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3796 (A > G)

General info

Mitimpact ID
MI.11768
Chr
chrM
Start
3796
Ref
A
Alt
G
Gene symbol
MT-ND1 Extended gene annotation
Gene position
490
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
ACC/GCC
AA pos
164
AA ref
T
AA alt
A
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3796A>G
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
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Conservation

PhyloP 100v
0.32 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.011 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
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
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
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
.

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
9730
Clinvar ALLELEID
24769
Clinvar CLNDISDB
Medgen:cn517202;

medgen:c0752197;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Not provided;

dystonia, adult-onset;

leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
3796A>G
MITOMAP Disease Clinical info
Adult-onset dystonia
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
-/+
MITOMAP General GenBank Freq
0.4727%
MITOMAP General GenBank Seqs
289
MITOMAP General GenBank Curated refs
12756609 19370763 21978175 17637808 18306232 19340307 31152278 15382008 11938495 15972314 18427623 29987491 24667788 16721903 32887465 21457906 14581685 15286228
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56424
Gnomad AC hom
466
Gnomad AF hom
0.0082589
Gnomad AC het
7
Gnomad AF het
0.000124
Gnomad filter
Pass
HelixMTdb AC hom
1980
HelixMTdb AF hom
0.0101029
HelixMTdb AC het
17
HelixMTdb AF het
8.67e-05
HelixMTdb mean ARF
0.62056
HelixMTdb max ARF
0.91489
ToMMo JPN54K AC
58
ToMMo JPN54K AF
0.001068
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs28357970

Residue interaction

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

Compensated Pathogenic Deviations

Frequency
2.67 CPD variant frequency
AA ref
T
CPD AA alt
A
Aln pos
165
RefSeq protein ID
NP_062467 , YP_778682 , YP_007625653 , YP_001874853 , YP_004062153 , YP_220667 , YP_659460 , YP_006460491 , YP_006460504 , YP_006460465 , YP_004425124 , YP_006460478 , YP_659473 , YP_004425111 , YP_659499 , YP_006460530 , YP_006460543 , NP_007835
Species name
Physeter catodon, Callorhinus ursinus, Hyaena hyaena, Panthera tigris, Panthera tigris amoyensis, Bradypus variegatus, Presbytis melalophos, Rhinopithecus strykeri, Rhinopithecus bieti 2 rl-2012, Rhinopithecus brelichi, Rhinopithecus bieti, Rhinopithecus bieti 1 rl-2012, Rhinopithecus roxellana, Rhinopithecus avunculus, Pygathrix nemaeus, Pygathrix cinerea 1 rl-2012, Pygathrix cinerea 2 rl-2012, Pongo abelii
Ncbi taxon ID
9755, 34884, 95912, 9694, 253258, 9355, 78451, 1194336, 1194335, 224329, 61621, 1194334, 61622, 66062, 54133, 1194332, 1194333, 9601

3796 (A > C)

General info

Mitimpact ID
MI.11767
Chr
chrM
Start
3796
Ref
A
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
490
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
ACC/CCC
AA pos
164
AA ref
T
AA alt
P
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3796A>C
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
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Conservation

PhyloP 100v
0.32 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.011 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly 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
Neutral 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
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
.
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
3796A>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
.

3796 (A > T)

General info

Mitimpact ID
MI.11769
Chr
chrM
Start
3796
Ref
A
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
490
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
ACC/TCC
AA pos
164
AA ref
T
AA alt
S
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3796A>T
HGNC ID
7455
RC complex
I
Ensembl gene ID
ENSG00000198888
Ensembl protein ID
ENSP00000354687
Ensembl transcript ID
ENST00000361390
Uniprot ID
P03886
Uniprot name
NU1M_HUMAN
Ncbi gene ID
4535
Ncbi protein ID
YP_003024026.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.32 Conservation Score
PhyloP 470way
0.58 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.011 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
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
Neutral Score and details of the predictor
PROVEAN
Tolerated 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
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
.

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
235654
Clinvar ALLELEID
237334
Clinvar CLNDISDB
Medgen:cn517202;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Not provided;

leigh syndrome
Clinvar CLNSIG
Benign/likely benign
MITOMAP Allele
3796A>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.3386%
MITOMAP General GenBank Seqs
207
MITOMAP General GenBank Curated refs
21041797 11938495
MITOMAP Variant Class
polymorphism
Gnomad AN
56433
Gnomad AC hom
495
Gnomad AF hom
0.0087714
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
267
HelixMTdb AF hom
0.0013623
HelixMTdb AC het
0
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
rs28357970

