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11778 (G > A)

General info

Mitimpact ID
MI.18470
Chr
chrM
Start
11778
Ref
G
Alt
A
Gene symbol
MT-ND4 Extended gene annotation
Gene position
1019
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
CGC/CAC
AA pos
340
AA ref
R
AA alt
H
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11778G>A
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
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Powered by MitoWheel

Conservation

PhyloP 100v
3.757 Conservation Score
PhyloP 470way
-1.057 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.009 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
Pathogenic Score and details of the predictor
MutationTaster
Disease automatic Score and details of the predictor
fathmm
Tolerated Score and details of the predictor
AlphaMissense
Likely pathogenic Score and details of the predictor
CADD
Deleterious 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
Damaging Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
Disease Score and details of the predictor
PhD-SNP
Disease Score and details of the predictor

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Pathogenic Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious 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
Disease Score and details of the meta-predictor

Cancer-specific predictors

PolyPhen2 transf
Low impact Score and details of the cancer-specific predictor
SIFT transf
Low impact Score and details of the cancer-specific predictor
MutationAssessor transf
High 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
9708
Clinvar ALLELEID
24747
Clinvar CLNDISDB
Medgen:cn169374;

mondo:mondo:0010640, medgen:c1839891, omim:308905, orphanet:104;

medgen:cn517202;

mondo:mondo:0044970, medgen:c0751651, orphanet:68380;

human phenotype ontology:hp:0001086, human phenotype ontology:hp:0001112, mondo:mondo:0010788, medgen:c0917796, omim:535000, orphanet:104
Clinvar CLNDN
Not specified;

leber optic atrophy, susceptibility to;

not provided;

mitochondrial disease;

