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4132 (G > A)

General info

Mitimpact ID
MI.12476
Chr
chrM
Start
4132
Ref
G
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
826
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GCA/ACA
AA pos
276
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4132G>A
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
2.646 Conservation Score
PhyloP 470way
-0.677 Conservation Score
PhastCons 100v
0.996 Conservation Score
PhastCons 470way
0.017 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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
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
.

Cancer-specific predictors

PolyPhen2 transf
High 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
377340
Clinvar ALLELEID
364218
Clinvar CLNDISDB
Medgen:cn517202;

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

leigh syndrome
Clinvar CLNSIG
Conflicting interpretations of pathogenicity
MITOMAP Allele
4132G>A
MITOMAP Disease Clinical info
NAion-associated
MITOMAP Disease Status
Reported [vus]
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.0147%
MITOMAP General GenBank Seqs
9
MITOMAP General GenBank Curated refs
29987491 17454741
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56433
Gnomad AC hom
11
Gnomad AF hom
0.0001949
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
80
HelixMTdb AF hom
0.0004081
HelixMTdb AC het
2
HelixMTdb AF het
1.02e-05
HelixMTdb mean ARF
0.13364
HelixMTdb max ARF
0.15493
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs1057520201

Residue interaction

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

Compensated Pathogenic Deviations

Frequency
8.31 CPD variant frequency
AA ref
A
CPD AA alt
T
Aln pos
277
RefSeq protein ID
YP_007625536 , NP_008225 , YP_007024891 , YP_009024983 , YP_007024904 , YP_009024996 , YP_214940 , YP_007024917 , YP_009047755 , YP_659460 , YP_214953 , YP_659486 , YP_007625614 , YP_659434 , YP_007024930 , YP_007024943 , YP_006460491 , YP_006460504 , YP_006460465 , YP_004425124 , YP_006460478 , YP_659473 , YP_004425111 , YP_659499 , YP_006460530 , YP_006460543 , YP_006460517 , YP_659447 , YP_007625627 , YP_009072450 , YP_009072463 , YP_002884226 , YP_008378969 , YP_009024892 , YP_008379060 , YP_007316909 , YP_008378930 , YP_009024866 , YP_009024905 , YP_008378917 , YP_008379086 , YP_009024918 , YP_009024879 , YP_001427422 , YP_009059459 , YP_238242 , YP_001427409 , NP_007835 , YP_003587305 , YP_006883018 , YP_003587382 , YP_008379099 , NP_007822 , YP_003587214 , YP_003587279 , NP_008199
Species name
Spalacopus cyanus, Pongo pygmaeus, Trachypithecus hatinhensis, Trachypithecus francoisi, Trachypithecus germaini, Trachypithecus cristatus, Trachypithecus obscurus, Trachypithecus shortridgei, Trachypithecus pileatus, Presbytis melalophos, Colobus guereza, Piliocolobus badius, Procolobus verus, Semnopithecus entellus, Trachypithecus vetulus, Trachypithecus johnii, 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, Pygathrix nigripes, Nasalis larvatus, Simias concolor, Macaca silenus, Macaca tonkeana, Macaca fascicularis, Erythrocebus patas, Cercopithecus diana, Lophocebus aterrimus, Papio kindae, Cercopithecus albogularis, Cercopithecus mitis, Cercocebus torquatus, Cercocebus chrysogaster, Mandrillus sphinx, Allenopithecus nigroviridis, Allochrocebus lhoesti, Chlorocebus pygerythrus, Chlorocebus cynosuros, Chlorocebus aethiops, Chlorocebus tantalus, Pongo abelii, Symphalangus syndactylus, Nomascus gabriellae, Nomascus siki, Nomascus leucogenys, Hylobates lar, Hylobates agilis, Hylobates pileatus, Pan paniscus
Ncbi taxon ID
61880, 9600, 867383, 54180, 271260, 122765, 54181, 1042121, 164651, 78451, 33548, 164648, 373033, 88029, 54137, 66063, 1194336, 1194335, 224329, 61621, 1194334, 61622, 66062, 54133, 1194332, 1194333, 310352, 43780, 170207, 54601, 40843, 9541, 9538, 36224, 75566, 208091, 867370, 36225, 9530, 75569, 9561, 54135, 100224, 60710, 460675, 9534, 60712, 9601, 9590, 61852, 9586, 61853, 9580, 9579, 9589, 9597

4132 (G > C)

General info

Mitimpact ID
MI.12475
Chr
chrM
Start
4132
Ref
G
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
826
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GCA/CCA
AA pos
276
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4132G>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
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
2.646 Conservation Score
PhyloP 470way
-0.677 Conservation Score
PhastCons 100v
0.996 Conservation Score
PhastCons 470way
0.017 Conservation Score

Pathogenicity predictors

PolyPhen2
Benign 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
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 pathogenic Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Tolerated 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
.
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
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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
4132G>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
.

