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10158 (T > G)

General info

Mitimpact ID
MI.15174
Chr
chrM
Start
10158
Ref
T
Alt
G
Gene symbol
MT-ND3 Extended gene annotation
Gene position
100
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/GCC
AA pos
34
AA ref
S
AA alt
A
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10158T>G
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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Conservation

PhyloP 100v
-2.594 Conservation Score
PhyloP 470way
-0.903 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.751 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
Tolerated Score and details of the predictor
Mutation Assessor
Neutral 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
Deleterious 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
Low 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
10158T>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
20304802
MITOMAP Variant Class
polymorphism
Gnomad AN
56433
Gnomad AC hom
1
Gnomad AF hom
1.77e-05
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
HelixMTdb AC hom
4
HelixMTdb AF hom
2.04e-05
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
.

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
.

10158 (T > A)

General info

Mitimpact ID
MI.15173
Chr
chrM
Start
10158
Ref
T
Alt
A
Gene symbol
MT-ND3 Extended gene annotation
Gene position
100
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/ACC
AA pos
34
AA ref
S
AA alt
T
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10158T>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-2.594 Conservation Score
PhyloP 470way
-0.903 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.751 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
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
Deleterious 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
693267
Clinvar ALLELEID
680157
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
10158T>A
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0016%
MITOMAP General GenBank Seqs
1
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
56434
Gnomad AC hom
3
Gnomad AF hom
5.31e-05
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
3
HelixMTdb AF hom
1.53e-05
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
rs199476117

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
.

10158 (T > C)

General info

Mitimpact ID
MI.15172
Chr
chrM
Start
10158
Ref
T
Alt
C
Gene symbol
MT-ND3 Extended gene annotation
Gene position
100
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
TCC/CCC
AA pos
34
AA ref
S
AA alt
P
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10158T>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-2.594 Conservation Score
PhyloP 470way
-0.903 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.751 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
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
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
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-pathogenic 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
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
9714
Clinvar ALLELEID
24753
Clinvar CLNDISDB
Mondo:mondo:0027068, medgen:c4746992, omim:500014;

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

medgen:cn517202;

mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Mitochondrial complex 1 deficiency, mitochondrial type 1;

mitochondrial disease;

not provided;

leigh syndrome
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
10158T>C
MITOMAP Disease Clinical info
Leigh disease / melas
MITOMAP Disease Status
Cfrm [p]
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
31996177 14684687 37038312 28429146 30128709 14764913 14705112 32371897 34732400 17152068 28050007 28522224 18402672 18977334 15972314 29054334 29237403 15372108 32504279 24642831 28916229 27914863 26741492 29500099 22115768 15576045 20064630 29987491 27742419 21364701 30095618 21457906 28883258 20972245
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
rs199476117

