MitImpact id |
MI.23738 |
MI.23740 |
MI.23739 |
Chr |
chrM |
chrM |
chrM |
Start |
14459 |
14459 |
14459 |
Ref |
G |
G |
G |
Alt |
A |
C |
T |
Gene symbol |
MT-ND6 |
MT-ND6 |
MT-ND6 |
Extended annotation |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 |
Gene position |
215 |
215 |
215 |
Gene start |
14149 |
14149 |
14149 |
Gene end |
14673 |
14673 |
14673 |
Gene strand |
- |
- |
- |
Codon substitution |
GCG/GTG |
GCG/GGG |
GCG/GAG |
AA position |
72 |
72 |
72 |
AA ref |
A |
A |
A |
AA alt |
V |
G |
E |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516006 |
516006 |
516006 |
HGVS |
NC_012920.1:g.14459G>A |
NC_012920.1:g.14459G>C |
NC_012920.1:g.14459G>T |
HGNC id |
7462 |
7462 |
7462 |
Respiratory Chain complex |
I |
I |
I |
Ensembl gene id |
ENSG00000198695 |
ENSG00000198695 |
ENSG00000198695 |
Ensembl transcript id |
ENST00000361681 |
ENST00000361681 |
ENST00000361681 |
Ensembl protein id |
ENSP00000354665 |
ENSP00000354665 |
ENSP00000354665 |
Uniprot id |
P03923 |
P03923 |
P03923 |
Uniprot name |
NU6M_HUMAN |
NU6M_HUMAN |
NU6M_HUMAN |
Ncbi gene id |
4541 |
4541 |
4541 |
Ncbi protein id |
YP_003024037.1 |
YP_003024037.1 |
YP_003024037.1 |
PhyloP 100V |
4.419 |
4.419 |
4.419 |
PhyloP 470Way |
0.848 |
0.848 |
0.848 |
PhastCons 100V |
1 |
1 |
1 |
PhastCons 470Way |
0.976 |
0.976 |
0.976 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1 |
1 |
1 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.3 |
0.2 |
0.25 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.001 |
0.002 |
0.0 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.4 |
0.25 |
0.15 |
VEST FDR |
0.5 |
0.45 |
0.4 |
Mitoclass.1 |
damaging |
damaging |
damaging |
SNPDryad |
Neutral |
Neutral |
Pathogenic |
SNPDryad score |
0.81 |
0.8 |
0.99 |
MutationTaster |
Disease |
Polymorphism |
Disease |
MutationTaster score |
1 |
0.999822 |
1 |
MutationTaster converted rankscore |
0.81001 |
0.20203 |
0.81001 |
MutationTaster model |
without_aae |
simple_aae |
complex_aae |
MutationTaster AAE |
. |
S37R |
S37* |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
2.27 |
2.17 |
2.16 |
fathmm converted rankscore |
0.17431 |
0.19020 |
0.19166 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.8611 |
0.7519 |
0.9792 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
4.081497 |
3.564245 |
3.883665 |
CADD phred |
23.7 |
23.1 |
23.5 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-3.98 |
-3.98 |
-4.98 |
MutationAssessor |
medium |
medium |
high |
MutationAssessor score |
3.215 |
3.07 |
3.765 |
EFIN SP |
Damaging |
Damaging |
Damaging |
EFIN SP score |
0.076 |
0.46 |
0.352 |
EFIN HD |
Damaging |
Neutral |
Damaging |
EFIN HD score |
0.15 |
0.46 |
0.194 |
MLC |
Deleterious |
Deleterious |
Deleterious |
MLC score |
0.83300139 |
0.83300139 |
0.83300139 |
PANTHER score |
0.614 |
. |
. |
PhD-SNP score |
0.919 |
. |
. |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.93 |
0.55 |
0.63 |
APOGEE2 |
Pathogenic |
VUS+ |
Likely-pathogenic |
APOGEE2 score |
0.925252754722916 |
0.712099908387641 |
0.767269110274587 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1.0 |
1.0 |
1.0 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.15 |
0.1 |
0.13 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
2 |
2 |
2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.87 |
0.84 |
0.9 |
DEOGEN2 |
Damaging |
Damaging |
Damaging |
DEOGEN2 score |
0.613447 |
0.585451 |
0.73832 |
DEOGEN2 converted rankscore |
0.87783 |
0.86490 |
0.92731 |
Meta-SNP |
Disease |
. |
. |
Meta-SNP score |
0.918 |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-3.55 |
-3.55 |
-3.55 |
SIFT_transf |
medium impact |
medium impact |
medium impact |
SIFT transf score |
0 |
-0.13 |
-0.06 |
MutationAssessor transf |
medium impact |
high impact |
high impact |
MutationAssessor transf score |
1.88 |
2.18 |
2.18 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.86 |
0.81 |
0.8 |
CHASM FDR |
0.9 |
0.85 |
0.85 |
ClinVar id |
9689.0 |
. |
. |
ClinVar Allele id |
24728.0 |
. |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MONDO:MONDO:0010772,MedGen:C1839040,OMIM:500001,Orphanet:99718|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MedGen:C1838951 |
. |
. |
ClinVar CLNDN |
Mitochondrial_disease|Leber_optic_atrophy_and_dystonia|Leber_optic_atrophy|Leigh_syndrome|Leigh_syndrome_due_to_mitochondrial_complex_I_deficiency |
. |
. |
ClinVar CLNSIG |
Pathogenic |
. |
. |
MITOMAP Disease Clinical info |
LDYT / Leigh Disease / dystonia / carotid atherosclerosis risk |
. |
. |
MITOMAP Disease Status |
Cfrm [P] |
. |
. |
MITOMAP Disease Hom/Het |
+/+ |
./. |
./. |
MITOMAP General GenBank Freq |
0.0049% |
. |
. |
MITOMAP General GenBank Seqs |
3 |
. |
. |
MITOMAP General Curated refs |
10426138;18674747;29670672;37038312;28429146;30461153;30128709;10072046;7654063;7760326;14520659;10894222;18402672;21067478;28951770;19714555;15972314;21749722;32220313;23847141;24398099;33717984;29253894;31221418;22879922;8622678;14735585;26741492;20301353;12205655;19268652;8680405;14735584;32045392;8016139;20064630;15126312;23874496;25834827;29987491;21364701;30095618;21457906;37587338;29408632 |
. |
. |
MITOMAP Variant Class |
disease |
. |
. |
gnomAD 3.1 AN |
56432.0 |
56431.0 |
. |
gnomAD 3.1 AC Homo |
0.0 |
0.0 |
. |
gnomAD 3.1 AF Hom |
0.0 |
0.0 |
. |
gnomAD 3.1 AC Het |
1.0 |
0.0 |
. |
gnomAD 3.1 AF Het |
1.77204e-05 |
0.0 |
. |
gnomAD 3.1 filter |
PASS |
npg |
. |
HelixMTdb AC Hom |
0.0 |
. |
. |
HelixMTdb AF Hom |
0.0 |
. |
. |
HelixMTdb AC Het |
1.0 |
. |
. |
HelixMTdb AF Het |
5.1024836e-06 |
. |
. |
HelixMTdb mean ARF |
0.14286 |
. |
. |
HelixMTdb max ARF |
0.14286 |
. |
. |
ToMMo 54KJPN AC |
. |
. |
. |
ToMMo 54KJPN AF |
. |
. |
. |
ToMMo 54KJPN AN |
. |
. |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs199476105 |
. |
. |