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8969 (G > A)

General info

Mitimpact ID
MI.946
Chr
chrM
Start
8969
Ref
G
Alt
A
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
443
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
AGC/AAC
AA pos
148
AA ref
S
AA alt
N
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8969G>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
9.61 Conservation Score
PhyloP 470way
0.965 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.247 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
Neutral 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
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
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
191364
Clinvar ALLELEID
189167
Clinvar CLNDISDB
Human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104;

mondo:mondo:0010789, medgen:c0162671, omim:540000, orphanet:550;

mondo:mondo:0010782, medgen:c4225415, omim:500011, orphanet:2598;

mondo:mondo:0044970, medgen:c0751651, orphanet:68380
Clinvar CLNDN
Leber optic atrophy;

juvenile myopathy, encephalopathy, lactic acidosis and stroke;

myopathy, lactic acidosis, and sideroblastic anemia 3;

mitochondrial disease
Clinvar CLNSIG
Likely pathogenic
MITOMAP Allele
8969G>A
MITOMAP Disease Clinical info
Mitochondrial myopathy, lactic acidosis and sideroblastic anemia (mlasa) / igg nephropathy
MITOMAP Disease Status
Cfrm [lp]
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
37988592 34732400 29350304 27450679 27812026 30763462 25037980
MITOMAP Variant Class
disease
Gnomad AN
56424
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
4
Gnomad AF het
7.08e-05
Gnomad filter
Pass
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
9
HelixMTdb AF het
4.59e-05
HelixMTdb mean ARF
0.13062
HelixMTdb max ARF
0.32634
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs794726857

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
.

8969 (G > C)

General info

Mitimpact ID
MI.945
Chr
chrM
Start
8969
Ref
G
Alt
C
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
443
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
AGC/ACC
AA pos
148
AA ref
S
AA alt
T
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8969G>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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Powered by MitoWheel

Conservation

PhyloP 100v
9.61 Conservation Score
PhyloP 470way
0.965 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.247 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
Neutral 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
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
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
8969G>C
MITOMAP Disease Clinical info
Suspected mito disease
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
Nr/nr
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
32858252
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56433
Gnomad AC hom
3
Gnomad AF hom
5.31e-05
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
8
HelixMTdb AF hom
4.08e-05
HelixMTdb AC het
2
HelixMTdb AF het
1.02e-05
HelixMTdb mean ARF
0.37364
HelixMTdb max ARF
0.52688
ToMMo JPN54K AC
1
ToMMo JPN54K AF
1.8e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs794726857

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
.

8969 (G > T)

