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3316 (G > C)

General info

Mitimpact ID
MI.10776
Chr
chrM
Start
3316
Ref
G
Alt
C
Gene symbol
MT-ND1 Extended gene annotation
Gene position
10
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GCC/CCC
AA pos
4
AA ref
A
AA alt
P
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3316G>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
-0.232 Conservation Score
PhyloP 470way
-0.376 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.001 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
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
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
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
692332
Clinvar ALLELEID
680869
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Uncertain significance
MITOMAP Allele
3316G>C
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
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
7
HelixMTdb AF hom
3.57e-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
rs2853516

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
.

3316 (G > A)

General info

Mitimpact ID
MI.10777
Chr
chrM
Start
3316
Ref
G
Alt
A
Gene symbol
MT-ND1 Extended gene annotation
Gene position
10
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GCC/ACC
AA pos
4
AA ref
A
AA alt
T
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3316G>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
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Powered by MitoWheel

Conservation

PhyloP 100v
-0.232 Conservation Score
PhyloP 470way
-0.376 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.001 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
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
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
692333
Clinvar ALLELEID
680868
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
3316G>A
MITOMAP Disease Clinical info
Diabetes / lhon / peo / vascular dementia
MITOMAP Disease Status
Reported; hg d1 d2 m33 r30 marker
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.9389%
MITOMAP General GenBank Seqs
574
MITOMAP General GenBank Curated refs
19370763 21978175 10520236 11238687 19199242 7733935 18691441 9384601 16477364 19818876 10636741 8858117 11938495 15972314 15338331 15638829 16076538 16714301 10924403 11733107 10395242 19733221 29464373 12436196 10704697 29387390 31798871 11961525 24002810 29987491 16409568 22333566 31797714 22949535 16331560 18368068 17264866 16414144
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56400
Gnomad AC hom
258
Gnomad AF hom
0.0045744
Gnomad AC het
15
Gnomad AF het
0.0002659
Gnomad filter
Pass
HelixMTdb AC hom
970
HelixMTdb AF hom
0.0049494
HelixMTdb AC het
50
HelixMTdb AF het
0.0002551
HelixMTdb mean ARF
0.4050599
HelixMTdb max ARF
0.90667
ToMMo JPN54K AC
371
ToMMo JPN54K AF
0.006832
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs2853516

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
.

3316 (G > T)

