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10398 (A > T)

General info

Mitimpact ID
MI.15682
Chr
chrM
Start
10398
Ref
A
Alt
T
Gene symbol
MT-ND3 Extended gene annotation
Gene position
340
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
ACC/TCC
AA pos
114
AA ref
T
AA alt
S
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10398A>T
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
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Powered by MitoWheel

Conservation

PhyloP 100v
-0.338 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.996 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
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
693288
Clinvar ALLELEID
680178
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506
Clinvar CLNDN
Leigh syndrome
Clinvar CLNSIG
Likely benign
MITOMAP Allele
10398A>T
MITOMAP Disease Clinical info
.
MITOMAP Disease Status
.
MITOMAP Disease Hom/Het
./.
MITOMAP General GenBank Freq
0.0115%
MITOMAP General GenBank Seqs
7
MITOMAP General GenBank Curated refs
22312186
MITOMAP Variant Class
polymorphism
Gnomad AN
56433
Gnomad AC hom
13
Gnomad AF hom
0.0002303
Gnomad AC het
0
Gnomad AF het
0.0
Gnomad filter
Pass
HelixMTdb AC hom
58
HelixMTdb AF hom
0.0002959
HelixMTdb AC het
0
HelixMTdb AF het
0.0
HelixMTdb mean ARF
0.0
HelixMTdb max ARF
.
ToMMo JPN54K AC
5630
ToMMo JPN54K AF
0.103679
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs2853826

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
.

10398 (A > C)

General info

Mitimpact ID
MI.15683
Chr
chrM
Start
10398
Ref
A
Alt
C
Gene symbol
MT-ND3 Extended gene annotation
Gene position
340
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
ACC/CCC
AA pos
114
AA ref
T
AA alt
P
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10398A>C
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.338 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.996 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
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
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
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
10398A>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
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
255
ToMMo JPN54K AF
0.004696
ToMMo JPN54K AN
54302
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
.

10398 (A > G)

General info

Mitimpact ID
MI.15681
Chr
chrM
Start
10398
Ref
A
Alt
G
Gene symbol
MT-ND3 Extended gene annotation
Gene position
340
Gene start
10059
Gene end
10404
Gene strand
+
Codon substitution
ACC/GCC
AA pos
114
AA ref
T
AA alt
A
Functional effect
missense
OMIM ID
516002
HGVS
NC_012920.1:g.10398A>G
HGNC ID
7458
RC complex
I
Ensembl gene ID
ENSG00000198840
Ensembl protein ID
ENSP00000355206
Ensembl transcript ID
ENST00000361227
Uniprot ID
P03897
Uniprot name
NU3M_HUMAN
Ncbi gene ID
4537
Ncbi protein ID
YP_003024033.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
-0.338 Conservation Score
PhyloP 470way
0.819 Conservation Score
PhastCons 100v
0 Conservation Score
PhastCons 470way
0.996 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
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
9713
Clinvar ALLELEID
24752
Clinvar CLNDISDB
Mondo:mondo:0009723, medgen:c0023264, omim:256000, orphanet:506;

medgen:c4016597
Clinvar CLNDN
Leigh syndrome;

parkinson disease, resistance to
Clinvar CLNSIG
Benign
MITOMAP Allele
10398A>G
MITOMAP Disease Clinical info
Pd protective factor / longevity / altered cell ph / metabolic syndrome / breast cancer risk / leigh syndrome risk / adhd / cognitive decline / sca2 age of onset / fuchs endothelial corneal dystrophy
MITOMAP Disease Status
Reported; lineage l & m marker, also hg ijk
MITOMAP Disease Hom/Het
+/-
MITOMAP General GenBank Freq
42.3692%
MITOMAP General GenBank Seqs
25902
MITOMAP General GenBank Curated refs
11406419 15470367 1634041 29997041 17288645 9384601 19732751 17886251 8102506 18545700 15465027 19497304 17603766 24467713 15637703 18590963 16901986 17701054 28648514 18806273 23756438 31358833 24470521 23111160 10924403 1968873 1910259 8037701 8304347 15234467 32943110 19076426 11095989 18458168 16624503 18709563 27217714 10996007 15896721 17510395 20691156 20939899 34120353 11931086 11179019 16364244 21457906 19370763 21281460 8769114 9027481 31478599 20043118 19022198 12827453 16532388 11349229 11935318 20566709 33420243 16530527 15126279 18820594 1732158 18402672 15771256 15638829 15827561 18679013 15488317 12670626 1346260 12888043 7689389 8728098 9302261 1757091 19390621 1442494 19586946 19167085 18226984 16172508 17003408 3472733 15483642 20304802 11669538 17300996 19546379 19398658 17627010 8016139 1346259 8104867 29486301 18639500 12031626 12375058 17331239 31798871 7942855 18177933 31797714 20067846 17264866 21978175 15108120 19050702 11553319 18223312 7688932 19188198 17033820 16140977 16418878 20728388 15804362 17452034 9443868 22561905 32094358 16705548 17072496 17698030 7901141 19026397 17406640 19151382 11571560 19062322 12022039 7864851 8147435 16404693 17942074 17620498 7688933 15286228 18775412 12713143 7635294 18286226 16895436 16773565 18931934 15694598 10737123 17617636 19427920 25199876 15210164 18262047 12436196 12618962 16960846 16955414 15707996 8978068 15670746 22333566 15555598 8302846 16048457 19092698 1899574 3201231 18668590 17429907 18322915 18853457 8659531 11820805 15786469 18691441 18587274 17496137 15262184 1463007 19130794 19818876 35146807 19703591 12112086 10712231 17434142 15591266 15708009 31152278 20627642 34045735 23304069 11938495 28793231 7646496 7689388 16714301 2043137 10680807 12802679 17620140 19733221 35801081 24667788 17698299 17174475 15975594 3025745 16050984 18386806 24917144 19324017 18810306 7874114 16955413 29987491 10936107 1764087 17341440 30446962 16982817
MITOMAP Variant Class
polymorphism;disease
Gnomad AN
56170
Gnomad AC hom
23506
Gnomad AF hom
0.41848
Gnomad AC het
8
Gnomad AF het
0.0001424
Gnomad filter
Pass
HelixMTdb AC hom
49322
HelixMTdb AF hom
0.2516647
HelixMTdb AC het
289
HelixMTdb AF het
0.0014746
HelixMTdb mean ARF
0.83138
HelixMTdb max ARF
0.97203
ToMMo JPN54K AC
.
ToMMo JPN54K AF
.
ToMMo JPN54K AN
.
COSMIC 90
.
dbSNP 156
rs2853826