General info

Mitimpact ID
MI.947
Chr
chrM
Start
8969
Ref
G
Alt
T
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
443
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
AGC/ATC
AA pos
148
AA ref
S
AA alt
I
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8969G>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
9.61 Conservation Score
PhyloP 470way
0.965 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.247 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
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
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
8969G>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
.
~ 8969 (G/A) 8969 (G/C) 8969 (G/T)
~ 8969 (AGC/AAC) 8969 (AGC/ACC) 8969 (AGC/ATC)
MitImpact id MI.946 MI.945 MI.947
Chr chrM chrM chrM
Start 8969 8969 8969
Ref G G G
Alt A C T
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 443 443 443
Gene start 8527 8527 8527
Gene end 9207 9207 9207
Gene strand + + +
Codon substitution AGC/AAC AGC/ACC AGC/ATC
AA position 148 148 148
AA ref S S S
AA alt N T I
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516060 516060 516060
HGVS NC_012920.1:g.8969G>A NC_012920.1:g.8969G>C NC_012920.1:g.8969G>T
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 9.61 9.61 9.61
PhyloP 470Way 0.965 0.965 0.965
PhastCons 100V 1 1 1
PhastCons 470Way 0.247 0.247 0.247
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 0.98 0.98 0.99
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 0.45 0.22 0.2
VEST FDR 0.65 0.65 0.65
Mitoclass.1 damaging damaging damaging
SNPDryad Neutral Neutral Pathogenic
SNPDryad score 0.88 0.67 1
MutationTaster Disease automatic Disease Disease
MutationTaster score 0.999997 0.999996 1.0
MutationTaster converted rankscore 0.58761 0.58761 0.81001
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE S148N S148T S148I
fathmm Tolerated Tolerated Tolerated
fathmm score 3.56 3.56 3.49
fathmm converted rankscore 0.04696 0.04696 0.05071
AlphaMissense likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.8997 0.7282 0.9357
CADD Deleterious Deleterious Deleterious
CADD score 3.628728 3.455574 4.157163
CADD phred 23.2 23.0 23.8
PROVEAN Damaging Damaging Damaging
PROVEAN score -2.76 -2.72 -5.48
MutationAssessor high high high
MutationAssessor score 5.335 5.335 5.335
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.47 0.514 0.492
EFIN HD Damaging Damaging Damaging
EFIN HD score 0.066 0.076 0.06
MLC Neutral Neutral Neutral
MLC score 0.01822681 0.01822681 0.01822681
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.57 0.5 0.48
APOGEE2 Likely-pathogenic VUS+ Likely-pathogenic
APOGEE2 score 0.837553028217724 0.67452196329104 0.781604418900294
CAROL deleterious deleterious deleterious
CAROL score 1 1 1
Condel neutral neutral neutral
Condel score 0.01 0.01 0.01
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 6 6 6
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.81 0.82 0.86
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.331145 0.218647 0.422588
DEOGEN2 converted rankscore 0.70125 0.58143 0.77361
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -2.36 -2.36 -2.65
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 2.84 2.36 2.84
CHASM Neutral Neutral Neutral
CHASM pvalue 0.44 0.71 0.68
CHASM FDR 0.9 0.9 0.9
ClinVar id 191364.0 . .
ClinVar Allele id 189167.0 . .
ClinVar CLNDISDB Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104|MONDO:MONDO:0010789,MedGen:C0162671,OMIM:540000,Orphanet:550|MONDO:MONDO:0010782,MedGen:C4225415,OMIM:500011,Orphanet:2598|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380 . .
ClinVar CLNDN Leber_optic_atrophy|Juvenile_myopathy,_encephalopathy,_lactic_acidosis_AND_stroke|Myopathy,_lactic_acidosis,_and_sideroblastic_anemia_3|Mitochondrial_disease . .
ClinVar CLNSIG Likely_pathogenic . .
MITOMAP Disease Clinical info Mitochondrial myopathy, lactic acidosis and sideroblastic anemia (MLASA) / IgG nephropathy Suspected mito disease .
MITOMAP Disease Status Cfrm [LP] Reported .
MITOMAP Disease Hom/Het -/+ nr/nr ./.
MITOMAP General GenBank Freq 0.0016% 0.0% .
MITOMAP General GenBank Seqs 1 0 .
MITOMAP General Curated refs 37988592;34732400;29350304;27450679;27812026;30763462;25037980 32858252 .
MITOMAP Variant Class disease polymorphism;disease .
gnomAD 3.1 AN 56424.0 56433.0 .
gnomAD 3.1 AC Homo 0.0 3.0 .
gnomAD 3.1 AF Hom 0.0 5.31604e-05 .
gnomAD 3.1 AC Het 4.0 1.0 .
gnomAD 3.1 AF Het 7.08918e-05 1.77201e-05 .
gnomAD 3.1 filter PASS PASS .
HelixMTdb AC Hom 0.0 8.0 .
HelixMTdb AF Hom 0.0 4.081987e-05 .
HelixMTdb AC Het 9.0 2.0 .
HelixMTdb AF Het 4.5922352e-05 1.0204967e-05 .
HelixMTdb mean ARF 0.13062 0.37364 .
HelixMTdb max ARF 0.32634 0.52688 .
ToMMo 54KJPN AC . 1 .
ToMMo 54KJPN AF . 1.8e-05 .
ToMMo 54KJPN AN . 54302 .
COSMIC 90 . . .
dbSNP 156 id rs794726857 rs794726857 .
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