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9185 (T > C)

General info

Mitimpact ID
MI.1401
Chr
chrM
Start
9185
Ref
T
Alt
C
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
659
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CTC/CCC
AA pos
220
AA ref
L
AA alt
P
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.9185T>C
HGNC ID
7414
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot ID
P00846
Uniprot name
ATP6_HUMAN
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
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Conservation

PhyloP 100v
7.687 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.986 Conservation Score
PhastCons 470way
0.701 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
Pathogenic Score and details of the predictor
MutationTaster
Disease automatic 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
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-pathogenic Score and details of the meta-predictor
CAROL
Deleterious 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
Low 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
9647
Clinvar ALLELEID
24686
Clinvar CLNDISDB
Mondo:mondo:0027069, medgen:c3275684, omim:500015;

mondo:mondo:0015626, medgen:c0007959, omim:ps118220, orphanet:166;

medgen:cn517202;

medgen:cn043634;

mondo:mondo:0044970, medgen:c0751651, orphanet:68380;

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:0007309, medgen:c0270911, omim:118220, orphanet:101081
Clinvar CLNDN
Mitochondrial complex 5 (atp synthase) deficiency, mitochondrial type 1;

charcot-marie-tooth disease;

not provided;

mitochondrial dna-associated leigh syndrome and narp;

mitochondrial disease;

leigh syndrome;

leber optic atrophy;

charcot-marie-tooth disease, type ia
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
9185T>C
MITOMAP Disease Clinical info
Leigh disease / ataxia syndromes / narp-like disease / episodic weakness and charcot-marie-tooth
MITOMAP Disease Status
Cfrm [p]
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
0.0049%
MITOMAP General GenBank Seqs
3
MITOMAP General GenBank Curated refs
25548692 22933740 19747204 28429146 29467576 30461153 37737178 30128709 27290639 29116603 22577227 17352390 24316278 24153443 32042921 23847141 30763462 31187502 32858252 33717984 29253894 29228836 28132834 34329598 36137325 21473984 31996241 28754700 16217706 18620007 27783406 20546952 18461509 29756269 21457906 31500933
MITOMAP Variant Class
disease
Gnomad AN
56421
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
2
Gnomad AF het
3.54e-05
Gnomad filter
Pass
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
2
HelixMTdb AF het
1.02e-05
HelixMTdb mean ARF
0.43429
HelixMTdb max ARF
0.45192
ToMMo JPN54K AC
1
ToMMo JPN54K AF
1.8e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs199476138

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
.

9185 (T > A)

General info

Mitimpact ID
MI.1403
Chr
chrM
Start
9185
Ref
T
Alt
A
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
659
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CTC/CAC
AA pos
220
AA ref
L
AA alt
H
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.9185T>A
HGNC ID
7414
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot ID
P00846
Uniprot name
ATP6_HUMAN
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
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Conservation

PhyloP 100v
7.687 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.986 Conservation Score
PhastCons 470way
0.701 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
Pathogenic Score and details of the predictor
MutationTaster
Disease 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
Neutral Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-pathogenic Score and details of the meta-predictor
CAROL
Deleterious 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
Low 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
9185T>A
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
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
.

9185 (T > G)

General info

Mitimpact ID
MI.1402
Chr
chrM
Start
9185
Ref
T
Alt
G
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
659
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CTC/CGC
AA pos
220
AA ref
L
AA alt
R
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.9185T>G
HGNC ID
7414
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot ID
P00846
Uniprot name
ATP6_HUMAN
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
7.687 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.986 Conservation Score
PhastCons 470way
0.701 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
Pathogenic Score and details of the predictor
MutationTaster
Disease 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
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
Deleterious 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
Low 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
9185T>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0098%
MITOMAP General GenBank Seqs
6
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56431
Gnomad AC hom
2
Gnomad AF hom
3.54e-05
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
15
HelixMTdb AF hom
7.65e-05
HelixMTdb AC het
3
HelixMTdb AF het
1.53e-05
HelixMTdb mean ARF
0.36981
HelixMTdb max ARF
0.85025
ToMMo JPN54K AC
14
ToMMo JPN54K AF
0.000258
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs199476138