4132 (G > T)

General info

Mitimpact ID
MI.12477
Chr
chrM
Start
4132
Ref
G
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
826
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GCA/TCA
AA pos
276
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.4132G>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
2.646 Conservation Score
PhyloP 470way
-0.677 Conservation Score
PhastCons 100v
0.996 Conservation Score
PhastCons 470way
0.017 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
Pathogenic 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
High 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
4132G>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0%
MITOMAP General GenBank Seqs
0
MITOMAP General GenBank Curated refs
.
MITOMAP Variant Class
polymorphism
Gnomad AN
0
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
.
Gnomad AF het
.
Gnomad filter
.
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
.
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
.
~ 4132 (G/A) 4132 (G/C) 4132 (G/T)
~ 4132 (GCA/ACA) 4132 (GCA/CCA) 4132 (GCA/TCA)
MitImpact id MI.12476 MI.12475 MI.12477
Chr chrM chrM chrM
Start 4132 4132 4132
Ref G G G
Alt A 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 826 826 826
Gene start 3307 3307 3307
Gene end 4262 4262 4262
Gene strand + + +
Codon substitution GCA/ACA GCA/CCA GCA/TCA
AA position 276 276 276
AA ref A A A
AA alt T P S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516000 516000 516000
HGVS NC_012920.1:g.4132G>A NC_012920.1:g.4132G>C NC_012920.1:g.4132G>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 2.646 2.646 2.646
PhyloP 470Way -0.677 -0.677 -0.677
PhastCons 100V 0.996 0.996 0.996
PhastCons 470Way 0.017 0.017 0.017
PolyPhen2 benign benign benign
PolyPhen2 score 0.0 0.36 0.0
SIFT neutral neutral neutral
SIFT score 0.41 0.23 0.44
SIFT4G Damaging Damaging Tolerated
SIFT4G score 0.033 0.0 1.0
VEST Neutral Pathogenic Neutral
VEST pvalue 0.15 0.04 0.2
VEST FDR 0.4 0.35 0.45
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.04 0.79 0.05
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 0.99995 0.999928 0.998821
MutationTaster converted rankscore 0.19072 0.19486 0.21877
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE A276T A276P A276S
fathmm Tolerated Tolerated Tolerated
fathmm score 2.86 2.65 2.87
fathmm converted rankscore 0.10482 0.12676 0.10386
AlphaMissense likely_benign likely_pathogenic likely_benign
AlphaMissense score 0.1694 0.9289 0.1318
CADD Neutral Neutral Neutral
CADD score 2.369834 2.133515 -0.818237
CADD phred 18.62 17.07 0.039
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score -0.08 -1.88 2.49
MutationAssessor neutral medium neutral
MutationAssessor score -1.085 2.145 -1.555
EFIN SP Neutral Damaging Neutral
EFIN SP score 0.694 0.534 0.662
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.802 0.408 0.806
MLC Deleterious Deleterious Deleterious
MLC score 0.61826302 0.61826302 0.61826302
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Pathogenic Neutral Pathogenic
APOGEE1 score 0.58 0.4 0.52
APOGEE2 Likely-benign VUS Benign
APOGEE2 score 0.0653780642282667 0.448956197151777 0.0470300847149953
CAROL neutral neutral neutral
CAROL score 0.59 0.73 0.55
Condel deleterious neutral deleterious
Condel score 0.71 0.44 0.72
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -3 -6
MtoolBox neutral deleterious neutral
MtoolBox DS 0.12 0.46 0.11
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.012017 0.17994 0.011347
DEOGEN2 converted rankscore 0.10632 0.53111 0.10136
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf high impact medium impact high impact
PolyPhen2 transf score 2.07 -0.52 2.07
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.19 -0.02 0.22
MutationAssessor transf low impact medium impact low impact
MutationAssessor transf score -1.49 1.17 -2.47
CHASM Neutral Neutral Neutral
CHASM pvalue 0.48 0.53 0.46
CHASM FDR 0.8 0.8 0.8
ClinVar id 377340.0 . .
ClinVar Allele id 364218.0 . .
ClinVar CLNDISDB MedGen:CN517202|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . .
ClinVar CLNDN not_provided|Leigh_syndrome . .
ClinVar CLNSIG Conflicting_interpretations_of_pathogenicity . .
MITOMAP Disease Clinical info NAION-associated . .
MITOMAP Disease Status Reported [VUS] . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.0147% . 0.0%
MITOMAP General GenBank Seqs 9 . 0
MITOMAP General Curated refs 29987491;17454741 . .
MITOMAP Variant Class polymorphism;disease . polymorphism
gnomAD 3.1 AN 56433.0 . .
gnomAD 3.1 AC Homo 11.0 . .
gnomAD 3.1 AF Hom 0.000194921 . .
gnomAD 3.1 AC Het 0.0 . .
gnomAD 3.1 AF Het 0.0 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 80.0 . 1.0
HelixMTdb AF Hom 0.00040819868 . 5.1024836e-06
HelixMTdb AC Het 2.0 . 0.0
HelixMTdb AF Het 1.0204967e-05 . 0.0
HelixMTdb mean ARF 0.13364 . .
HelixMTdb max ARF 0.15493 . .
ToMMo 54KJPN AC . . .
ToMMo 54KJPN AF . . .
ToMMo 54KJPN AN . . .
COSMIC 90 . . .
dbSNP 156 id rs1057520201 . .
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