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12397 (A > G)

General info

Mitimpact ID
MI.19351
Chr
chrM
Start
12397
Ref
A
Alt
G
Gene symbol
MT-ND5 Extended gene annotation
Gene position
61
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
ACC/GCC
AA pos
21
AA ref
T
AA alt
A
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.12397A>G
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
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Conservation

PhyloP 100v
-7.131 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.004 Conservation Score

Pathogenicity predictors

PolyPhen2
Unknown 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
9705
Clinvar ALLELEID
24744
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

mondo:mondo:0011613, medgen:c1853833, omim:605909, orphanet:2828
Clinvar CLNDN
Leigh syndrome;

autosomal recessive early-onset parkinson disease 6
Clinvar CLNSIG
Benign
MITOMAP Allele
12397A>G
MITOMAP Disease Clinical info
Pd, early onset
MITOMAP Disease Status
Reported
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
0.6183%
MITOMAP General GenBank Seqs
378
MITOMAP General GenBank Curated refs
21978175 32094358 24467713 17429907 18524835 29987491 30242360 21457906 22487888
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56432
Gnomad AC hom
186
Gnomad AF hom
0.003296
Gnomad AC het
3
Gnomad AF het
5.31e-05
Gnomad filter
Pass
HelixMTdb AC hom
697
HelixMTdb AF hom
0.0035564
HelixMTdb AC het
12
HelixMTdb AF het
6.12e-05
HelixMTdb mean ARF
0.60862
HelixMTdb max ARF
0.91304
ToMMo JPN54K AC
81
ToMMo JPN54K AF
0.001492
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs1556424100

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
.

12397 (A > C)

General info

Mitimpact ID
MI.19350
Chr
chrM
Start
12397
Ref
A
Alt
C
Gene symbol
MT-ND5 Extended gene annotation
Gene position
61
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
ACC/CCC
AA pos
21
AA ref
T
AA alt
P
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.12397A>C
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
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Powered by MitoWheel

Conservation

PhyloP 100v
-7.131 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.004 Conservation Score

Pathogenicity predictors

PolyPhen2
Unknown 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
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
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
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
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
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
12397A>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
.

12397 (A > T)

General info

Mitimpact ID
MI.19352
Chr
chrM
Start
12397
Ref
A
Alt
T
Gene symbol
MT-ND5 Extended gene annotation
Gene position
61
Gene start
12337
Gene end
14148
Gene strand
+
Codon substitution
ACC/TCC
AA pos
21
AA ref
T
AA alt
S
Functional effect
missense
OMIM ID
516005
HGVS
NC_012920.1:g.12397A>T
HGNC ID
7461
RC complex
I
Ensembl gene ID
ENSG00000198786
Ensembl protein ID
ENSP00000354813
Ensembl transcript ID
ENST00000361567
Uniprot ID
P03915
Uniprot name
NU5M_HUMAN
Ncbi gene ID
4540
Ncbi protein ID
YP_003024036.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-7.131 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.004 Conservation Score

