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10197 (G > A)

General info

Mitimpact ID
MI.15259
Chr
chrM
Start
10197
Ref
G
Alt
A
Gene symbol
MT-ND3 Extended gene annotation
Gene position
139
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
GCC/ACC
AA pos
47
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10197G>A
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
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Powered by MitoWheel

Conservation

PhyloP 100v
4.687 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.007 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
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 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
Medium 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
Deleterious Score and details of the predictor
PANTHER
Neutral Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor

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
Damaging 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
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
9715
Clinvar ALLELEID
24754
Clinvar CLNDISDB
Mondo:mondo:0027068, medgen:c4746992, omim:500014;

medgen:cn169374;

medgen:cn517202;

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

medgen:cn043634;

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

mondo:mondo:0010772, medgen:c1839040, omim:500001, orphanet:99718
Clinvar CLNDN
Mitochondrial complex 1 deficiency, mitochondrial type 1;

not specified;

not provided;

mitochondrial disease;

mitochondrial dna-associated leigh syndrome and narp;

leigh syndrome;

leber optic atrophy and dystonia
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
10197G>A
MITOMAP Disease Clinical info
Leigh disease / dystonia / stroke / ldyt
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
21978175 37038312 30899856 28429146 30461153 30128709 17413873 18800376 17152068 18977334 35715829 30978515 15372108 19458970 29253894 11130070 30199507 32045392 38465286 20064630 12509511 21364701 30095618 30978516 20972245
MITOMAP Variant Class
disease
Gnomad AN
56422
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Npg
HelixMTdb AC hom
0
HelixMTdb AF hom
0.0
HelixMTdb AC het
7
HelixMTdb AF het
3.57e-05
HelixMTdb mean ARF
0.15194
HelixMTdb max ARF
0.25
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs267606891

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
.

10197 (G > C)

General info

Mitimpact ID
MI.15260
Chr
chrM
Start
10197
Ref
G
Alt
C
Gene symbol
MT-ND3 Extended gene annotation
Gene position
139
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
GCC/CCC
AA pos
47
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10197G>C
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
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Powered by MitoWheel

Conservation

PhyloP 100v
4.687 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.007 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
Pathogenic Score and details of the predictor
MitoClass 1
Damaging 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
Ambiguous Score and details of the predictor
CADD
Deleterious Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
Medium 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
Deleterious 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
Damaging 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
10197G>C
MITOMAP Disease Clinical info
Leigh disease
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
38437941
MITOMAP Variant Class
disease
Gnomad AN
56433
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Npg
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
.

10197 (G > T)

