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8701 (A > C)

General info

Mitimpact ID
MI.373
Chr
chrM
Start
8701
Ref
A
Alt
C
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
175
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ACC/CCC
AA pos
59
AA ref
T
AA alt
P
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8701A>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
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Powered by MitoWheel

Conservation

PhyloP 100v
-5.681 Conservation Score
PhyloP 470way
-0.238 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.004 Conservation Score

Pathogenicity predictors

PolyPhen2
Possibly damaging 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
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
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
8701A>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
0
Gnomad AF hom
0.0
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Npg
HelixMTdb AC hom
2
HelixMTdb AF hom
1.02e-05
HelixMTdb AC het
0
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
1
ToMMo JPN54K AF
1.8e-05
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs2000975

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
.

8701 (A > G)

General info

Mitimpact ID
MI.374
Chr
chrM
Start
8701
Ref
A
Alt
G
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
175
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ACC/GCC
AA pos
59
AA ref
T
AA alt
A
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8701A>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
-5.681 Conservation Score
PhyloP 470way
-0.238 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.004 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
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
692955
Clinvar ALLELEID
681491
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Benign
MITOMAP Allele
8701A>G
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
31.2821%
MITOMAP General GenBank Seqs
19124
MITOMAP General GenBank Curated refs
18619472 29997041 17288645 19732751 18545700 19497304 24467713 15466285 15637703 31358833 24470521 32337946 16120352 8037701 32943110 19076426 16624503 10996007 20939899 15896721 26993169 20691156 12840039 19370763 21281460 8769114 31478599 19022198 11349229 33420243 15126279 11811990 15771256 15338331 7689389 8728098 1757091 1442494 19586946 19167085 16172508 17003408 20304802 12870132 17300996 19546379 8016139 18639500 12375058 17331239 18177933 20067846 17264866 21978175 18223312 19188198 17033820 17452034 20728388 21144833 32094358 17698030 19026397 12022039 18775412 16895436 17617636 15670746 22333566 15555598 16048457 19460299 3201231 17170302 18691441 18587274 15262184 19818876 19703591 20045353 17434142 15708009 20627642 23304069 11938495 16714301 17620140 19733221 24667788 17698299 12504210 16050984 18386806 2025303 19349200 19324017 7874114 16955413 27783406 17072496 17341440 30446962
MITOMAP Variant Class
polymorphism
Gnomad AN
56285
Gnomad AC hom
17065
Gnomad AF hom
0.303189
Gnomad AC het
7
Gnomad AF het
0.0001243
Gnomad filter
Pass
HelixMTdb AC hom
17154
HelixMTdb AF hom
0.087528
HelixMTdb AC het
47
HelixMTdb AF het
0.0002398
HelixMTdb mean ARF
0.72788
HelixMTdb max ARF
0.96581
ToMMo JPN54K AC
34608
ToMMo JPN54K AF
0.637325
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs2000975

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
.

8701 (A > T)