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
.
~ 10398 (A/T) 10398 (A/C) 10398 (A/G)
~ 10398 (ACC/TCC) 10398 (ACC/CCC) 10398 (ACC/GCC)
MitImpact id MI.15682 MI.15683 MI.15681
Chr chrM chrM chrM
Start 10398 10398 10398
Ref A A A
Alt T C G
Gene symbol MT-ND3 MT-ND3 MT-ND3
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3
Gene position 340 340 340
Gene start 10059 10059 10059
Gene end 10404 10404 10404
Gene strand + + +
Codon substitution ACC/TCC ACC/CCC ACC/GCC
AA position 114 114 114
AA ref T T T
AA alt S P A
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516002 516002 516002
HGVS NC_012920.1:g.10398A>T NC_012920.1:g.10398A>C NC_012920.1:g.10398A>G
HGNC id 7458 7458 7458
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198840 ENSG00000198840 ENSG00000198840
Ensembl transcript id ENST00000361227 ENST00000361227 ENST00000361227
Ensembl protein id ENSP00000355206 ENSP00000355206 ENSP00000355206
Uniprot id P03897 P03897 P03897
Uniprot name NU3M_HUMAN NU3M_HUMAN NU3M_HUMAN
Ncbi gene id 4537 4537 4537
Ncbi protein id YP_003024033.1 YP_003024033.1 YP_003024033.1
PhyloP 100V -0.338 -0.338 -0.338
PhyloP 470Way 0.819 0.819 0.819
PhastCons 100V 0 0 0
PhastCons 470Way 0.996 0.996 0.996
PolyPhen2 benign benign benign
PolyPhen2 score 0.02 0.08 0.0
SIFT neutral neutral neutral
SIFT score 0.77 0.3 0.83
SIFT4G Tolerated Damaging Tolerated
SIFT4G score 0.054 0.003 1.0
VEST Neutral Neutral Neutral
VEST pvalue 0.5 0.2 0.36
VEST FDR 0.6 0.45 0.5
Mitoclass.1 neutral neutral neutral
SNPDryad Neutral Neutral Neutral
SNPDryad score 0.36 0.68 0.0
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 T114S T114P T114A
fathmm Tolerated Tolerated Tolerated
fathmm score 2.0 1.92 2.04
fathmm converted rankscore 0.21473 0.23082 0.20808
AlphaMissense likely_benign likely_benign likely_benign
AlphaMissense score 0.0953 0.2218 0.064
CADD Neutral Neutral Neutral
CADD score 0.505482 1.820969 -0.988289
CADD phred 7.473 15.11 0.017
PROVEAN Tolerated Damaging Tolerated
PROVEAN score -1.4 -3.18 -1.39
MutationAssessor neutral medium neutral
MutationAssessor score 0.345 2.185 -0.6
EFIN SP Neutral Neutral Neutral
EFIN SP score 0.84 0.618 0.952
EFIN HD Neutral Neutral Neutral
EFIN HD score 0.81 0.314 0.886
MLC Deleterious Deleterious Deleterious
MLC score 0.57858048 0.57858048 0.57858048
PANTHER score . . .
PhD-SNP score . . .
APOGEE1 Neutral Neutral Neutral
APOGEE1 score 0.33 0.41 0.44
APOGEE2 Benign VUS- Benign
APOGEE2 score 0.022281682853002 0.387398046596952 0.0401688759009998
CAROL neutral neutral neutral
CAROL score 0.19 0.66 0.17
Condel deleterious deleterious deleterious
Condel score 0.88 0.61 0.92
COVEC WMV neutral neutral neutral
COVEC WMV score -6 -3 -6
MtoolBox neutral neutral neutral
MtoolBox DS 0.09 0.2 0.04
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.180211 0.492561 0.176709
DEOGEN2 converted rankscore 0.53147 0.81647 0.52674
Meta-SNP . . .
Meta-SNP score . . .
PolyPhen2 transf medium impact medium impact medium impact
PolyPhen2 transf score 0.81 0.24 1.99
SIFT_transf medium impact medium impact medium impact
SIFT transf score 0.48 -0.01 0.57
MutationAssessor transf medium impact medium impact low impact
MutationAssessor transf score -0.22 0.84 -1.33
CHASM Neutral Neutral Neutral
CHASM pvalue 0.52 0.37 0.37
CHASM FDR 0.8 0.8 0.8
ClinVar id 693288.0 . 9713.0
ClinVar Allele id 680178.0 . 24752.0
