MitImpact id |
MI.23468 |
MI.23467 |
MI.23466 |
Chr |
chrM |
chrM |
chrM |
Start |
14325 |
14325 |
14325 |
Ref |
T |
T |
T |
Alt |
C |
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 |
349 |
349 |
349 |
Gene start |
14149 |
14149 |
14149 |
Gene end |
14673 |
14673 |
14673 |
Gene strand |
- |
- |
- |
Codon substitution |
AAC/GAC |
AAC/TAC |
AAC/CAC |
AA position |
117 |
117 |
117 |
AA ref |
N |
N |
N |
AA alt |
D |
Y |
H |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516006 |
516006 |
516006 |
HGVS |
NC_012920.1:g.14325T>C |
NC_012920.1:g.14325T>A |
NC_012920.1:g.14325T>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 |
-3.847 |
-3.847 |
-3.847 |
PhyloP 470Way |
0.361 |
0.361 |
0.361 |
PhastCons 100V |
0 |
0 |
0 |
PhastCons 470Way |
0.009 |
0.009 |
0.009 |
PolyPhen2 |
possibly_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
0.49 |
0.94 |
0.91 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.42 |
1.0 |
0.56 |
SIFT4G |
Tolerated |
Tolerated |
Tolerated |
SIFT4G score |
0.649 |
0.052 |
0.104 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.59 |
0.32 |
0.46 |
VEST FDR |
0.65 |
0.5 |
0.55 |
Mitoclass.1 |
neutral |
neutral |
neutral |
SNPDryad |
Neutral |
Neutral |
Neutral |
SNPDryad score |
0.11 |
0.76 |
0.41 |
MutationTaster |
Disease automatic |
Polymorphism |
Polymorphism |
MutationTaster score |
4.63429e-08 |
1 |
1 |
MutationTaster converted rankscore |
0.08975 |
0.08975 |
0.08975 |
MutationTaster model |
without_aae |
without_aae |
without_aae |
MutationTaster AAE |
. |
. |
. |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
1.71 |
1.65 |
1.65 |
fathmm converted rankscore |
0.26737 |
0.27650 |
0.27650 |
AlphaMissense |
likely_benign |
likely_benign |
likely_benign |
AlphaMissense score |
0.0675 |
0.2095 |
0.1226 |
CADD |
Neutral |
Deleterious |
Neutral |
CADD score |
-0.044599 |
2.894288 |
2.255099 |
CADD phred |
2.178 |
21.8 |
17.87 |
PROVEAN |
Tolerated |
Damaging |
Tolerated |
PROVEAN score |
0.7 |
-2.72 |
-1.41 |
MutationAssessor |
neutral |
neutral |
neutral |
MutationAssessor score |
0.205 |
-1.05 |
0.345 |
EFIN SP |
Neutral |
Neutral |
Neutral |
EFIN SP score |
0.914 |
0.878 |
0.804 |
EFIN HD |
Neutral |
Neutral |
Neutral |
EFIN HD score |
0.984 |
0.83 |
0.64 |
MLC |
Neutral |
Neutral |
Neutral |
MLC score |
0.26259883 |
0.26259883 |
0.26259883 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Pathogenic |
Neutral |
Neutral |
APOGEE1 score |
0.54 |
0.28 |
0.27 |
APOGEE2 |
Benign |
Likely-benign |
Likely-benign |
APOGEE2 score |
0.0187627764746114 |
0.17280501327238 |
0.208094692610728 |
CAROL |
neutral |
neutral |
neutral |
CAROL score |
0.56 |
0.94 |
0.9 |
Condel |
neutral |
deleterious |
neutral |
Condel score |
0.47 |
0.53 |
0.33 |
COVEC WMV |
neutral |
neutral |
deleterious |
COVEC WMV score |
-3 |
-2 |
1 |
MtoolBox |
neutral |
deleterious |
deleterious |
MtoolBox DS |
0.4 |
0.72 |
0.64 |
DEOGEN2 |
Tolerated |
Damaging |
Tolerated |
DEOGEN2 score |
0.190626 |
0.587173 |
0.369743 |
DEOGEN2 converted rankscore |
0.54522 |
0.86571 |
0.73440 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
PolyPhen2 transf |
medium impact |
low impact |
low impact |
PolyPhen2 transf score |
-0.78 |
-1.89 |
-1.72 |
SIFT_transf |
medium impact |
high impact |
medium impact |
SIFT transf score |
0.13 |
1.87 |
0.27 |
MutationAssessor transf |
medium impact |
medium impact |
medium impact |
MutationAssessor transf score |
-0.34 |
0.39 |
0.68 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.65 |
0.63 |
0.54 |
CHASM FDR |
0.8 |
0.8 |
0.8 |
ClinVar id |
65512.0 |
. |
. |
ClinVar Allele id |
76420.0 |
. |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 |
. |
. |
ClinVar CLNDN |
Leigh_syndrome|Leber_optic_atrophy |
. |
. |
ClinVar CLNSIG |
Benign |
. |
. |
MITOMAP Disease Clinical info |
LHON |
. |
. |
MITOMAP Disease Status |
Reported |
. |
. |
MITOMAP Disease Hom/Het |
+/- |
./. |
./. |
MITOMAP General GenBank Freq |
0.0932% |
. |
. |
MITOMAP General GenBank Seqs |
57 |
. |
. |
MITOMAP General Curated refs |
21041797;24467713;15382008;29987491;20301353;31152278;12736867;16714301 |
. |
. |
MITOMAP Variant Class |
polymorphism;disease |
. |
. |
gnomAD 3.1 AN |
56428.0 |
. |
. |
gnomAD 3.1 AC Homo |
78.0 |
. |
. |
gnomAD 3.1 AF Hom |
0.00138229 |
. |
. |
gnomAD 3.1 AC Het |
1.0 |
. |
. |
gnomAD 3.1 AF Het |
1.77217e-05 |
. |
. |
gnomAD 3.1 filter |
PASS |
. |
. |
HelixMTdb AC Hom |
228.0 |
. |
. |
HelixMTdb AF Hom |
0.0011633663 |
. |
. |
HelixMTdb AC Het |
17.0 |
. |
. |
HelixMTdb AF Het |
8.674222e-05 |
. |
. |
HelixMTdb mean ARF |
0.46131 |
. |
. |
HelixMTdb max ARF |
0.89547 |
. |
. |
ToMMo 54KJPN AC |
132 |
. |
. |
ToMMo 54KJPN AF |
0.002431 |
. |
. |
ToMMo 54KJPN AN |
54302 |
. |
. |
COSMIC 90 |
COSM1155553 |
. |
. |
dbSNP 156 id |
rs397515505 |
. |
. |