General info

Mitimpact ID
MI.15258
Chr
chrM
Start
10197
Ref
G
Alt
T
Gene symbol
MT-ND3 Extended gene annotation
Gene position
139
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
GCC/TCC
AA pos
47
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10197G>T
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
4.687 Conservation Score
PhyloP 470way
0.848 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.007 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
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
Deleterious 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
Damaging Score and details of the predictor
EFIN HD
Neutral Score and details of the predictor
MLC
Deleterious 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
Deleterious 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
High 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
10197G>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
.
~ 10197 (G/A) 10197 (G/C) 10197 (G/T)
~ 10197 (GCC/ACC) 10197 (GCC/CCC) 10197 (GCC/TCC)
MitImpact id MI.15259 MI.15260 MI.15258
Chr chrM chrM chrM
Start 10197 10197 10197
Ref G G G
Alt A C T
Gene symbol MT-ND3 MT-ND3 MT-ND3
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3
Gene position 139 139 139
Gene start 10059 10059 10059
Gene end 10404 10404 10404
Gene strand + + +
Codon substitution GCC/ACC GCC/CCC GCC/TCC
AA position 47 47 47
AA ref A A A
AA alt T P S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516002 516002 516002
HGVS NC_012920.1:g.10197G>A NC_012920.1:g.10197G>C NC_012920.1:g.10197G>T
HGNC id 7458 7458 7458
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198840 ENSG00000198840 ENSG00000198840
Ensembl transcript id ENST00000361227 ENST00000361227 ENST00000361227
Ensembl protein id ENSP00000355206 ENSP00000355206 ENSP00000355206
Uniprot id P03897 P03897 P03897
Uniprot name NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN
Ncbi gene id 4537 4537 4537
Ncbi protein id YP_003024033.1 YP_003024033.1 YP_003024033.1
PhyloP 100V 4.687 4.687 4.687
PhyloP 470Way 0.848 0.848 0.848
PhastCons 100V 1 1 1
PhastCons 470Way 0.007 0.007 0.007
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0 1.0
SIFT neutral neutral neutral
SIFT score 0.52 0.32 1.0
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.0 0.001 0.007
VEST Neutral Pathogenic Neutral
VEST pvalue 0.17 0.04 0.26
VEST FDR 0.45 0.35 0.45
Mitoclass.1 damaging damaging neutral
SNPDryad Pathogenic Pathogenic Pathogenic
SNPDryad score 0.93 0.96 0.98
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 3.23265e-07 1 0.999992
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE A47T A47P A47S
fathmm Tolerated Tolerated Tolerated
fathmm score 0.89 0.82 0.98
fathmm converted rankscore 0.45636 0.48142 0.42122
AlphaMissense likely_benign ambiguous likely_benign
AlphaMissense score 0.2513 0.4019 0.1583
CADD Deleterious Deleterious Deleterious
CADD score 4.196092 3.865291 3.717795
CADD phred 23.9 23.5 23.3
PROVEAN Damaging Damaging Damaging
PROVEAN score -3.52 -4.73 -2.76
MutationAssessor medium medium low
MutationAssessor score 2.045 2.03 1.14
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.094 0.39 0.456
EFIN HD Neutral Damaging Neutral
EFIN HD score 0.38 0.236 0.366
MLC Deleterious Deleterious Deleterious
MLC score 0.55232663 0.55232663 0.55232663
PANTHER score 0.309 . .
PhD-SNP score 0.797 . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.88 0.46 0.39
APOGEE2 Likely-pathogenic VUS+ VUS
APOGEE2 score 0.843686040876126 0.645176820055587 0.498126916021381
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 1.0
Condel neutral neutral deleterious
Condel score 0.26 0.16 0.5
COVEC WMV deleterious deleterious neutral
COVEC WMV score 1 1 -2
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.79 0.84 0.75
DEOGEN2 Damaging Damaging Tolerated
DEOGEN2 score 0.52544 0.539619 0.495506
DEOGEN2 converted rankscore 0.83481 0.84213 0.81820
Meta-SNP Disease . .
Meta-SNP score 0.623 . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.43 -3.43 -3.43
SIFT_transf medium impact medium impact high impact
SIFT transf score 0.21 0.01 1.85
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 1.22 1.39 0.51
CHASM Neutral Neutral Neutral
CHASM pvalue 0.76 0.31 0.21
CHASM FDR 0.85 0.8 0.8
ClinVar id 9715.0 . .
ClinVar Allele id 24754.0 . .
ClinVar CLNDISDB MONDO:MONDO:0027068,MedGen:C4746992,OMIM:500014|MedGen:CN169374|MedGen:CN517202|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MedGen:CN043634|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0010772,MedGen:C1839040,OMIM:500001,Orphanet:99718 . .
ClinVar CLNDN Mitochondrial_complex_1_deficiency,_mitochondrial_type_1|not_specified|not_provided|Mitochondrial_disease|Mitochondrial_DNA-Associated_Leigh_Syndrome_and_NARP|Leigh_syndrome|Leber_optic_atrophy_and_dystonia . .
ClinVar CLNSIG Pathogenic . .
MITOMAP Disease Clinical info Leigh Disease / Dystonia / Stroke / LDYT Leigh Disease .
MITOMAP Disease Status Cfrm [P] Reported .
MITOMAP Disease Hom/Het +/+ -/+ ./.
MITOMAP General GenBank Freq 0.0049% 0.0% .
MITOMAP General GenBank Seqs 3 0 .
MITOMAP General Curated refs 21978175;37038312;30899856;28429146;30461153;30128709;17413873;18800376;17152068;18977334;35715829;30978515;15372108;19458970;29253894;11130070;30199507;32045392;38465286;20064630;12509511;21364701;30095618;30978516;20972245 38437941 .
MITOMAP Variant Class disease disease .
gnomAD 3.1 AN 56422.0 56433.0 .
gnomAD 3.1 AC Homo 0.0 0.0 .
gnomAD 3.1 AF Hom 0.0 0.0 .
gnomAD 3.1 AC Het 0.0 0.0 .
gnomAD 3.1 AF Het 0.0 0.0 .
gnomAD 3.1 filter npg npg .
HelixMTdb AC Hom 0.0 . .
HelixMTdb AF Hom 0.0 . .
HelixMTdb AC Het 7.0 . .
HelixMTdb AF Het 3.5717385e-05 . .
HelixMTdb mean ARF 0.15194 . .
HelixMTdb max ARF 0.25 . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs267606891 . .
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