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9176 (T > G)

General info

Mitimpact ID
MI.1385
Chr
chrM
Start
9176
Ref
T
Alt
G
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
650
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CTA/CGA
AA pos
217
AA ref
L
AA alt
R
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.9176T>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
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Powered by MitoWheel

Conservation

PhyloP 100v
5.978 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.911 Conservation Score
PhastCons 470way
0.825 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
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
9650
Clinvar ALLELEID
24689
Clinvar CLNDISDB
Mondo:mondo:0027069, medgen:c3275684, omim:500015;

medgen:cn517202;

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

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
Mitochondrial complex 5 (atp synthase) deficiency, mitochondrial type 1;

not provided;

mitochondrial disease;

leber optic atrophy;

leigh syndrome
Clinvar CLNSIG
Likely pathogenic
MITOMAP Allele
9176T>G
MITOMAP Disease Clinical info
Leigh disease / spastic paraplegia / spinocerebellar ataxia
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
19160410 11119722 15176724 19875463 38465286 18402672 29307858 11382202 30763462 11245730 29253894 11731285
MITOMAP Variant Class
disease
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
rs199476135

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
.

9176 (T > A)

General info

Mitimpact ID
MI.1383
Chr
chrM
Start
9176
Ref
T
Alt
A
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
650
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CTA/CAA
AA pos
217
AA ref
L
AA alt
Q
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.9176T>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
5.978 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.911 Conservation Score
PhastCons 470way
0.825 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
9176T>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
.

9176 (T > C)

General info

Mitimpact ID
MI.1384
Chr
chrM
Start
9176
Ref
T
Alt
C
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
650
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
CTA/CCA
AA pos
217
AA ref
L
AA alt
P
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.9176T>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
5.978 Conservation Score
PhyloP 470way
0.742 Conservation Score
PhastCons 100v
0.911 Conservation Score
PhastCons 470way
0.825 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
Disease Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
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
Disease Score and details of the meta-predictor

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
9644
Clinvar ALLELEID
24683
Clinvar CLNDISDB
Mondo:mondo:0017917, medgen:c4755299, orphanet:320360;

mondo:mondo:0027069, medgen:c3275684, omim:500015;

medgen:cn517202;

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

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

mondo:mondo:0010774, medgen:c1839022, omim:500003;

human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104
Clinvar CLNDN
Maternally-inherited spastic paraplegia;

mitochondrial complex 5 (atp synthase) deficiency, mitochondrial type 1;

not provided;

mitochondrial disease;

leigh syndrome;

striatonigral degeneration, infantile, mitochondrial;

leber optic atrophy
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
9176T>C
MITOMAP Disease Clinical info
Fbsn / leigh disease / spinocerebellar ataxia
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
19370763 20656066 19747204 21819970 28429146 30128709 31625254 9631394 20074547 18402672 24153443 30136164 32042921 9270604 30763462 31187502 32858252 29253894 29038134 24642831 15753359 31424416 9501263 32686207 31996241 19160410 20056103 20064630 10862082 18620007 7668837 29756269 21457906 34037856 16120341
MITOMAP Variant Class
disease
Gnomad AN
56433
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
3
Gnomad AF het
5.31e-05
Gnomad filter
Pass
HelixMTdb AC hom
1
HelixMTdb AF hom
5.1e-06
HelixMTdb AC het
0
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
1
ToMMo JPN54K AF
1.8e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs199476135