Pathogenicity predictors

PolyPhen2
Unknown 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
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
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
12397A>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
.
~ 12397 (A/G) 12397 (A/C) 12397 (A/T)
~ 12397 (ACC/GCC) 12397 (ACC/CCC) 12397 (ACC/TCC)
MitImpact id MI.19351 MI.19350 MI.19352
Chr chrM chrM chrM
Start 12397 12397 12397
Ref A A A
Alt G C T
Gene symbol MT-ND5 MT-ND5 MT-ND5
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5
Gene position 61 61 61
Gene start 12337 12337 12337
Gene end 14148 14148 14148
Gene strand + + +
Codon substitution ACC/GCC ACC/CCC ACC/TCC
AA position 21 21 21
AA ref T T T
AA alt A P S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516005 516005 516005
HGVS NC_012920.1:g.12397A>G NC_012920.1:g.12397A>C NC_012920.1:g.12397A>T
HGNC id 7461 7461 7461
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198786 ENSG00000198786 ENSG00000198786
Ensembl transcript id ENST00000361567 ENST00000361567 ENST00000361567
Ensembl protein id ENSP00000354813 ENSP00000354813 ENSP00000354813
Uniprot id P03915 P03915 P03915
Uniprot name NU5M_HUMAN NU5M_HUMAN NU5M_HUMAN
Ncbi gene id 4540 4540 4540
Ncbi protein id YP_003024036.1 YP_003024036.1 YP_003024036.1
PhyloP 100V -7.131 -7.131 -7.131
PhyloP 470Way 0.819 0.819 0.819
PhastCons 100V 0 0 0
PhastCons 470Way 0.004 0.004 0.004
PolyPhen2 unknown unknown unknown
PolyPhen2 score . . .
SIFT neutral neutral neutral
SIFT score 0.46 0.36 0.43
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 0.233 0.069 0.263
VEST Neutral Neutral Neutral
VEST pvalue 0.66 0.42 0.68
VEST FDR 0.7 0.55 0.7
Mitoclass.1 neutral damaging neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.02 0.2 0.04
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1 1 1
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE T21A T21P T21S
fathmm Tolerated Tolerated Tolerated
fathmm score 0.98 0.88 0.92
fathmm converted rankscore 0.42122 0.46028 0.44461
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.0736 0.1777 0.0999
CADD Neutral Neutral Neutral
CADD score 0.011306 0.427103 -0.090454
CADD phred 2.695 6.846 1.802
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score -0.74 -1.52 -1.09
MutationAssessor neutral medium low
MutationAssessor score 0.1 2.145 1.25
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.88 0.738 0.86
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.938 0.708 0.954
MLC Neutral Neutral Neutral
MLC score 0.2846581 0.2846581 0.2846581
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.5 0.38 0.41
APOGEE2 Benign Likely-benign Benign
APOGEE2 score 0.0123413636497991 0.120041245612278 0.0265606965013206
CAROL neutral neutral neutral
CAROL score 0.54 0.64 0.57
Condel deleterious deleterious deleterious
Condel score 0.73 0.68 0.72
COVEC WMV neutral neutral neutral
COVEC WMV score -4 -4 -4
MtoolBox neutral neutral neutral
MtoolBox DS 0.26 0.43 0.25
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.014168 0.029744 0.021865
DEOGEN2 converted rankscore 0.12111 0.21243 0.16957
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf high impact high impact high impact
PolyPhen2 transf score 2.1 2.1 2.1
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.19 0.1 0.17
MutationAssessor transf low impact medium impact medium impact
MutationAssessor transf score -1.88 -0.15 -0.15
CHASM Neutral Neutral Neutral
CHASM pvalue 0.32 0.7 0.61
CHASM FDR 0.8 0.85 0.8
ClinVar id 9705.0 . .
ClinVar Allele id 24744.0 . .
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0011613,MedGen:C1853833,OMIM:605909,Orphanet:2828 . .
ClinVar CLNDN Leigh_syndrome|Autosomal_recessive_early-onset_Parkinson_disease_6 . .
ClinVar CLNSIG Benign . .
MITOMAP Disease Clinical info PD, early onset . .
MITOMAP Disease Status Reported . .
MITOMAP Disease Hom/Het +/- ./. ./.
MITOMAP General GenBank Freq 0.6183% . .
MITOMAP General GenBank Seqs 378 . .
MITOMAP General Curated refs 21978175;32094358;24467713;17429907;18524835;29987491;30242360;21457906;22487888 . .
MITOMAP Variant Class polymorphism;disease . .
gnomAD 3.1 AN 56432.0 . .
gnomAD 3.1 AC Homo 186.0 . .
gnomAD 3.1 AF Hom 0.003296 . .
gnomAD 3.1 AC Het 3.0 . .
gnomAD 3.1 AF Het 5.31613e-05 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 697.0 . .
HelixMTdb AF Hom 0.0035564308 . .
HelixMTdb AC Het 12.0 . .
HelixMTdb AF Het 6.12298e-05 . .
HelixMTdb mean ARF 0.60862 . .
HelixMTdb max ARF 0.91304 . .
ToMMo 54KJPN AC 81 . .
ToMMo 54KJPN AF 0.001492 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs1556424100 . .
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