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 |
. |
. |