General info

Mitimpact ID
MI.10775
Chr
chrM
Start
3316
Ref
G
Alt
T
Gene symbol
MT-ND1 Extended gene annotation
Gene position
10
Gene start
3307
Gene end
4262
Gene strand
+
Codon substitution
GCC/TCC
AA pos
4
AA ref
A
AA alt
S
Functional effect
missense
OMIM ID
516000
HGVS
NC_012920.1:g.3316G>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
-0.232 Conservation Score
PhyloP 470way
-0.376 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.001 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
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
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
3316G>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
56433
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
1
Gnomad AF het
1.77e-05
Gnomad filter
Pass
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
.
~ 3316 (G/C) 3316 (G/A) 3316 (G/T)
~ 3316 (GCC/CCC) 3316 (GCC/ACC) 3316 (GCC/TCC)
MitImpact id MI.10776 MI.10777 MI.10775
Chr chrM chrM chrM
Start 3316 3316 3316
Ref G G G
Alt C A 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 10 10 10
Gene start 3307 3307 3307
Gene end 4262 4262 4262
Gene strand + + +
Codon substitution GCC/CCC GCC/ACC GCC/TCC
AA position 4 4 4
AA ref A A A
AA alt P T S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516000 516000 516000
HGVS NC_012920.1:g.3316G>C NC_012920.1:g.3316G>A NC_012920.1:g.3316G>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 -0.232 -0.232 -0.232
PhyloP 470Way -0.376 -0.376 -0.376
PhastCons 100V 0 0 0
PhastCons 470Way 0.001 0.001 0.001
PolyPhen2 benign benign benign
PolyPhen2 score 0.22 0.0 0.05
SIFT neutral neutral neutral
SIFT score 0.23 0.49 0.47
SIFT4G Damaging Tolerated Damaging
SIFT4G score 0.001 0.115 0.039
VEST Neutral Neutral Neutral
VEST pvalue 0.07 0.3 0.26
VEST FDR 0.35 0.45 0.45
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.33 0.05 0.12
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1 1 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE A4P A4T A4S
fathmm Tolerated Tolerated Tolerated
fathmm score 2.67 2.71 2.7
fathmm converted rankscore 0.12473 0.12055 0.12162
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.217 0.1098 0.1289
CADD Neutral Neutral Neutral
CADD score 1.742374 1.042328 1.578948
CADD phred 14.65 10.9 13.74
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score -1.63 0.05 -0.77
MutationAssessor low neutral neutral
MutationAssessor score 1.585 -0.39 0.44
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.772 0.942 0.846
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.468 0.904 0.726
MLC Neutral Neutral Neutral
MLC score 0.14418492 0.14418492 0.14418492
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.34 0.44 0.38
APOGEE2 VUS Benign Likely-benign
APOGEE2 score 0.400439515832731 0.0282673207031084 0.0735147878300974
CAROL neutral neutral neutral
CAROL score 0.73 0.51 0.49
Condel deleterious deleterious deleterious
Condel score 0.51 0.75 0.71
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -6 -6
MtoolBox neutral neutral neutral
MtoolBox DS 0.32 0.09 0.15
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.063233 0.006362 0.017008
DEOGEN2 converted rankscore 0.32122 0.05794 0.13954
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact high impact medium impact
PolyPhen2 transf score -0.24 2.07 0.45
SIFT_transf medium impact medium impact medium impact
SIFT transf score -0.02 0.27 0.25
MutationAssessor transf medium impact low impact low impact
MutationAssessor transf score -0.04 -1.85 -1.12
CHASM Neutral Neutral Neutral
CHASM pvalue 0.52 0.43 0.39
CHASM FDR 0.8 0.8 0.8
ClinVar id 692332.0 692333.0 .
ClinVar Allele id 680869.0 680868.0 .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 .
ClinVar CLNDN Leigh_syndrome Leigh_syndrome .
ClinVar CLNSIG Uncertain_significance Benign .
MITOMAP Disease Clinical info . Diabetes / LHON / PEO / vascular dementia .
MITOMAP Disease Status . Reported; hg D1 D2 M33 R30 marker .
MITOMAP Disease Hom/Het ./. +/- ./.
MITOMAP General GenBank Freq 0.0% 0.9389% .
MITOMAP General GenBank Seqs 0 574 .
MITOMAP General Curated refs . 19370763;21978175;10520236;11238687;19199242;7733935;18691441;9384601;16477364;19818876;10636741;8858117;11938495;15972314;15338331;15638829;16076538;16714301;10924403;11733107;10395242;19733221;29464373;12436196;10704697;29387390;31798871;11961525;24002810;29987491;16409568;22333566;31797714;22949535;16331560;18368068;17264866;16414144 .
MITOMAP Variant Class polymorphism polymorphism;disease .
gnomAD 3.1 AN 56433.0 56400.0 56433.0
gnomAD 3.1 AC Homo 1.0 258.0 0.0
gnomAD 3.1 AF Hom 1.77201e-05 0.00457447 0.0
gnomAD 3.1 AC Het 1.0 15.0 1.0
gnomAD 3.1 AF Het 1.77201e-05 0.000265957 1.77201e-05
gnomAD 3.1 filter PASS PASS PASS
HelixMTdb AC Hom 7.0 970.0 .
HelixMTdb AF Hom 3.5717385e-05 0.004949409 .
HelixMTdb AC Het 0.0 50.0 .
HelixMTdb AF Het 0.0 0.00025512418 .
HelixMTdb mean ARF . 0.40506 .
HelixMTdb max ARF . 0.90667 .
ToMMo 54KJPN AC . 371 .
ToMMo 54KJPN AF . 0.006832 .
ToMMo 54KJPN AN . 54302 .
COSMIC 90 . . .
dbSNP 156 id rs2853516 rs2853516 .
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