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4917 (A > G)

General info

Mitimpact ID
MI.13701
Chr
chrM
Start
4917
Ref
A
Alt
G
Gene symbol
MT-ND2 Extended gene annotation
Gene position
448
Gene start
4470
Gene end
5511
Gene strand
+
Codon substitution
AAC/GAC
AA pos
150
AA ref
N
AA alt
D
Functional effect
missense
OMIM ID
516001
HGVS
NC_012920.1:g.4917A>G
HGNC ID
7456
RC complex
I
Ensembl gene ID
ENSG00000198763
Ensembl protein ID
ENSP00000355046
Ensembl transcript ID
ENST00000361453
Uniprot ID
P03891
Uniprot name
NU2M_HUMAN
Ncbi gene ID
4536
Ncbi protein ID
YP_003024027.1
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Conservation

PhyloP 100v
2.233 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
0.499 Conservation Score
PhastCons 470way
0.002 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
Disease 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-benign Score and details of the meta-predictor
CAROL
Neutral 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
Neutral 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
Medium 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
9716
Clinvar ALLELEID
24755
Clinvar CLNDISDB
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
Leber optic atrophy;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
4917A>G
MITOMAP Disease Clinical info
Lhon / insulin resistance / amd / nrti-pn
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
5.0741%
MITOMAP General GenBank Seqs
3102
MITOMAP General GenBank Curated refs
10720328 19370763 19050702 9027481 11062027 18477584 16132471 11820805 8593537 19005266 17562939 11349229 1550131 10545708 15465027 18495510 32094358 24467713 7977345 8899049 18461138 11938495 17406640 15972314 7599217 19151382 16759180 31152278 16404693 16901986 17454741 18806273 7635294 8071952 16996290 10680807 9302261 12802679 16773565 18308428 18931934 20211276 10737123 24667788 19427920 7770132 7599218 1900003 16172508 17003408 8680405 18216301 10234520 16050984 28267784 29486301 23563965 10803467 9150158 17684475 19383124 29987491 10936107 11179019 21457906 18445251 11339587
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56429
Gnomad AC hom
3247
Gnomad AF hom
0.0575413
Gnomad AC het
4
Gnomad AF het
7.08e-05
Gnomad filter
Pass
HelixMTdb AC hom
17602
HelixMTdb AF hom
0.0898139
HelixMTdb AC het
42
HelixMTdb AF het
0.0002143
HelixMTdb mean ARF
0.80987
HelixMTdb max ARF
0.9619
ToMMo JPN54K AC
19
ToMMo JPN54K AF
0.00035
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs28357980

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
.

4917 (A > C)

General info

Mitimpact ID
MI.13702
Chr
chrM
Start
4917
Ref
A
Alt
C
Gene symbol
MT-ND2 Extended gene annotation
Gene position
448
Gene start
4470
Gene end
5511
Gene strand
+
Codon substitution
AAC/CAC
AA pos
150
AA ref
N
AA alt
H
Functional effect
missense
OMIM ID
516001
HGVS
NC_012920.1:g.4917A>C
HGNC ID
7456
RC complex
I
Ensembl gene ID
ENSG00000198763
Ensembl protein ID
ENSP00000355046
Ensembl transcript ID
ENST00000361453
Uniprot ID
P03891
Uniprot name
NU2M_HUMAN
Ncbi gene ID
4536
Ncbi protein ID
YP_003024027.1
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Conservation

PhyloP 100v
2.233 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
0.499 Conservation Score
PhastCons 470way
0.002 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
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
Medium 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
Vus- Score and details of the meta-predictor
CAROL
Neutral 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
4917A>C
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
.

4917 (A > T)