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
.
~ 9185 (T/C) 9185 (T/A) 9185 (T/G)
~ 9185 (CTC/CCC) 9185 (CTC/CAC) 9185 (CTC/CGC)
MitImpact id MI.1401 MI.1403 MI.1402
Chr chrM chrM chrM
Start 9185 9185 9185
Ref T T T
Alt C A G
Gene symbol MT-ATP6 MT-ATP6 MT-ATP6
Extended annotation mitochondrially encoded ATP synthase membrane subunit 6 mitochondrially encoded ATP synthase membrane subunit 6 mitochondrially encoded ATP synthase membrane subunit 6
Gene position 659 659 659
Gene start 8527 8527 8527
Gene end 9207 9207 9207
Gene strand + + +
Codon substitution CTC/CCC CTC/CAC CTC/CGC
AA position 220 220 220
AA ref L L L
AA alt P H R
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516060 516060 516060
HGVS NC_012920.1:g.9185T>C NC_012920.1:g.9185T>A NC_012920.1:g.9185T>G
HGNC id 7414 7414 7414
Respiratory Chain complex V V V
Ensembl gene id ENSG00000198899 ENSG00000198899 ENSG00000198899
Ensembl transcript id ENST00000361899 ENST00000361899 ENST00000361899
Ensembl protein id ENSP00000354632 ENSP00000354632 ENSP00000354632
Uniprot id P00846 P00846 P00846
Uniprot name ATP6_HUMAN ATP6_HUMAN ATP6_HUMAN
Ncbi gene id 4508 4508 4508
Ncbi protein id YP_003024031.1 YP_003024031.1 YP_003024031.1
PhyloP 100V 7.687 7.687 7.687
PhyloP 470Way 0.742 0.742 0.742
PhastCons 100V 0.986 0.986 0.986
PhastCons 470Way 0.701 0.701 0.701
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0 1.0
SIFT deleterious deleterious deleterious
SIFT score 0 0 0
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.0 0.0 0.0
VEST Neutral Neutral Neutral
VEST pvalue 0.2 0.22 0.19
VEST FDR 0.65 0.65 0.65
Mitoclass.1 damaging damaging damaging
SNPDryad Pathogenic Pathogenic Pathogenic
SNPDryad score 1 0.97 0.99
MutationTaster Disease automatic Disease Disease
MutationTaster score 1.0 0.999996 0.999998
MutationTaster converted rankscore 0.81001 0.58761 0.58761
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE L220P L220H L220R
fathmm Tolerated Tolerated Tolerated
fathmm score 4.14 4.14 4.15
fathmm converted rankscore 0.02839 0.02839 0.02815
AlphaMissense likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.9687 0.8652 0.7344
CADD Deleterious Deleterious Deleterious
CADD score 3.986474 4.222825 4.316557
CADD phred 23.6 23.9 24.0
PROVEAN Damaging Damaging Damaging
PROVEAN score -6.22 -6.2 -5.32
MutationAssessor high high high
MutationAssessor score 5.285 5.285 5.285
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.202 0.378 0.152
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.422 0.384 0.344
MLC Neutral Neutral Neutral
MLC score 0.08002897 0.08002897 0.08002897
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.94 0.66 0.95
APOGEE2 Likely-pathogenic Likely-pathogenic VUS+
APOGEE2 score 0.904565643418929 0.810281980867029 0.569699360876384
CAROL deleterious deleterious deleterious
CAROL score 1 1 1
Condel neutral neutral neutral
Condel score 0 0 0
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 6 6 6
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.89 0.87 0.9
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.321284 0.321284 0.313807
DEOGEN2 converted rankscore 0.69240 0.69240 0.68553
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.6 -3.6 -3.6
SIFT_transf low impact low impact low impact
SIFT transf score -1.4 -1.4 -1.4
MutationAssessor transf high impact high impact high impact
MutationAssessor transf score 2.59 2.59 2.59
CHASM Neutral Neutral Neutral
CHASM pvalue 0.48 0.58 0.54
CHASM FDR 0.9 0.9 0.9
ClinVar id 9647.0 . .
ClinVar Allele id 24686.0 . .
ClinVar CLNDISDB MONDO:MONDO:0027069,MedGen:C3275684,OMIM:500015|MONDO:MONDO:0015626,MedGen:C0007959,OMIM:PS118220,Orphanet:166|MedGen:CN517202|MedGen:CN043634|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|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:0007309,MedGen:C0270911,OMIM:118220,Orphanet:101081 . .
ClinVar CLNDN Mitochondrial_complex_5_(ATP_synthase)_deficiency,_mitochondrial_type_1|Charcot-Marie-Tooth_disease|not_provided|Mitochondrial_DNA-Associated_Leigh_Syndrome_and_NARP|Mitochondrial_disease|Leigh_syndrome|Leber_optic_atrophy|Charcot-Marie-Tooth_disease,_type_IA . .
ClinVar CLNSIG Pathogenic . .
MITOMAP Disease Clinical info Leigh Disease / Ataxia syndromes / NARP-like disease / Episodic weakness and Charcot-Marie-Tooth . .
MITOMAP Disease Status Cfrm [P] . .
MITOMAP Disease Hom/Het +/+ ./. ./.
MITOMAP General GenBank Freq 0.0049% 0.0016% 0.0098%
MITOMAP General GenBank Seqs 3 1 6
MITOMAP General Curated refs 25548692;22933740;19747204;28429146;29467576;30461153;37737178;30128709;27290639;29116603;22577227;17352390;24316278;24153443;32042921;23847141;30763462;31187502;32858252;33717984;29253894;29228836;28132834;34329598;36137325;21473984;31996241;28754700;16217706;18620007;27783406;20546952;18461509;29756269;21457906;31500933 . .
MITOMAP Variant Class disease polymorphism polymorphism
gnomAD 3.1 AN 56421.0 . 56431.0
gnomAD 3.1 AC Homo 0.0 . 2.0
gnomAD 3.1 AF Hom 0.0 . 3.54415e-05
gnomAD 3.1 AC Het 2.0 . 1.0
gnomAD 3.1 AF Het 3.54478e-05 . 1.77208e-05
gnomAD 3.1 filter PASS . PASS
HelixMTdb AC Hom 0.0 . 15.0
HelixMTdb AF Hom 0.0 . 7.653725e-05
HelixMTdb AC Het 2.0 . 3.0
HelixMTdb AF Het 1.0204967e-05 . 1.530745e-05
HelixMTdb mean ARF 0.43429 . 0.36981
HelixMTdb max ARF 0.45192 . 0.85025
ToMMo 54KJPN AC 1 . 14
ToMMo 54KJPN AF 1.8e-05 . 0.000258
ToMMo 54KJPN AN 54302 . 54302
COSMIC 90 . . .
dbSNP 156 id rs199476138 . rs199476138
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