt
T
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9355A>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
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Powered by MitoWheel

Conservation

PhyloP 100v
0.212 Conservation Score
PhyloP 470way
-0.43 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.026 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
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
High 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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
9355A>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
.

9355 (A > G)

General info

Mitimpact ID
MI.6951
Chr
chrM
Start
9355
Ref
A
Alt
G
Gene symbol
MT-CO3 Extended gene annotation
Gene position
149
Gene start
9207
Gene end
9990
Gene strand
+
Codon substitution
AAC/AGC
AA pos
50
AA ref
N
AA alt
S
Functional effect
missense
OMIM ID
516050
HGVS
NC_012920.1:g.9355A>G
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
0.212 Conservation Score
PhyloP 470way
-0.43 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.026 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign Score and details of the predictor
SIFT
Deleterious Score and details of the predictor
SIFT4G
Tolerated 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
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
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
Tolerated Score and details of the meta-predictor
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
693155
Clinvar ALLELEID
681691
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
9355A>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0376%
MITOMAP General GenBank Seqs
23
MITOMAP General GenBank Curated refs
16895436 21041797
MITOMAP Variant Class
polymorphism
Gnomad AN
56429
Gnomad AC hom
13
Gnomad AF hom
0.0002303
Gnomad AC het
2
Gnomad AF het
3.54e-05
Gnomad filter
Pass
HelixMTdb AC hom
49
HelixMTdb AF hom
0.00025
HelixMTdb AC het
4
HelixMTdb AF het
2.04e-05
HelixMTdb mean ARF
0.22522
HelixMTdb max ARF
0.31818
ToMMo JPN54K AC
48
ToMMo JPN54K AF
0.000884
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs1556423663