leber optic atrophy
Clinvar CLNSIG
Pathogenic
MITOMAP Allele
11778G>A
MITOMAP Disease Clinical info
Lhon / progressive dystonia
MITOMAP Disease Status
Cfrm [p]
MITOMAP Disease Hom/Het
+/+
MITOMAP General GenBank Freq
0.3108%
MITOMAP General GenBank Seqs
190
MITOMAP General GenBank Curated refs
10520236 32969847 16083845 30516647 35791239 37988592 8448903 10976107 11741983 25342621 20301353 26892229 1734726 8680405 20019878 29955763 15060117 26438859 15033723 29587845 7745422 30369864 19726426 30597069 36358916 8250088 8071960 2286378 8195807 7710535 26647310 1763894 22194643 32284191 27177320 27746671 9302261 27787713 20837795 2346190 19268652 17003408 8489402 26959136 20064630 8023847 1532593 16083844 14671420 20809775 2566116 7735876 20632027 26606867 29649796 31939618 1575231 33185792 15548492 15026512 7612556 17942074 14620678 7649539 30968497 7635294 11754070 22410442 32991883 7770132 20123042 35623556 30304398 8101084 12464729 18320530 37878684 31040363 7916404 21414825 12464728 12807863 33477675 32991388 18214789 8457609 33584522 1353825 12815198 8071952 28392196 36350566 15126312 32259370 30572950 9561832 34122299 16331570 1635296 8931573 10545708 15720387 11169561 28093355 2390098 33298565 1977373 16120317 18771762 10939569 17886296 9012411 2222273 1770665 15629832 34584057 8255489 1900003 14748908 23091534 7611298 31817256 19015050 17122117 27071925 37587338 20676915 16705513 34467602 38710404 29427840 19370763 28716668 1895564 37737178 15282189 16532388 29049835 34415266 7629530 8600429 10216058 8556281 20454697 16617593 8240103 29047345 29253894 21788663 30081212 29428506 12888043 34417770 20491810 24525545 1770533 8053461 7599218 32704028 20471050 8662757 33159657 8240101 7617199 31584786 15883259 20625049 17197509 27749593 20728388 31776719 27721048 32516135 26404827 17724295 7603534 7901141 12446713 15342361 19026397 8401538 11754915 22108605 36565700 23297368 20232220 11074292 11001192 21063443 36565701 8489411 12436196 15728653 18363168 34670133 20599858 11523562 10413253 18674747 8742999 37038312 28481993 32105823 32723871 18848389 17460303 28314831 4003041 19319978 11331900 8165962 22669418 30831606 8449667 32740724 16528519 11853713 1959619 20211598 22039503 17204919 9175737 8755941 19800080 11579587 7926004 2817063 18676632 10611124 28994349 27119776 21482521 24508359 32220313 17479363 18806273 19525327 38768545 29890302 18647627 28040497 28640805 33706792 14750573 16624503 15896721 20691156 11124301 21694444 31226990 7823072 12185132 15282179 36361994 26410888 29980632 24404670 35190400 33552719 12518276 2566021 19936068 34573281 18235013 9541429 27847334 29116953 25909222 32096343 7832241 29554000 12379308 25192510 33911213 7924787 2575667 10426138 16829155 27427386 20435583 30936345 16477364 36827238 2346203 34146515 17406640 7801223 8213820 35723074 16380918 1937476 21253496 7601652 9412783 8474822 8320863 3201231 11162998 20628600 32887465 26605371 8941270 19255150 28219504 34667002 8240102 1444915 28650878 30558558 12402246 16050984 22523243 27127184 34915201 19710181 8024249 27631475 25338955 18619472 1346348 7853025 22110754 31718067 16044424 17366829 19098324 9685604 28647203 27159682 21067478 33709232 15629831 29133642 38346855 31932089 16972023 10087740 20407791 12711217 7707093 2039048 18216301 8270249 12638016 29454364 8023848 16120371 31727544 21457906 2757028 17292333 1352537 8118464 9125387 19247386 10636656 15804271 11937918 7639060 33451738 17573650 12402249 34168607 9541428 17300996 25053773 34310464 7617193 7763260 9150158 34673906 21397051 21859767 12560876 8867076 15838728 29189152 34108929 35104579 7814218 7977345 17296905 15972314 23847141 18775412 8103501 24369379 20943885 24457989 35778412 1866007 12409182 16564802 28991104 20111055 7821467 15707996 29387390 16431939 29983856 35690699 16120433 35858578 7760326 27426279 21887510 18070226 16148621 32504279 33095398 32277753 31896800 28233183 21145289 8659512 21810891 17072496 11339587
MITOMAP Variant Class
disease
Gnomad AN
56423
Gnomad AC hom
11
Gnomad AF hom
0.0001949
Gnomad AC het
13
Gnomad AF het
0.0002304
Gnomad filter
Pass
HelixMTdb AC hom
44
HelixMTdb AF hom
0.0002245
HelixMTdb AC het
34
HelixMTdb AF het
0.0001734
HelixMTdb mean ARF
0.37469
HelixMTdb max ARF
0.91005
ToMMo JPN54K AC
27
ToMMo JPN54K AF
0.000497
ToMMo JPN54K AN
54302
COSMIC 90
.
dbSNP 156
rs199476112

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
.

11778 (G > C)

General info

Mitimpact ID
MI.18469
Chr
chrM
Start
11778
Ref
G
Alt
C
Gene symbol
MT-ND4 Extended gene annotation
Gene position
1019
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
CGC/CCC
AA pos
340
AA ref
R
AA alt
P
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11778G>C
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.757 Conservation Score
PhyloP 470way
-1.057 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.009 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious Score and details of the predictor
SIFT4G
Damaging Score and details of the predictor
VEST
Pathogenic Score and details of the predictor
MitoClass 1
Damaging Score and details of the predictor
SNPDryad
Pathogenic 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
Deleterious 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
Damaging Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-pathogenic Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious 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
Low impact Score and details of the cancer-specific predictor
SIFT transf
Low impact Score and details of the cancer-specific predictor
MutationAssessor transf
High 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
11778G>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
.

