Logo MitImpact
Home Description Output legend Molecular Dynamics How to cite License

8860 (A > T)

General info

Mitimpact ID
MI.707
Chr
chrM
Start
8860
Ref
A
Alt
T
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
334
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ACA/TCA
AA pos
112
AA ref
T
AA alt
S
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8860A>T
HGNC ID
7414
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot ID
P00846
Uniprot name
ATP6_HUMAN
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.266 Conservation Score
PhyloP 470way
-1.251 Conservation Score
PhastCons 100v
0.001 Conservation Score
PhastCons 470way
0.352 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
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
Damaging Score and details of the predictor
Mutation Assessor
High 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
.
Clinvar ALLELEID
.
Clinvar CLNDISDB
.
Clinvar CLNDN
.
Clinvar CLNSIG
.
MITOMAP Allele
8860A>T
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
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
5343
ToMMo JPN54K AF
0.377864
ToMMo JPN54K AN
14140
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
.

8860 (A > C)

General info

Mitimpact ID
MI.709
Chr
chrM
Start
8860
Ref
A
Alt
C
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
334
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ACA/CCA
AA pos
112
AA ref
T
AA alt
P
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8860A>C
HGNC ID
7414
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot ID
P00846
Uniprot name
ATP6_HUMAN
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.266 Conservation Score
PhyloP 470way
-1.251 Conservation Score
PhastCons 100v
0.001 Conservation Score
PhastCons 470way
0.352 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
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 pathogenic Score and details of the predictor
CADD
Neutral Score and details of the predictor
PROVEAN
Damaging Score and details of the predictor
Mutation Assessor
High 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
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
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
8860A>C
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0033%
MITOMAP General GenBank Seqs
2
MITOMAP General GenBank Curated refs
23332919
MITOMAP Variant Class
polymorphism
Gnomad AN
56433
Gnomad AC hom
0
Gnomad AF hom
0.0
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Npg
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
284
ToMMo JPN54K AF
0.020085
ToMMo JPN54K AN
14140
COSMIC 90
.
dbSNP 156
rs2001031

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
.

8860 (A > G)

General info

Mitimpact ID
MI.708
Chr
chrM
Start
8860
Ref
A
Alt
G
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
334
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ACA/GCA
AA pos
112
AA ref
T
AA alt
A
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8860A>G
HGNC ID
7414
RC complex
V
Ensembl gene ID
ENSG00000198899
Ensembl protein ID
ENSP00000354632
Ensembl transcript ID
ENST00000361899
Uniprot ID
P00846
Uniprot name
ATP6_HUMAN
Ncbi gene ID
4508
Ncbi protein ID
YP_003024031.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
0.266 Conservation Score
PhyloP 470way
-1.251 Conservation Score
PhastCons 100v
0.001 Conservation Score
PhastCons 470way
0.352 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
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
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
693004
Clinvar ALLELEID
681540
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
8860A>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
98.7895%
MITOMAP General GenBank Seqs
60394
MITOMAP General GenBank Curated refs
18619472 1634041 19732751 15465027 19497304 24467713 14978686 15922297 15637703 12112111 23756438 24470521 1968873 16120352 8304347 7723627 11095989 30351437 16624503 15286157 20939899 20153673 26993169 20691156 11931086 18445251 2112427 19370763 14699607 21281460 8769114 19022198 16532388 11349229 11935318 20566709 18495510 18820594 1732158 15771256 2268345 10508508 1346260 7689389 19167085 2124116 16172508 3472733 17003408 20304802 19546379 17300996 19398658 8104867 8016139 1346259 18639500 12031626 17331239 7942855 17264866 21978175 7688932 19188198 17452034 20728388 21144833 12271374 16705548 17698030 14681830 19026397 17406640 17434445 19062322 12022039 8147435 18775412 7688933 17085680 10909988 16895436 7726182 15707996 19555656 22333566 15555598 8302846 16048457 1899574 19460299 3201231 22291763 11820805 18691441 18587274 19394449 19818876 17434142 15591266 15708009 20627642 23304069 9771776 11938495 16714301 2043137 20211276 17620140 19733221 24667788 17698299 3025745 12504210 16050984 18386806 19349200 19324017 16380089 7874114 16955413 10936107 18590963 17341440
MITOMAP Variant Class
polymorphism
Gnomad AN
56418
Gnomad AC hom
56069
Gnomad AF hom
0.993814
Gnomad AC het
9
Gnomad AF het
0.0001595
Gnomad filter
Pass
HelixMTdb AC hom
193581
HelixMTdb AF hom
0.9877438
HelixMTdb AC het
40
HelixMTdb AF het
0.000204
HelixMTdb mean ARF
0.75608
HelixMTdb max ARF
0.90698
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs2001031