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
.
~ 10158 (T/G) 10158 (T/A) 10158 (T/C)
~ 10158 (TCC/GCC) 10158 (TCC/ACC) 10158 (TCC/CCC)
MitImpact id MI.15174 MI.15173 MI.15172
Chr chrM chrM chrM
Start 10158 10158 10158
Ref T T T
Alt G A C
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 100 100 100
Gene start 10059 10059 10059
Gene end 10404 10404 10404
Gene strand + + +
Codon substitution TCC/GCC TCC/ACC TCC/CCC
AA position 34 34 34
AA ref S S S
AA alt A T P
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516002 516002 516002
HGVS NC_012920.1:g.10158T>G NC_012920.1:g.10158T>A NC_012920.1:g.10158T>C
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 -2.594 -2.594 -2.594
PhyloP 470Way -0.903 -0.903 -0.903
PhastCons 100V 0 0 0
PhastCons 470Way 0.751 0.751 0.751
PolyPhen2 benign benign possibly_damaging
PolyPhen2 score 0.0 0.0 0.47
SIFT neutral neutral neutral
SIFT score 0.57 0.45 0.34
SIFT4G Tolerated Tolerated Damaging
SIFT4G score 0.395 0.179 0.015
VEST Neutral Neutral Neutral
VEST pvalue 0.31 0.3 0.1
VEST FDR 0.45 0.45 0.4
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.06 0.02 0.59
MutationTaster Polymorphism Polymorphism Disease automatic
MutationTaster score 1 1 6.31977e-12
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE S34A S34T S34P
fathmm Tolerated Tolerated Tolerated
fathmm score 0.95 0.92 0.88
fathmm converted rankscore 0.43279 0.44461 0.46028
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.0816 0.0985 0.2714
CADD Neutral Neutral Neutral
CADD score -0.198984 0.58993 2.250192
CADD phred 1.103 8.086 17.84
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score 0.51 0.1 -2.09
MutationAssessor neutral low low
MutationAssessor score 0.66 1.165 1.145
EFIN SP Neutral Neutral Damaging
EFIN SP score 0.864 0.852 0.196
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.976 0.988 0.416
MLC Deleterious Deleterious Deleterious
MLC score 0.52064096 0.52064096 0.52064096
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Pathogenic
APOGEE1 score 0.31 0.37 0.95
APOGEE2 Benign Benign Likely-pathogenic
APOGEE2 score 0.0470810836355675 0.0271625478344544 0.84413850510661
CAROL neutral neutral neutral
CAROL score 0.42 0.54 0.62
Condel deleterious deleterious neutral
Condel score 0.79 0.73 0.44
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -3
MtoolBox neutral neutral neutral
MtoolBox DS 0.1 0.1 0.4
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.167297 0.186349 0.436351
DEOGEN2 converted rankscore 0.51388 0.53961 0.78277
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score 1.99 1.99 -0.67
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.26 0.14 0.03
MutationAssessor transf low impact medium impact medium impact
MutationAssessor transf score -1.1 -0.46 0.52
CHASM Neutral Neutral Neutral
CHASM pvalue 0.28 0.34 0.13
CHASM FDR 0.8 0.8 0.8
ClinVar id . 693267.0 9714.0
ClinVar Allele id . 680157.0 24753.0
ClinVar CLNDISDB . MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 MONDO:MONDO:0027068,MedGen:C4746992,OMIM:500014|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506
ClinVar CLNDN . Leigh_syndrome Mitochondrial_complex_1_deficiency,_mitochondrial_type_1|Mitochondrial_disease|not_provided|Leigh_syndrome
ClinVar CLNSIG . Uncertain_significance Pathogenic
MITOMAP Disease Clinical info . . Leigh Disease / MELAS
MITOMAP Disease Status . . Cfrm [P]
MITOMAP Disease Hom/Het ./. ./. +/+
MITOMAP General GenBank Freq 0.0016% 0.0016% 0.0%
MITOMAP General GenBank Seqs 1 1 0
MITOMAP General Curated refs 20304802 . 31996177;14684687;37038312;28429146;30128709;14764913;14705112;32371897;34732400;17152068;28050007;28522224;18402672;18977334;15972314;29054334;29237403;15372108;32504279;24642831;28916229;27914863;26741492;29500099;22115768;15576045;20064630;29987491;27742419;21364701;30095618;21457906;28883258;20972245
MITOMAP Variant Class polymorphism polymorphism disease
gnomAD 3.1 AN 56433.0 56434.0 .
gnomAD 3.1 AC Homo 1.0 3.0 .
gnomAD 3.1 AF Hom 1.77201e-05 5.31594e-05 .
gnomAD 3.1 AC Het 1.0 0.0 .
gnomAD 3.1 AF Het 1.77201e-05 0.0 .
gnomAD 3.1 filter PASS PASS .
HelixMTdb AC Hom 4.0 3.0 .
HelixMTdb AF Hom 2.0409934e-05 1.530745e-05 .
HelixMTdb AC Het 0.0 0.0 .
HelixMTdb AF Het 0.0 0.0 .
HelixMTdb mean ARF . . .
HelixMTdb max ARF . . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id . rs199476117 rs199476117
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