11778 (G > T)

General info

Mitimpact ID
MI.18468
Chr
chrM
Start
11778
Ref
G
Alt
T
Gene symbol
MT-ND4 Extended gene annotation
Gene position
1019
Gene start
10760
Gene end
12137
Gene strand
+
Codon substitution
CGC/CTC
AA pos
340
AA ref
R
AA alt
L
Functional effect
missense
OMIM ID
516003
HGVS
NC_012920.1:g.11778G>T
HGNC ID
7459
RC complex
I
Ensembl gene ID
ENSG00000198886
Ensembl protein ID
ENSP00000354961
Ensembl transcript ID
ENST00000361381
Uniprot ID
P03905
Uniprot name
NU4M_HUMAN
Ncbi gene ID
4538
Ncbi protein ID
YP_003024035.1
Powered by NGL Viewer
Powered by MitoWheel

Conservation

PhyloP 100v
3.757 Conservation Score
PhyloP 470way
-1.057 Conservation Score
PhastCons 100v
1 Conservation Score
PhastCons 470way
0.009 Conservation Score

Pathogenicity predictors

PolyPhen2
Probably damaging Score and details of the predictor
SIFT
Deleterious 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
Pathogenic 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
Deleterious 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
Damaging Score and details of the predictor
EFIN HD
Damaging Score and details of the predictor
MLC
Deleterious Score and details of the predictor
PANTHER
.
PhD-SNP
.