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
.
~ 8860 (A/T) 8860 (A/C) 8860 (A/G)
~ 8860 (ACA/TCA) 8860 (ACA/CCA) 8860 (ACA/GCA)
MitImpact id MI.707 MI.709 MI.708
Chr chrM chrM chrM
Start 8860 8860 8860
Ref A A A
Alt T C G
Gene symbol MT-ATP6 MT-ATP6 MT-ATP6
Extended annotation mitochondrially encoded ATP synthase membrane subunit 6 mitochondrially encoded ATP synthase membrane subunit 6 mitochondrially encoded ATP synthase membrane subunit 6
Gene position 334 334 334
Gene start 8527 8527 8527
Gene end 9207 9207 9207
Gene strand + + +
Codon substitution ACA/TCA ACA/CCA ACA/GCA
AA position 112 112 112
AA ref T T T
AA alt S P A
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516060 516060 516060
HGVS NC_012920.1:g.8860A>T NC_012920.1:g.8860A>C NC_012920.1:g.8860A>G
HGNC id 7414 7414 7414
Respiratory Chain complex V V V
Ensembl gene id ENSG00000198899 ENSG00000198899 ENSG00000198899
Ensembl transcript id ENST00000361899 ENST00000361899 ENST00000361899
Ensembl protein id ENSP00000354632 ENSP00000354632 ENSP00000354632
Uniprot id P00846 P00846 P00846
Uniprot name ATP6_HUMAN ATP6_HUMAN ATP6_HUMAN
Ncbi gene id 4508 4508 4508
Ncbi protein id YP_003024031.1 YP_003024031.1 YP_003024031.1
PhyloP 100V 0.266 0.266 0.266
PhyloP 470Way -1.251 -1.251 -1.251
PhastCons 100V 0.001 0.001 0.001
PhastCons 470Way 0.352 0.352 0.352
PolyPhen2 benign benign benign
PolyPhen2 score 0.07 0.28 0.0
SIFT neutral neutral neutral
SIFT score 0.4 0.22 0.61
SIFT4G Damaging Damaging Tolerated
SIFT4G score 0.001 0.0 0.095
VEST Neutral Neutral Neutral
VEST pvalue 0.39 0.11 0.47
VEST FDR 0.65 0.65 0.65
Mitoclass.1 damaging damaging neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.38 0.79 0
MutationTaster Polymorphism Polymorphism Polymorphism
MutationTaster score 1.0 1.0 1.0
MutationTaster converted rankscore 0.08975 0.08975 0.08975
MutationTaster model simple_aae simple_aae simple_aae
MutationTaster AAE T112S T112P T112A
fathmm Tolerated Tolerated Tolerated
fathmm score 4.28 4.23 4.3
fathmm converted rankscore 0.02487 0.02616 0.02437
AlphaMissense likely_benign likely_pathogenic likely_benign
AlphaMissense score 0.312 0.7363 0.1103
CADD Neutral Neutral Neutral
CADD score 1.394277 1.811232 0.345861
CADD phred 12.76 15.05 6.128
PROVEAN Damaging Damaging Damaging
PROVEAN score -3.36 -5.25 -3.97
MutationAssessor high high medium
MutationAssessor score 3.565 4.535 2.21
EFIN SP Neutral Damaging Neutral
EFIN SP score 0.636 0.522 0.962
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.614 0.442 0.906
MLC Neutral Neutral Neutral
MLC score 0.05691351 0.05691351 0.05691351
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.34 0.35 0.27
APOGEE2 Likely-benign VUS- Likely-benign
APOGEE2 score 0.123868246072304 0.355846030282563 0.0742010447563555
CAROL neutral neutral neutral
CAROL score 0.55 0.74 0.38