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
.
~ 9355 (A/T) 9355 (A/C) 9355 (A/G)
~ 9355 (AAC/ATC) 9355 (AAC/ACC) 9355 (AAC/AGC)
MitImpact id MI.6952 MI.6953 MI.6951
Chr chrM chrM chrM
Start 9355 9355 9355
Ref A A A
Alt T C G
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 149 149 149
Gene start 9207 9207 9207
Gene end 9990 9990 9990
Gene strand + + +
Codon substitution AAC/ATC AAC/ACC AAC/AGC
AA position 50 50 50
AA ref N N N
AA alt I T S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516050 516050 516050
HGVS NC_012920.1:g.9355A>T NC_012920.1:g.9355A>C NC_012920.1:g.9355A>G
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 0.212 0.212 0.212
PhyloP 470Way -0.43 -0.43 -0.43
PhastCons 100V 0 0 0
PhastCons 470Way 0.026 0.026 0.026
PolyPhen2 benign benign benign
PolyPhen2 score 0.2 0.0 0.0
SIFT neutral neutral deleterious
SIFT score 1 0.4 0.04
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 0.585 0.939 0.073
VEST Neutral Neutral Neutral
VEST pvalue 0.13 0.21 0.37
VEST FDR 0.4 0.45 0.5
Mitoclass.1 neutral neutral damaging
SNPDryad Pathogenic Neutral Neutral
SNPDryad score 0.98 0.73 0.83
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1.0 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE N50I N50T N50S
fathmm Tolerated Tolerated Tolerated
fathmm score 2.73 2.67 2.61
fathmm converted rankscore 0.11839 0.12473 0.13095
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.2265 0.0926 0.0656
CADD Neutral Neutral Neutral
CADD score 1.797216 -0.969697 -0.022363
CADD phred 14.97 0.018 2.377
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score 2.07 1.97 0.49
MutationAssessor neutral neutral neutral
MutationAssessor score -1.215 -1.65 0.24
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.774 0.722 0.736
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.78 0.786 0.782
MLC Neutral Neutral Neutral
MLC score 0.25608063 0.25608063 0.25608063
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Pathogenic Pathogenic
APOGEE1 score 0.37 0.51 0.54
APOGEE2 Benign Likely-benign Benign
APOGEE2 score 0.0368570887703306 0.0625113181467775 0.0441178693244919
CAROL neutral neutral neutral
CAROL score 0.2 0.6 0.96
Condel deleterious deleterious deleterious
Condel score 0.9 0.7 0.52
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -2
MtoolBox neutral neutral neutral
MtoolBox DS 0.31 0.1 0.1
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.003627 0.003581 0.005531
DEOGEN2 converted rankscore 0.03030 0.02990 0.04982
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact high impact high impact
PolyPhen2 transf score -0.28 2.05 2.05
SIFT_transf high impact medium impact medium impact
SIFT transf score 1.9 0.09 -0.6
MutationAssessor transf low impact low impact medium impact
MutationAssessor transf score -2.85 -2.47 -0.88
CHASM Neutral Neutral Neutral
CHASM pvalue 0.27 0.41 0.35
CHASM FDR 0.8 0.8 0.8
ClinVar id 523307.0 . 693155.0
ClinVar Allele id 514152.0 . 681691.0
ClinVar CLNDISDB Human_Phenotype_Ontology:HP:0001251,Human_Phenotype_Ontology:HP:0001253,Human_Phenotype_Ontology:HP:0002513,Human_Phenotype_Ontology:HP:0007050,Human_Phenotype_Ontology:HP:0007157,MONDO:MONDO:0000437,MedGen:C0007758,Orphanet:102002|Human_Phenotype_Ontology:HP:0002355,Human_Phenotype_Ontology:HP:0007101,Human_Phenotype_Ontology:HP:0009030,MedGen:C0311394|Human_Phenotype_Ontology:HP:0001509,Human_Phenotype_Ontology:HP:0003501,Human_Phenotype_Ontology:HP:0003507,Human_Phenotype_Ontology:HP:0003512,Human_Phenotype_Ontology:HP:0003518,Human_Phenotype_Ontology:HP:0003519,Human_Phenotype_Ontology:HP:0004322,Human_Phenotype_Ontology:HP:0008871,Human_Phenotype_Ontology:HP:0008882,Human_Phenotype_Ontology:HP:0008888,Human_Phenotype_Ontology:HP:0008913,MedGen:C0349588|Human_Phenotype_Ontology:HP:0000365,Human_Phenotype_Ontology:HP:0000404,Human_Phenotype_Ontology:HP:0001728,Human_Phenotype_Ontology:HP:0001729,Human_Phenotype_Ontology:HP:0001754,Human_Phenotype_Ontology:HP:0008560,Human_Phenotype_Ontology:HP:0008563,MONDO:MONDO:0005365,MedGen:C1384666|Human_Phenotype_Ontology:HP:0001494,Human_Phenotype_Ontology:HP:0012048,MONDO:MONDO:0019771,MedGen:C2242577,Orphanet:93958|Human_Phenotype_Ontology:HP:0008316,MedGen:C4021546|Human_Phenotype_Ontology:HP:0003546,MedGen:C0424551|Human_Phenotype_Ontology:HP:0010535,MONDO:MONDO:0005296,MedGen:C0037315|Human_Phenotype_Ontology:HP:0001031,MedGen:C1403035|Human_Phenotype_Ontology:HP:0008504,MedGen:C4024664|Human_Phenotype_Ontology:HP:0006554,Human_Phenotype_Ontology:HP:0006556,MONDO:MONDO:0019542,MeSH:D017114,MedGen:C0162557,Orphanet:90062|Human_Phenotype_Ontology:HP:0012432,MedGen:C0518656|Human_Phenotype_Ontology:HP:0000102,Human_Phenotype_Ontology:HP:0000787,MONDO:MONDO:0008171,MedGen:C0392525 . MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506
ClinVar CLNDN Cerebellar_ataxia|Difficulty_walking|Short_stature|Hearing_impairment|Oromandibular_dystonia|Abnormal_mitochondria_in_muscle_tissue|Exercise_intolerance|Sleep_apnea|Subcutaneous_lipoma|Moderate_sensorineural_hearing_impairment|Acute_hepatic_failure|Chronic_fatigue|Nephrolithiasis . Leigh_syndrome
ClinVar CLNSIG Uncertain_significance . Benign
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 0.0% . 0.0376%
MITOMAP General GenBank Seqs 0 . 23
MITOMAP General Curated refs . . 16895436;21041797
MITOMAP Variant Class polymorphism . polymorphism
gnomAD 3.1 AN . . 56429.0
gnomAD 3.1 AC Homo . . 13.0
gnomAD 3.1 AF Hom . . 0.000230378
gnomAD 3.1 AC Het . . 2.0
gnomAD 3.1 AF Het . . 3.54428e-05
gnomAD 3.1 filter . . PASS
HelixMTdb AC Hom 6.0 . 49.0
HelixMTdb AF Hom 3.06149e-05 . 0.0002500217
HelixMTdb AC Het 0.0 . 4.0
HelixMTdb AF Het 0.0 . 2.0409934e-05
HelixMTdb mean ARF . . 0.22522
HelixMTdb max ARF . . 0.31818
ToMMo 54KJPN AC . . 48
ToMMo 54KJPN AF . . 0.000884
ToMMo 54KJPN AN . . 54302
COSMIC 90 . . .
dbSNP 156 id rs1556423663 . rs1556423663
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