Pathogenicity meta-predictors

APOGEE1
Pathogenic Score and details of the meta-predictor
APOGEE2
Likely-pathogenic Score and details of the meta-predictor
CAROL
Deleterious Score and details of the meta-predictor
Condel
Neutral Score and details of the meta-predictor
COVEC WMV
Deleterious 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
Low impact Score and details of the cancer-specific predictor
SIFT transf
Low impact Score and details of the cancer-specific predictor
MutationAssessor transf
High 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
11778G>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
.
~ 11778 (G/A) 11778 (G/C) 11778 (G/T)
~ 11778 (CGC/CAC) 11778 (CGC/CCC) 11778 (CGC/CTC)
MitImpact id MI.18470 MI.18469 MI.18468
Chr chrM chrM chrM
Start 11778 11778 11778
Ref G G G
Alt A C T
Gene symbol MT-ND4 MT-ND4 MT-ND4
Extended annotation mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4
Gene position 1019 1019 1019
Gene start 10760 10760 10760
Gene end 12137 12137 12137
Gene strand + + +
Codon substitution CGC/CAC CGC/CCC CGC/CTC
AA position 340 340 340
AA ref R R R
AA alt H P L
Functional effect general missense missense missense
Functional effect detailed missense missense missense
OMIM id 516003 516003 516003
HGVS NC_012920.1:g.11778G>A NC_012920.1:g.11778G>C NC_012920.1:g.11778G>T
HGNC id 7459 7459 7459
Respiratory Chain complex I I I
Ensembl gene id ENSG00000198886 ENSG00000198886 ENSG00000198886
Ensembl transcript id ENST00000361381 ENST00000361381 ENST00000361381
Ensembl protein id ENSP00000354961 ENSP00000354961 ENSP00000354961
Uniprot id P03905 P03905 P03905
Uniprot name NU4M_HUMAN NU4M_HUMAN NU4M_HUMAN
Ncbi gene id 4538 4538 4538
Ncbi protein id YP_003024035.1 YP_003024035.1 YP_003024035.1
PhyloP 100V 3.757 3.757 3.757
PhyloP 470Way -1.057 -1.057 -1.057
PhastCons 100V 1 1 1
PhastCons 470Way 0.009 0.009 0.009
PolyPhen2 probably_damaging probably_damaging probably_damaging
PolyPhen2 score 1.0 1.0 1.0
SIFT deleterious deleterious deleterious
SIFT score 0.0 0.0 0.0
SIFT4G Damaging Damaging Damaging
SIFT4G score 0.0 0.001 0.0
VEST Neutral Pathogenic Neutral
VEST pvalue 0.21 0.03 0.06
VEST FDR 0.45 0.35 0.35
Mitoclass.1 damaging damaging damaging
SNPDryad Pathogenic Pathogenic Pathogenic
SNPDryad score 1.0 0.99 1.0
MutationTaster Disease automatic Polymorphism Polymorphism
MutationTaster score 5.51739e-05 0.99992 0.999975
MutationTaster converted rankscore 0.19238 0.19486 0.18612
MutationTaster model complex_aae complex_aae complex_aae
MutationTaster AAE R340H R340P R340L
fathmm Tolerated Tolerated Tolerated
fathmm score 4.44 4.44 4.45
fathmm converted rankscore 0.02139 0.02139 0.02121
AlphaMissense likely_pathogenic likely_pathogenic likely_pathogenic
AlphaMissense score 0.8615 0.987 0.9724
CADD Deleterious Deleterious Deleterious
CADD score 4.556305 4.349779 4.461447
CADD phred 24.4 24.1 24.2
PROVEAN Damaging Damaging Damaging
PROVEAN score -4.74 -6.64 -6.64
MutationAssessor high high medium
MutationAssessor score 5.07 5.07 3.405
EFIN SP Damaging Damaging Damaging
EFIN SP score 0.178 0.402 0.394
EFIN HD Damaging Damaging Damaging
EFIN HD score 0.126 0.196 0.258
MLC Deleterious Deleterious Deleterious
MLC score 0.87926248 0.87926248 0.87926248
PANTHER score 0.63 . .
PhD-SNP score 0.933 . .
APOGEE1 Pathogenic Pathogenic Pathogenic
APOGEE1 score 0.97 0.76 0.81
APOGEE2 Pathogenic Likely-pathogenic Likely-pathogenic
APOGEE2 score 0.926042202256757 0.837464517623008 0.818322642772869
CAROL deleterious deleterious deleterious
CAROL score 1.0 1.0 1.0
Condel neutral neutral neutral
Condel score 0.0 0.0 0.0
COVEC WMV deleterious deleterious deleterious
COVEC WMV score 6 6 6
MtoolBox deleterious deleterious deleterious
MtoolBox DS 0.85 0.83 0.84
DEOGEN2 Tolerated Tolerated Tolerated
DEOGEN2 score 0.237204 0.395348 0.209901
DEOGEN2 converted rankscore 0.60484 0.75425 0.57024
Meta-SNP Disease . .
Meta-SNP score 0.724 . .
PolyPhen2 transf low impact low impact low impact
PolyPhen2 transf score -3.54 -3.54 -3.54
SIFT_transf low impact low impact low impact
SIFT transf score -1.48 -1.48 -1.48
MutationAssessor transf high impact high impact high impact
MutationAssessor transf score 3.44 3.44 2.4
CHASM Neutral Neutral Neutral
CHASM pvalue 0.77 0.13 0.02
CHASM FDR 0.85 0.8 0.8
ClinVar id 9708.0 . .
ClinVar Allele id 24747.0 . .
ClinVar CLNDISDB MedGen:CN169374|MONDO:MONDO:0010640,MedGen:C1839891,OMIM:308905,Orphanet:104|MedGen:CN517202|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 . .
ClinVar CLNDN not_specified|Leber_optic_atrophy,_susceptibility_to|not_provided|Mitochondrial_disease|Leber_optic_atrophy . .