Condel deleterious deleterious deleterious
Condel score 0.67 0.47 0.81
COVEC WMV neutral neutral neutral
COVEC WMV score -3 -3 -3
MtoolBox neutral deleterious neutral
MtoolBox DS 0.22 0.54 0.14
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.060609 0.168726 0.068386
DEOGEN2 converted rankscore 0.31433 0.51584 0.33443
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact medium impact high impact
PolyPhen2 transf score 0.31 -0.37 2.09
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.19 -0.02 0.4
MutationAssessor transf medium impact medium impact medium impact
MutationAssessor transf score 0.89 1.54 0.75
CHASM Neutral Neutral Neutral
CHASM pvalue 0.72 0.6 0.43
CHASM FDR 0.9 0.9 0.9
ClinVar id . . 693004.0
ClinVar Allele id . . 681540.0
ClinVar CLNDISDB . . MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506
ClinVar CLNDN . . Leigh_syndrome
ClinVar CLNSIG . . Benign
MITOMAP Disease Clinical info . . .
MITOMAP Disease Status . . .
MITOMAP Disease Hom/Het ./. ./. ./.
MITOMAP General GenBank Freq 0.0016% 0.0033% 98.7895%
MITOMAP General GenBank Seqs 1 2 60394
MITOMAP General Curated refs . 23332919 18619472;1634041;19732751;15465027;19497304;24467713;14978686;15922297;15637703;12112111;23756438;24470521;1968873;16120352;8304347;7723627;11095989;30351437;16624503;15286157;20939899;20153673;26993169;20691156;11931086;18445251;2112427;19370763;14699607;21281460;8769114;19022198;16532388;11349229;11935318;20566709;18495510;18820594;1732158;15771256;2268345;10508508;1346260;7689389;19167085;2124116;16172508;3472733;17003408;20304802;19546379;17300996;19398658;8104867;8016139;1346259;18639500;12031626;17331239;7942855;17264866;21978175;7688932;19188198;17452034;20728388;21144833;12271374;16705548;17698030;14681830;19026397;17406640;17434445;19062322;12022039;8147435;18775412;7688933;17085680;10909988;16895436;7726182;15707996;19555656;22333566;15555598;8302846;16048457;1899574;19460299;3201231;22291763;11820805;18691441;18587274;19394449;19818876;17434142;15591266;15708009;20627642;23304069;9771776;11938495;16714301;2043137;20211276;17620140;19733221;24667788;17698299;3025745;12504210;16050984;18386806;19349200;19324017;16380089;7874114;16955413;10936107;18590963;17341440
MITOMAP Variant Class polymorphism polymorphism polymorphism
gnomAD 3.1 AN . 56433.0 56418.0
gnomAD 3.1 AC Homo . 0.0 56069.0
gnomAD 3.1 AF Hom . 0.0 0.993814
gnomAD 3.1 AC Het . 0.0 9.0
gnomAD 3.1 AF Het . 0.0 0.000159524
gnomAD 3.1 filter . npg PASS
HelixMTdb AC Hom . . 193581.0
HelixMTdb AF Hom . . 0.98774385
HelixMTdb AC Het . . 40.0
HelixMTdb AF Het . . 0.00020409934
HelixMTdb mean ARF . . 0.75608
HelixMTdb max ARF . . 0.90698
ToMMo 54KJPN AC 5343 284 .
ToMMo 54KJPN AF 0.377864 0.020085 .
ToMMo 54KJPN AN 14140 14140 .
COSMIC 90 . . .
dbSNP 156 id . rs2001031 rs2001031
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