MitImpact id |
MI.23971 |
MI.23970 |
MI.23969 |
Chr |
chrM |
chrM |
chrM |
Start |
14568 |
14568 |
14568 |
Ref |
C |
C |
C |
Alt |
T |
A |
G |
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 |
106 |
106 |
106 |
Gene start |
14149 |
14149 |
14149 |
Gene end |
14673 |
14673 |
14673 |
Gene strand |
- |
- |
- |
Codon substitution |
GGT/AGT |
GGT/TGT |
GGT/CGT |
AA position |
36 |
36 |
36 |
AA ref |
G |
G |
G |
AA alt |
S |
C |
R |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516006 |
516006 |
516006 |
HGVS |
NC_012920.1:g.14568C>T |
NC_012920.1:g.14568C>A |
NC_012920.1:g.14568C>G |
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 |
2.344 |
2.344 |
2.344 |
PhyloP 470Way |
0.65 |
0.65 |
0.65 |
PhastCons 100V |
0.907 |
0.907 |
0.907 |
PhastCons 470Way |
0.336 |
0.336 |
0.336 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1 |
1 |
1 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.64 |
0.23 |
0.33 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.036 |
0.001 |
0.0 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.42 |
0.21 |
0.13 |
VEST FDR |
0.55 |
0.45 |
0.4 |
Mitoclass.1 |
neutral |
damaging |
damaging |
SNPDryad |
Pathogenic |
Pathogenic |
Pathogenic |
SNPDryad score |
1.0 |
0.97 |
1.0 |
MutationTaster |
Disease |
Disease |
Disease |
MutationTaster score |
1 |
1 |
1 |
MutationTaster converted rankscore |
0.81001 |
0.81001 |
0.81001 |
MutationTaster model |
complex_aae |
complex_aae |
complex_aae |
MutationTaster AAE |
R1M |
R1M |
R1M |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
2.47 |
2.31 |
2.29 |
fathmm converted rankscore |
0.14783 |
0.16794 |
0.17113 |
AlphaMissense |
ambiguous |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.5263 |
0.8987 |
0.9918 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
4.270399 |
4.536784 |
3.986131 |
CADD phred |
24.0 |
24.3 |
23.6 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-5.99 |
-8.98 |
-7.98 |
MutationAssessor |
neutral |
medium |
medium |
MutationAssessor score |
0.565 |
2.19 |
2.995 |
EFIN SP |
Damaging |
Neutral |
Neutral |
EFIN SP score |
0.266 |
0.672 |
0.612 |
EFIN HD |
Damaging |
Damaging |
Damaging |
EFIN HD score |
0.228 |
0.274 |
0.26 |
MLC |
Neutral |
Neutral |
Neutral |
MLC score |
0.13377392 |
0.13377392 |
0.13377392 |
PANTHER score |
0.225 |
. |
. |
PhD-SNP score |
0.704 |
. |
. |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.9 |
0.53 |
0.57 |
APOGEE2 |
Likely-pathogenic |
VUS+ |
Likely-pathogenic |
APOGEE2 score |
0.834105016797609 |
0.711721415386645 |
0.75963680264494 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1.0 |
1.0 |
1.0 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.32 |
0.12 |
0.17 |
COVEC WMV |
neutral |
deleterious |
deleterious |
COVEC WMV score |
-2 |
1 |
2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.73 |
0.88 |
0.89 |
DEOGEN2 |
Damaging |
Damaging |
Damaging |
DEOGEN2 score |
0.530048 |
0.573241 |
0.69744 |
DEOGEN2 converted rankscore |
0.83721 |
0.85905 |
0.91258 |
Meta-SNP |
Neutral |
. |
. |
Meta-SNP score |
0.352 |
. |
. |
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 |
0.35 |
-0.09 |
0.04 |
MutationAssessor transf |
medium impact |
medium impact |
medium impact |
MutationAssessor transf score |
0.3 |
1.58 |
1.88 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.77 |
0.79 |
0.76 |
CHASM FDR |
0.85 |
0.85 |
0.85 |
ClinVar id |
65515.0 |
. |
. |
ClinVar Allele id |
76423.0 |
. |
. |
ClinVar CLNDISDB |
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 |
Mitochondrial_disease|Leber_optic_atrophy |
. |
. |
ClinVar CLNSIG |
Likely_pathogenic |
. |
. |
MITOMAP Disease Clinical info |
LHON |
. |
. |
MITOMAP Disease Status |
Cfrm [LP] |
. |
. |
MITOMAP Disease Hom/Het |
+/- |
./. |
./. |
MITOMAP General GenBank Freq |
0.0098% |
0.0% |
. |
MITOMAP General GenBank Seqs |
6 |
0 |
. |
MITOMAP General Curated refs |
22879922;29253894;12150954;20064630;15972314;19319978;20301353;12324878;9177303;10447650 |
. |
. |
MITOMAP Variant Class |
disease |
polymorphism |
. |
gnomAD 3.1 AN |
56434.0 |
56433.0 |
. |
gnomAD 3.1 AC Homo |
1.0 |
0.0 |
. |
gnomAD 3.1 AF Hom |
1.77198e-05 |
0.0 |
. |
gnomAD 3.1 AC Het |
1.0 |
0.0 |
. |
gnomAD 3.1 AF Het |
1.77198e-05 |
0.0 |
. |
gnomAD 3.1 filter |
PASS |
npg |
. |
HelixMTdb AC Hom |
2.0 |
0.0 |
. |
HelixMTdb AF Hom |
1.0204967e-05 |
0.0 |
. |
HelixMTdb AC Het |
1.0 |
1.0 |
. |
HelixMTdb AF Het |
5.1024836e-06 |
5.1024836e-06 |
. |
HelixMTdb mean ARF |
0.32326 |
0.14658 |
. |
HelixMTdb max ARF |
0.32326 |
0.14658 |
. |
ToMMo 54KJPN AC |
. |
. |
. |
ToMMo 54KJPN AF |
. |
. |
. |
ToMMo 54KJPN AN |
. |
. |
. |
COSMIC 90 |
. |
COSM1138273 |
. |
dbSNP 156 id |
rs397515506 |
. |
. |