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
.
~ 9176 (T/G) 9176 (T/A) 9176 (T/C)
~ 9176 (CTA/CGA) 9176 (CTA/CAA) 9176 (CTA/CCA)
MitImpact id MI.1385 MI.1383 MI.1384
Chr chrM chrM chrM
Start 9176 9176 9176
Ref T T T
Alt G A C
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 650 650 650
Gene start 8527 8527 8527
Gene end 9207 9207 9207
Gene strand + + +
Codon substitution CTA/CGA CTA/CAA CTA/CCA
AA position 217 217 217
AA ref L L L
AA alt R Q P
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516060 516060 516060
HGVS NC_012920.1:g.9176T>G NC_012920.1:g.9176T>A NC_012920.1:g.9176T>C
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 5.978 5.978 5.978
PhyloP 470Way 0.742 0.742 0.742
PhastCons 100V 0.911 0.911 0.911
PhastCons 470Way 0.825 0.825 0.825
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 0.11 0.11 0.12
VEST FDR 0.65 0.65 0.65
Mitoclass.1 damaging damaging damaging
SNPDryad Pathogenic Pathogenic Pathogenic
SNPDryad score 0.99 0.98 1
MutationTaster Disease automatic Disease Disease automatic
MutationTaster score 0.901141 0.879972 0.999997
MutationTaster converted rankscore 0.36175 0.35731 0.58761
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE L217R L217Q L217P
fathmm Tolerated Tolerated Tolerated
fathmm score 2.25 2.25 2.25
fathmm converted rankscore 0.17761 0.17761 0.17761
AlphaMissense likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.929 0.957 0.9528
CADD Deleterious Deleterious Deleterious
CADD score 4.286375 4.125377 3.995894
CADD phred 24.0 23.8 23.6
PROVEAN Damaging Damaging Damaging
PROVEAN score -5.36 -5.35 -6.26
MutationAssessor high high high
MutationAssessor score 5.33 5.33 4.985
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.178 0.408 0.058
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.364 0.448 0.436
MLC Neutral Neutral Neutral
MLC score 0.0871507 0.0871507 0.0871507
PANTHER score . . .
PhD-SNP score . . 0.873
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.9 0.66 0.92
APOGEE2 Pathogenic Likely-pathogenic Pathogenic
APOGEE2 score 0.957153322162873 0.901111889759993 0.969106537719339
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 0.92 0.87 0.92
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.410791 0.410791 0.418285
DEOGEN2 converted rankscore 0.76543 0.76543 0.77068
Meta-SNP . . Disease
Meta-SNP score . . 0.906
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 2.82 2.82 2.52
CHASM Neutral Neutral Neutral
CHASM pvalue 0.37 0.61 0.54
CHASM FDR 0.9 0.9 0.9
ClinVar id 9650.0 . 9644.0
ClinVar Allele id 24689.0 . 24683.0
ClinVar CLNDISDB MONDO:MONDO:0027069,MedGen:C3275684,OMIM:500015|MedGen:CN517202|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|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 . MONDO:MONDO:0017917,MedGen:C4755299,Orphanet:320360|MONDO:MONDO:0027069,MedGen:C3275684,OMIM:500015|MedGen:CN517202|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0010774,MedGen:C1839022,OMIM:500003|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104
ClinVar CLNDN Mitochondrial_complex_5_(ATP_synthase)_deficiency,_mitochondrial_type_1|not_provided|Mitochondrial_disease|Leber_optic_atrophy|Leigh_syndrome . Maternally-inherited_spastic_paraplegia|Mitochondrial_complex_5_(ATP_synthase)_deficiency,_mitochondrial_type_1|not_provided|Mitochondrial_disease|Leigh_syndrome|Striatonigral_degeneration,_infantile,_mitochondrial|Leber_optic_atrophy
ClinVar CLNSIG Likely_pathogenic . Pathogenic
MITOMAP Disease Clinical info Leigh Disease / Spastic Paraplegia / Spinocerebellar Ataxia . FBSN / Leigh Disease / Spinocerebellar Ataxia
MITOMAP Disease Status Cfrm [LP] . Cfrm [P]
MITOMAP Disease Hom/Het +/+ ./. +/+
MITOMAP General GenBank Freq 0.0016% . 0.0049%
MITOMAP General GenBank Seqs 1 . 3
MITOMAP General Curated refs 19160410;11119722;15176724;19875463;38465286;18402672;29307858;11382202;30763462;11245730;29253894;11731285 . 19370763;20656066;19747204;21819970;28429146;30128709;31625254;9631394;20074547;18402672;24153443;30136164;32042921;9270604;30763462;31187502;32858252;29253894;29038134;24642831;15753359;31424416;9501263;32686207;31996241;19160410;20056103;20064630;10862082;18620007;7668837;29756269;21457906;34037856;16120341
MITOMAP Variant Class disease . disease
gnomAD 3.1 AN . . 56433.0
gnomAD 3.1 AC Homo . . 0.0
gnomAD 3.1 AF Hom . . 0.0
gnomAD 3.1 AC Het . . 3.0
gnomAD 3.1 AF Het . . 5.31604e-05
gnomAD 3.1 filter . . PASS
HelixMTdb AC Hom . . 1.0
HelixMTdb AF Hom . . 5.1024836e-06
HelixMTdb AC Het . . 0.0
HelixMTdb AF Het . . 0.0
HelixMTdb mean ARF . . .
HelixMTdb max ARF . . .
ToMMo 54KJPN AC . . 1
ToMMo 54KJPN AF . . 1.8e-05
ToMMo 54KJPN AN . . 54302
COSMIC 90 . . .
dbSNP 156 id rs199476135 . rs199476135
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