ClinVar CLNDISDB MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 . MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MedGen:C4016597
ClinVar CLNDN Leigh_syndrome . Leigh_syndrome|Parkinson_disease,_resistance_to
ClinVar CLNSIG Likely_benign . Benign
MITOMAP Disease Clinical info . . PD protective factor / longevity / altered cell pH / metabolic syndrome / breast cancer risk / Leigh Syndrome risk / ADHD / cognitive decline / SCA2 age of onset / Fuchs endothelial corneal dystrophy
MITOMAP Disease Status . . Reported; lineage L & M marker, also hg IJK
MITOMAP Disease Hom/Het ./. ./. +/-
MITOMAP General GenBank Freq 0.0115% . 42.3692%
MITOMAP General GenBank Seqs 7 . 25902
MITOMAP General Curated refs 22312186 . 11406419;15470367;1634041;29997041;17288645;9384601;19732751;17886251;8102506;18545700;15465027;19497304;17603766;24467713;15637703;18590963;16901986;17701054;28648514;18806273;23756438;31358833;24470521;23111160;10924403;1968873;1910259;8037701;8304347;15234467;32943110;19076426;11095989;18458168;16624503;18709563;27217714;10996007;15896721;17510395;20691156;20939899;34120353;11931086;11179019;16364244;21457906;19370763;21281460;8769114;9027481;31478599;20043118;19022198;12827453;16532388;11349229;11935318;20566709;33420243;16530527;15126279;18820594;1732158;18402672;15771256;15638829;15827561;18679013;15488317;12670626;1346260;12888043;7689389;8728098;9302261;1757091;19390621;1442494;19586946;19167085;18226984;16172508;17003408;3472733;15483642;20304802;11669538;17300996;19546379;19398658;17627010;8016139;1346259;8104867;29486301;18639500;12031626;12375058;17331239;31798871;7942855;18177933;31797714;20067846;17264866;21978175;15108120;19050702;11553319;18223312;7688932;19188198;17033820;16140977;16418878;20728388;15804362;17452034;9443868;22561905;32094358;16705548;17072496;17698030;7901141;19026397;17406640;19151382;11571560;19062322;12022039;7864851;8147435;16404693;17942074;17620498;7688933;15286228;18775412;12713143;7635294;18286226;16895436;16773565;18931934;15694598;10737123;17617636;19427920;25199876;15210164;18262047;12436196;12618962;16960846;16955414;15707996;8978068;15670746;22333566;15555598;8302846;16048457;19092698;1899574;3201231;18668590;17429907;18322915;18853457;8659531;11820805;15786469;18691441;18587274;17496137;15262184;1463007;19130794;19818876;35146807;19703591;12112086;10712231;17434142;15591266;15708009;31152278;20627642;34045735;23304069;11938495;28793231;7646496;7689388;16714301;2043137;10680807;12802679;17620140;19733221;35801081;24667788;17698299;17174475;15975594;3025745;16050984;18386806;24917144;19324017;18810306;7874114;16955413;29987491;10936107;1764087;17341440;30446962;16982817
MITOMAP Variant Class polymorphism . polymorphism;disease
gnomAD 3.1 AN 56433.0 56433.0 56170.0
gnomAD 3.1 AC Homo 13.0 0.0 23506.0
gnomAD 3.1 AF Hom 0.000230362 0.0 0.41848
gnomAD 3.1 AC Het 0.0 0.0 8.0
gnomAD 3.1 AF Het 0.0 0.0 0.000142425
gnomAD 3.1 filter PASS npg PASS
HelixMTdb AC Hom 58.0 . 49322.0
HelixMTdb AF Hom 0.00029594405 . 0.2516647
HelixMTdb AC Het 0.0 . 289.0
HelixMTdb AF Het 0.0 . 0.0014746177
HelixMTdb mean ARF . . 0.83138
HelixMTdb max ARF . . 0.97203
ToMMo 54KJPN AC 5630 255 .
ToMMo 54KJPN AF 0.103679 0.004696 .
ToMMo 54KJPN AN 54302 54302 .
COSMIC 90 . . .
dbSNP 156 id rs2853826 . rs2853826
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