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8932 (C > T)

General info

Mitimpact ID
MI.863
Chr
chrM
Start
8932
Ref
C
Alt
T
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
406
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CCC/TCC
AA pos
136
AA ref
P
AA alt
S
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8932C>T
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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Powered by MitoWheel

Conservation

PhyloP 100v
-0.087 Conservation Score
PhyloP 470way
0.724 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.026 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
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
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
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
Likely-benign 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
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
235343
Clinvar ALLELEID
237030
Clinvar CLNDISDB
Mondo:mondo:0044970, medgen:c0751651, orphanet:68380;

medgen:cn517202;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Mitochondrial disease;

not provided;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
8932C>T
MITOMAP Disease Clinical info
Prostate tumor / neuromuscular disorder
MITOMAP Disease Status
Reported [b]
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.4008%
MITOMAP General GenBank Seqs
245
MITOMAP General GenBank Curated refs
11406419 26993169 18850577 15647368
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56428
Gnomad AC hom
749
Gnomad AF hom
0.0132736
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
383
HelixMTdb AF hom
0.0019542
HelixMTdb AC het
2
HelixMTdb AF het
1.02e-05
HelixMTdb mean ARF
0.92632
HelixMTdb max ARF
0.92647
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs878853013

Residue interaction

EVmutation
Site A-B InterP
Site A-B IntraP
ΔΔG intra
ΔΔG intra interface
ΔΔG inter

Compensated Pathogenic Deviations

Frequency
5.48 CPD variant frequency
AA ref
P
CPD AA alt
S
Aln pos
137
RefSeq protein ID
YP_008379208 , YP_006073049 , YP_005087600 , YP_004891280 , YP_007024974 , YP_004935510 , YP_007024961 , YP_004021636 , YP_002381175 , YP_002791021 , YP_004123235 , YP_008999715 , YP_004123355 , YP_002791216 , YP_004123193 , YP_004123275 , YP_004123316 , YP_004123407 , YP_007025973 , YP_002791060 , YP_665634 , YP_009024858 , YP_004300438 , YP_004300464 , YP_004935497 , NP_149962 , YP_003331228 , YP_003331125 , YP_626399 , YP_004891157 , YP_001876474 , YP_220568 , NP_904333 , YP_220555 , YP_001686703 , YP_002791047 , NP_659381
Species name
Plecturocebus cupreus, Apodemus chevrieri, Apodemus chejuensis, Apodemus peninsulae, Apodemus latronum, Apodemus agrarius, Apodemus draco, Leggadina lakedownensis, Rattus tanezumi, Rattus rattus, Rattus lutreolus, Rattus niobe, Rattus fuscipes, Rattus praetor, Rattus leucopus, Rattus tunneyi, Rattus villosissimus, Rattus sordidus, Niviventer excelsior, Rattus exulans, Rattus norvegicus, Niviventer confucianus, Microtus fortis fortis, Microtus fortis calamorum, Myodes regulus, Microtus kikuchii, Eothenomys chinensis, Proedromys liangshanensis, Microtus levis, Neodon irene, Mus terricolor, Mus musculus molossinus, Mus musculus, Mus musculus domesticus, Mus musculus musculus, Mus musculus castaneus, Tamandua tetradactyla
Ncbi taxon ID
202457, 129246, 754351, 105297, 214933, 39030, 129247, 81936, 35732, 10117, 472760, 472762, 10119, 349711, 10115, 10121, 10122, 10120, 349709, 34854, 10116, 248811, 311338, 311220, 82464, 100899, 577681, 575527, 537919, 798166, 254704, 57486, 10090, 10092, 39442, 10091, 48850

8932 (C > A)

General info

Mitimpact ID
MI.862
Chr
chrM
Start
8932
Ref
C
Alt
A
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
406
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CCC/ACC
AA pos
136
AA ref
P
AA alt
T
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8932C>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
-0.087 Conservation Score
PhyloP 470way
0.724 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.026 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
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
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
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
Likely-benign 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
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
8932C>A
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
.