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
.
~ 3796 (A/G) 3796 (A/C) 3796 (A/T)
~ 3796 (ACC/GCC) 3796 (ACC/CCC) 3796 (ACC/TCC)
MitImpact id MI.11768 MI.11767 MI.11769
Chr chrM chrM chrM
Start 3796 3796 3796
Ref A A A
Alt G C T
Gene symbol MT-ND1 MT-ND1 MT-ND1
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1
Gene position 490 490 490
Gene start 3307 3307 3307
Gene end 4262 4262 4262
Gene strand + + +
Codon substitution ACC/GCC ACC/CCC ACC/TCC
AA position 164 164 164
AA ref T T T
AA alt A P S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516000 516000 516000
HGVS NC_012920.1:g.3796A>G NC_012920.1:g.3796A>C NC_012920.1:g.3796A>T
HGNC id 7455 7455 7455
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198888 ENSG00000198888 ENSG00000198888
Ensembl transcript id ENST00000361390 ENST00000361390 ENST00000361390
Ensembl protein id ENSP00000354687 ENSP00000354687 ENSP00000354687
Uniprot id P03886 P03886 P03886
Uniprot name NU1M_HUMAN NU1M_HUMAN NU1M_HUMAN
Ncbi gene id 4535 4535 4535
Ncbi protein id YP_003024026.1 YP_003024026.1 YP_003024026.1
PhyloP 100V 0.32 0.32 0.32
PhyloP 470Way 0.58 0.58 0.58
PhastCons 100V 0 0 0
PhastCons 470Way 0.011 0.011 0.011
PolyPhen2 benign possibly_damaging benign
PolyPhen2 score 0.02 0.65 0.03
SIFT neutral neutral neutral
SIFT score 0.51 0.2 0.41
SIFT4G Tolerated Damaging Tolerated
SIFT4G score 0.066 0.001 0.172
VEST Neutral Pathogenic Neutral
VEST pvalue 0.29 0.05 0.3
VEST FDR 0.45 0.35 0.45
Mitoclass.1 neutral damaging neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.01 0.79 0.21
MutationTaster Disease automatic Polymorphism Disease automatic
MutationTaster score 2.23873e-10 1.0 3.1068e-09
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE T164A T164P T164S
fathmm Tolerated Tolerated Tolerated
fathmm score 2.82 2.72 2.83
fathmm converted rankscore 0.10871 0.11947 0.10771
AlphaMissense likely_benign ambiguous likely_benign
AlphaMissense score 0.112 0.3913 0.1402
CADD Neutral Deleterious Neutral
CADD score 0.918142 3.576323 0.669441
CADD phred 10.18 23.2 8.626
PROVEAN Damaging Damaging Tolerated
PROVEAN score -3.3 -4.32 -2.25
MutationAssessor low medium low
MutationAssessor score 1.47 3.465 1.245
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.906 0.604 0.856
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.898 0.334 0.918
MLC Neutral Neutral Neutral
MLC score 0.29724184 0.29724184 0.29724184
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.38 0.37 0.3
APOGEE2 Likely-benign VUS+ Benign
APOGEE2 score 0.0687214979878696 0.651496288507949 0.0372362855038056
CAROL neutral neutral neutral
CAROL score 0.47 0.82 0.57
Condel deleterious neutral deleterious
Condel score 0.75 0.28 0.69
COVEC WMV neutral . neutral
COVEC WMV score -6 0 -6
MtoolBox neutral deleterious neutral
MtoolBox DS 0.13 0.52 0.13
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.096009 0.111428 0.043845
DEOGEN2 converted rankscore 0.39736 0.42692 0.26629
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact low impact medium impact
PolyPhen2 transf score 0.84 -1 0.67
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.29 -0.06 0.19
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score -0.18 1.52 -0.59
CHASM Neutral Neutral Neutral
CHASM pvalue 0.46 0.42 0.55
CHASM FDR 0.8 0.8 0.8
ClinVar id 9730.0 . 235654.0
ClinVar Allele id 24769.0 . 237334.0
ClinVar CLNDISDB MedGen:CN517202|MedGen:C0752197|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506
ClinVar CLNDN not_provided|Dystonia,_adult-onset|Leigh_syndrome . not_provided|Leigh_syndrome
ClinVar CLNSIG Benign . Benign/Likely_benign
MITOMAP Disease Clinical info Adult-Onset Dystonia . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het -/+ ./. ./.
MITOMAP General GenBank Freq 0.4727% . 0.3386%
MITOMAP General GenBank Seqs 289 . 207
MITOMAP General Curated refs 12756609;19370763;21978175;17637808;18306232;19340307;31152278;15382008;11938495;15972314;18427623;29987491;24667788;16721903;32887465;21457906;14581685;15286228 . 21041797;11938495
MITOMAP Variant Class polymorphism;disease . polymorphism
gnomAD 3.1 AN 56424.0 . 56433.0
gnomAD 3.1 AC Homo 466.0 . 495.0
gnomAD 3.1 AF Hom 0.0082589 . 0.00877146
gnomAD 3.1 AC Het 7.0 . 0.0
gnomAD 3.1 AF Het 0.000124061 . 0.0
gnomAD 3.1 filter PASS . PASS
HelixMTdb AC Hom 1980.0 . 267.0
HelixMTdb AF Hom 0.010102917 . 0.0013623631
HelixMTdb AC Het 17.0 . 0.0
HelixMTdb AF Het 8.674222e-05 . 0.0
HelixMTdb mean ARF 0.62056 . .
HelixMTdb max ARF 0.91489 . .
ToMMo 54KJPN AC 58 . .
ToMMo 54KJPN AF 0.001068 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs28357970 . rs28357970
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