General info

Mitimpact ID
MI.372
Chr
chrM
Start
8701
Ref
A
Alt
T
Gene symbol
MT-ATP6 Extended gene annotation
Gene position
175
Gene start
8527
Gene end
9207
Gene strand
+
Codon substitution
ACC/TCC
AA pos
59
AA ref
T
AA alt
S
Functional effect
missense
OMIM ID
516060
HGVS
NC_012920.1:g.8701A>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
-5.681 Conservation Score
PhyloP 470way
-0.238 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.004 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
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
8701A>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
56434
Gnomad AC hom
2
Gnomad AF hom
3.54e-05
Gnomad AC het
0
Gnomad AF het
0.0
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
.
~ 8701 (A/C) 8701 (A/G) 8701 (A/T)
~ 8701 (ACC/CCC) 8701 (ACC/GCC) 8701 (ACC/TCC)
MitImpact id MI.373 MI.374 MI.372
Chr chrM chrM chrM
Start 8701 8701 8701
Ref A A A
Alt C G T
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 175 175 175
Gene start 8527 8527 8527
Gene end 9207 9207 9207
Gene strand + + +
Codon substitution ACC/CCC ACC/GCC ACC/TCC
AA position 59 59 59
AA ref T T T
AA alt P A S
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516060 516060 516060
HGVS NC_012920.1:g.8701A>C NC_012920.1:g.8701A>G NC_012920.1:g.8701A>T
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 -5.681 -5.681 -5.681
PhyloP 470Way -0.238 -0.238 -0.238
PhastCons 100V 0 0 0
PhastCons 470Way 0.004 0.004 0.004
PolyPhen2 possibly_damaging benign benign
PolyPhen2 score 0.48 0.01 0.14
SIFT neutral neutral neutral
SIFT score 0.24 0.6 0.51
SIFT4G Tolerated Tolerated Tolerated
SIFT4G score 0.12 0.512 0.722
VEST Neutral Neutral Neutral
VEST pvalue 0.4 0.73 0.81
VEST FDR 0.65 0.75 0.85
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.74 0.03 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 T59P T59A T59S
fathmm Tolerated Tolerated Tolerated
fathmm score 4.37 4.44 4.51
fathmm converted rankscore 0.02277 0.02139 0.02015
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.1536 0.0634 0.0891
CADD Neutral Neutral Neutral
CADD score 0.454889 -0.661909 -1.226065
CADD phred 7.076 0.088 0.006
PROVEAN Tolerated Tolerated Tolerated
PROVEAN score -2.35 -0.94 -0.64
MutationAssessor medium neutral neutral
MutationAssessor score 2.105 0.62 0.285
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.848 0.984 0.9
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.522 0.984 0.98
MLC Neutral Neutral Neutral
MLC score 0.02806446 0.02806446 0.02806446
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.3 0.29 0.42
APOGEE2 Likely-benign Benign Benign
APOGEE2 score 0.166575323363085 0.025634712412579 0.0163743681189181
CAROL neutral neutral neutral
CAROL score 0.73 0.39 0.4
Condel neutral deleterious deleterious
Condel score 0.38 0.8 0.69
COVEC WMV neutral neutral neutral
COVEC WMV score -3 -6 -6
MtoolBox deleterious neutral neutral
MtoolBox DS 0.58 0.07 0.19
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.056313 0.018173 0.014263
DEOGEN2 converted rankscore 0.30253 0.14695 0.12177
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score -0.72 1.14 -0.01
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.01 0.39 0.3
MutationAssessor transf medium impact medium impact low impact
MutationAssessor transf score 0.22 -0.79 -1.32
CHASM Neutral Neutral Neutral
CHASM pvalue 0.72 0.36 0.83
CHASM FDR 0.9 0.9 0.9
ClinVar id . 692955.0 .
ClinVar Allele id . 681491.0 .
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 0.0% 31.2821% 0.0016%
MITOMAP General GenBank Seqs 0 19124 1
MITOMAP General Curated refs . 18619472;29997041;17288645;19732751;18545700;19497304;24467713;15466285;15637703;31358833;24470521;32337946;16120352;8037701;32943110;19076426;16624503;10996007;20939899;15896721;26993169;20691156;12840039;19370763;21281460;8769114;31478599;19022198;11349229;33420243;15126279;11811990;15771256;15338331;7689389;8728098;1757091;1442494;19586946;19167085;16172508;17003408;20304802;12870132;17300996;19546379;8016139;18639500;12375058;17331239;18177933;20067846;17264866;21978175;18223312;19188198;17033820;17452034;20728388;21144833;32094358;17698030;19026397;12022039;18775412;16895436;17617636;15670746;22333566;15555598;16048457;19460299;3201231;17170302;18691441;18587274;15262184;19818876;19703591;20045353;17434142;15708009;20627642;23304069;11938495;16714301;17620140;19733221;24667788;17698299;12504210;16050984;18386806;2025303;19349200;19324017;7874114;16955413;27783406;17072496;17341440;30446962 .
MITOMAP Variant Class polymorphism polymorphism polymorphism
gnomAD 3.1 AN 56433.0 56285.0 56434.0
gnomAD 3.1 AC Homo 0.0 17065.0 2.0
gnomAD 3.1 AF Hom 0.0 0.303189 3.54396e-05
gnomAD 3.1 AC Het 0.0 7.0 0.0
gnomAD 3.1 AF Het 0.0 0.000124367 0.0
gnomAD 3.1 filter npg PASS PASS
HelixMTdb AC Hom 2.0 17154.0 4.0
HelixMTdb AF Hom 1.0204967e-05 0.087528 2.0409934e-05
HelixMTdb AC Het 0.0 47.0 0.0
HelixMTdb AF Het 0.0 0.00023981671 0.0
HelixMTdb mean ARF . 0.72788 .
HelixMTdb max ARF . 0.96581 .
ToMMo 54KJPN AC 1 34608 .
ToMMo 54KJPN AF 1.8e-05 0.637325 .
ToMMo 54KJPN AN 54302 54302 .
COSMIC 90 . . .
dbSNP 156 id rs2000975 rs2000975 .
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