8932 (C > G)

General info

Mitimpact ID
MI.861
Chr
chrM
Start
8932
Ref
C
Alt
G
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
406
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CCC/GCC
AA pos
136
AA ref
P
AA alt
A
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8932C>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
-0.087 Conservation Score
PhyloP 470way
0.724 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.026 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging 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
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
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Neutral 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
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
8932C>G
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
.
~ 8932 (C/T) 8932 (C/A) 8932 (C/G)
~ 8932 (CCC/TCC) 8932 (CCC/ACC) 8932 (CCC/GCC)
MitImpact id MI.863 MI.862 MI.861
Chr chrM chrM chrM
Start 8932 8932 8932
Ref C C C
Alt T 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 406 406 406
Gene start 8527 8527 8527
Gene end 9207 9207 9207
Gene strand + + +
Codon substitution CCC/TCC CCC/ACC CCC/GCC
AA position 136 136 136
AA ref P P P
AA alt S T A
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516060 516060 516060
HGVS NC_012920.1:g.8932C>T NC_012920.1:g.8932C>A NC_012920.1:g.8932C>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 -0.087 -0.087 -0.087
PhyloP 470Way 0.724 0.724 0.724
PhastCons 100V 0 0 0
PhastCons 470Way 0.026 0.026 0.026
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0 1.0
SIFT neutral neutral neutral
SIFT score 0.41 0.4 0.53
SIFT4G Damaging Damaging Tolerated
SIFT4G score 0.033 0.038 0.067
VEST Neutral Neutral Neutral
VEST pvalue 0.38 0.29 0.34
VEST FDR 0.65 0.65 0.65
Mitoclass.1 damaging damaging neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.13 0.68 0.56
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1.0 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE P136S P136T P136A
fathmm Tolerated Tolerated Tolerated
fathmm score 4.42 4.42 4.55
fathmm converted rankscore 0.02177 0.02177 0.01948
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.2137 0.1615 0.0897
CADD Deleterious Deleterious Neutral
CADD score 2.861114 2.62171 1.900435
CADD phred 21.7 20.3 15.59
PROVEAN Damaging Damaging Damaging
PROVEAN score -5.13 -5.02 -4.96
MutationAssessor high high low
MutationAssessor score 3.815 3.72 1.58
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.89 0.884 0.888
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.732 0.644 0.776
MLC Neutral Neutral Neutral
MLC score 0.08033074 0.08033074 0.08033074
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.46 0.41 0.38
APOGEE2 Likely-benign Likely-benign Benign
APOGEE2 score 0.14301930695681 0.1282773336742 0.0581943669842741
CAROL deleterious deleterious deleterious
CAROL score 1 1 1
Condel neutral neutral neutral
Condel score 0.21 0.2 0.27
COVEC WMV deleterious deleterious neutral
COVEC WMV score 1 1 -2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.74 0.75 0.71
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.078674 0.107552 0.068591
DEOGEN2 converted rankscore 0.35949 0.41986 0.33496
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.6 -3.6 -3.6
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.2 0.19 0.32
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 1.08 1.37 -0.46
CHASM Neutral Neutral Neutral
CHASM pvalue 0.5 0.8 0.77
CHASM FDR 0.9 0.9 0.9
ClinVar id 235343.0 . .
ClinVar Allele id 237030.0 . .
ClinVar CLNDISDB MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN Mitochondrial_disease|not_provided|Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info Prostate tumor / Neuromuscular disorder . .
MITOMAP Disease Status Reported [B] . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.4008% . .
MITOMAP General GenBank Seqs 245 . .
MITOMAP General Curated refs 11406419;26993169;18850577;15647368 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56428.0 . .
gnomAD 3.1 AC Homo 749.0 . .
gnomAD 3.1 AF Hom 0.0132736 . .
gnomAD 3.1 AC Het 1.0 . .
gnomAD 3.1 AF Het 1.77217e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 383.0 . .
HelixMTdb AF Hom 0.0019542512 . .
HelixMTdb AC Het 2.0 . .
HelixMTdb AF Het 1.0204967e-05 . .
HelixMTdb mean ARF 0.92632 . .
HelixMTdb max ARF 0.92647 . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs878853013 . .
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