ClinVar CLNSIG Pathogenic . .
MITOMAP Disease Clinical info LHON / Progressive Dystonia . .
MITOMAP Disease Status Cfrm [P] . .
MITOMAP Disease Hom/Het +/+ ./. ./.
MITOMAP General GenBank Freq 0.3108% . .
MITOMAP General GenBank Seqs 190 . .
MITOMAP General Curated refs 10520236;32969847;16083845;30516647;35791239;37988592;8448903;10976107;11741983;25342621;20301353;26892229;1734726;8680405;20019878;29955763;15060117;26438859;15033723;29587845;7745422;30369864;19726426;30597069;36358916;8250088;8071960;2286378;8195807;7710535;26647310;1763894;22194643;32284191;27177320;27746671;9302261;27787713;20837795;2346190;19268652;17003408;8489402;26959136;20064630;8023847;1532593;16083844;14671420;20809775;2566116;7735876;20632027;26606867;29649796;31939618;1575231;33185792;15548492;15026512;7612556;17942074;14620678;7649539;30968497;7635294;11754070;22410442;32991883;7770132;20123042;35623556;30304398;8101084;12464729;18320530;37878684;31040363;7916404;21414825;12464728;12807863;33477675;32991388;18214789;8457609;33584522;1353825;12815198;8071952;28392196;36350566;15126312;32259370;30572950;9561832;34122299;16331570;1635296;8931573;10545708;15720387;11169561;28093355;2390098;33298565;1977373;16120317;18771762;10939569;17886296;9012411;2222273;1770665;15629832;34584057;8255489;1900003;14748908;23091534;7611298;31817256;19015050;17122117;27071925;37587338;20676915;16705513;34467602;38710404;29427840;19370763;28716668;1895564;37737178;15282189;16532388;29049835;34415266;7629530;8600429;10216058;8556281;20454697;16617593;8240103;29047345;29253894;21788663;30081212;29428506;12888043;34417770;20491810;24525545;1770533;8053461;7599218;32704028;20471050;8662757;33159657;8240101;7617199;31584786;15883259;20625049;17197509;27749593;20728388;31776719;27721048;32516135;26404827;17724295;7603534;7901141;12446713;15342361;19026397;8401538;11754915;22108605;36565700;23297368;20232220;11074292;11001192;21063443;36565701;8489411;12436196;15728653;18363168;34670133;20599858;11523562;10413253;18674747;8742999;37038312;28481993;32105823;32723871;18848389;17460303;28314831;4003041;19319978;11331900;8165962;22669418;30831606;8449667;32740724;16528519;11853713;1959619;20211598;22039503;17204919;9175737;8755941;19800080;11579587;7926004;2817063;18676632;10611124;28994349;27119776;21482521;24508359;32220313;17479363;18806273;19525327;38768545;29890302;18647627;28040497;28640805;33706792;14750573;16624503;15896721;20691156;11124301;21694444;31226990;7823072;12185132;15282179;36361994;26410888;29980632;24404670;35190400;33552719;12518276;2566021;19936068;34573281;18235013;9541429;27847334;29116953;25909222;32096343;7832241;29554000;12379308;25192510;33911213;7924787;2575667;10426138;16829155;27427386;20435583;30936345;16477364;36827238;2346203;34146515;17406640;7801223;8213820;35723074;16380918;1937476;21253496;7601652;9412783;8474822;8320863;3201231;11162998;20628600;32887465;26605371;8941270;19255150;28219504;34667002;8240102;1444915;28650878;30558558;12402246;16050984;22523243;27127184;34915201;19710181;8024249;27631475;25338955;18619472;1346348;7853025;22110754;31718067;16044424;17366829;19098324;9685604;28647203;27159682;21067478;33709232;15629831;29133642;38346855;31932089;16972023;10087740;20407791;12711217;7707093;2039048;18216301;8270249;12638016;29454364;8023848;16120371;31727544;21457906;2757028;17292333;1352537;8118464;9125387;19247386;10636656;15804271;11937918;7639060;33451738;17573650;12402249;34168607;9541428;17300996;25053773;34310464;7617193;7763260;9150158;34673906;21397051;21859767;12560876;8867076;15838728;29189152;34108929;35104579;7814218;7977345;17296905;15972314;23847141;18775412;8103501;24369379;20943885;24457989;35778412;1866007;12409182;16564802;28991104;20111055;7821467;15707996;29387390;16431939;29983856;35690699;16120433;35858578;7760326;27426279;21887510;18070226;16148621;32504279;33095398;32277753;31896800;28233183;21145289;8659512;21810891;17072496;11339587 . .
MITOMAP Variant Class disease . .
gnomAD 3.1 AN 56423.0 . .
gnomAD 3.1 AC Homo 11.0 . .
gnomAD 3.1 AF Hom 0.000194956 . .
gnomAD 3.1 AC Het 13.0 . .
gnomAD 3.1 AF Het 0.000230402 . .
gnomAD 3.1 filter PASS . .
HelixMTdb AC Hom 44.0 . .
HelixMTdb AF Hom 0.00022450926 . .
HelixMTdb AC Het 34.0 . .
HelixMTdb AF Het 0.00017348444 . .
HelixMTdb mean ARF 0.37469 . .
HelixMTdb max ARF 0.91005 . .
ToMMo 54KJPN AC 27 . .
ToMMo 54KJPN AF 0.000497 . .
ToMMo 54KJPN AN 54302 . .
COSMIC 90 . . .
dbSNP 156 id rs199476112 . .
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