General info

Mitimpact ID
MI.13700
Chr
chrM
Start
4917
Ref
A
Alt
T
Gene symbol
MT-ND2 Extended gene annotation
Gene position
448
Gene start
4470
Gene end
5511
Gene strand
+
Codon substitution
AAC/TAC
AA pos
150
AA ref
N
AA alt
Y
Functional effect
missense
OMIM ID
516001
HGVS
NC_012920.1:g.4917A>T
HGNC ID
7456
RC complex
I
Ensembl gene ID
ENSG00000198763
Ensembl protein ID
ENSP00000355046
Ensembl transcript ID
ENST00000361453
Uniprot ID
P03891
Uniprot name
NU2M_HUMAN
Ncbi gene ID
4536
Ncbi protein ID
YP_003024027.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
2.233 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
0.499 Conservation Score
PhastCons 470way
0.002 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
Polymorphism 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
Medium 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
Vus Score and details of the meta-predictor
CAROL
Neutral Score and details of the meta-predictor
Condel
Deleterious 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
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
4917A>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
.
~ 4917 (A/G) 4917 (A/C) 4917 (A/T)
~ 4917 (AAC/GAC) 4917 (AAC/CAC) 4917 (AAC/TAC)
MitImpact id MI.13701 MI.13702 MI.13700
Chr chrM chrM chrM
Start 4917 4917 4917
Ref A A A
Alt G C T
Gene symbol MT-ND2 MT-ND2 MT-ND2
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 2
Gene position 448 448 448
Gene start 4470 4470 4470
Gene end 5511 5511 5511
Gene strand + + +
Codon substitution AAC/GAC AAC/CAC AAC/TAC
AA position 150 150 150
AA ref N N N
AA alt D H Y
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516001 516001 516001
HGVS NC_012920.1:g.4917A>G NC_012920.1:g.4917A>C NC_012920.1:g.4917A>T
HGNC id 7456 7456 7456
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198763 ENSG00000198763 ENSG00000198763
Ensembl transcript id ENST00000361453 ENST00000361453 ENST00000361453
Ensembl protein id ENSP00000355046 ENSP00000355046 ENSP00000355046
Uniprot id P03891 P03891 P03891
Uniprot name NU2M_HUMAN NU2M_HUMAN NU2M_HUMAN
Ncbi gene id 4536 4536 4536
Ncbi protein id YP_003024027.1 YP_003024027.1 YP_003024027.1
PhyloP 100V 2.233 2.233 2.233
PhyloP 470Way 0.58 0.58 0.58
PhastCons 100V 0.499 0.499 0.499
PhastCons 470Way 0.002 0.002 0.002
PolyPhen2 benign probably_damaging probably_damaging
PolyPhen2 score 0.06 0.97 0.97
SIFT neutral neutral neutral
SIFT score 0.22 0.54 1.0
SIFT4G Tolerated Damaging Damaging
SIFT4G score 0.077 0.01 0.006
VEST Neutral Neutral Neutral
VEST pvalue 0.4 0.32 0.15
VEST FDR 0.5 0.5 0.4
Mitoclass.1 neutral neutral damaging
SNPDryad Neutral Neutral Pathogenic
SNPDryad score 0.35 0.81 0.95
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1.0 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE N150D N150H N150Y
fathmm Tolerated Tolerated Tolerated
fathmm score 4.6 4.58 4.54
fathmm converted rankscore 0.01868 0.01901 0.01963
AlphaMissense likely_benign likely_benign likely_pathogenic
AlphaMissense score 0.0797 0.2081 0.5928
CADD Neutral Deleterious Deleterious
CADD score 0.696056 2.940145 3.588028
CADD phred 8.801 22.0 23.2
PROVEAN Damaging Damaging Damaging
PROVEAN score -3.86 -4.55 -7.36
MutationAssessor low medium medium
MutationAssessor score 1.695 2.85 3.31
EFIN SP Damaging Neutral Neutral
EFIN SP score 0.398 0.846 0.872
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.784 0.524 0.44
MLC Neutral Neutral Neutral
MLC score 0.20094755 0.20094755 0.20094755
PANTHER score 0.662 . .
PhD-SNP score 0.563 . .
APOGEE1 Pathogenic Neutral Neutral
APOGEE1 score 0.71 0.2 0.24
APOGEE2 Likely-benign VUS- VUS
APOGEE2 score 0.231533092953379 0.29852078152496 0.513065920419832
CAROL neutral neutral neutral
CAROL score 0.76 0.96 0.97
Condel deleterious neutral deleterious
Condel score 0.58 0.29 0.52
COVEC WMV neutral neutral deleterious
COVEC WMV score -6 -2 1
MtoolBox neutral deleterious deleterious
MtoolBox DS 0.27 0.78 0.82
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.058693 0.062855 0.072106
DEOGEN2 converted rankscore 0.30911 0.32026 0.34371
Meta-SNP Disease . .
Meta-SNP score 0.576 . .
PolyPhen2 transf medium impact low impact low impact
PolyPhen2 transf score 0.3 -2.18 -2.18
SIFT_transf medium impact medium impact high impact
SIFT transf score -0.1 0.25 1.87
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 0.03 0.28 0.86
CHASM Neutral Neutral Neutral
CHASM pvalue 0.32 0.13 0.17
CHASM FDR 0.8 0.8 0.8
ClinVar id 9716.0 . .
ClinVar Allele id 24755.0 . .
ClinVar CLNDISDB 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 Leber_optic_atrophy|Leigh_syndrome . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info LHON / Insulin Resistance / AMD / NRTI-PN . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 5.0741% . .
MITOMAP General GenBank Seqs 3102 . .
MITOMAP General Curated refs 10720328;19370763;19050702;9027481;11062027;18477584;16132471;11820805;8593537;19005266;17562939;11349229;1550131;10545708;15465027;18495510;32094358;24467713;7977345;8899049;18461138;11938495;17406640;15972314;7599217;19151382;16759180;31152278;16404693;16901986;17454741;18806273;7635294;8071952;16996290;10680807;9302261;12802679;16773565;18308428;18931934;20211276;10737123;24667788;19427920;7770132;7599218;1900003;16172508;17003408;8680405;18216301;10234520;16050984;28267784;29486301;23563965;10803467;9150158;17684475;19383124;29987491;10936107;11179019;21457906;18445251;11339587 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56429.0 . .
gnomAD 3.1 AC Homo 3247.0 . .
gnomAD 3.1 AF Hom 0.0575413 . .
gnomAD 3.1 AC Het 4.0 . .
gnomAD 3.1 AF Het 7.08855e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 17602.0 . .
HelixMTdb AF Hom 0.08981391 . .
HelixMTdb AC Het 42.0 . .
HelixMTdb AF Het 0.0002143043 . .
HelixMTdb mean ARF 0.80987 . .
HelixMTdb max ARF 0.9619 . .
ToMMo 54KJPN AC 19 . .
ToMMo 54KJPN AF 0.00035 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs28357980 . .
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