MitImpact id |
MI.11153 |
MI.11155 |
MI.11154 |
MI.11157 |
MI.11158 |
MI.11156 |
Chr |
chrM |
chrM |
chrM |
chrM |
chrM |
chrM |
Start |
3496 |
3496 |
3496 |
3497 |
3497 |
3497 |
Ref |
G |
G |
G |
C |
C |
C |
Alt |
A |
C |
T |
A |
G |
T |
Gene symbol |
MT-ND1 |
MT-ND1 |
MT-ND1 |
MT-ND1 |
MT-ND1 |
MT-ND1 |
Extended annotation |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
Gene position |
190 |
190 |
190 |
191 |
191 |
191 |
Gene start |
3307 |
3307 |
3307 |
3307 |
3307 |
3307 |
Gene end |
4262 |
4262 |
4262 |
4262 |
4262 |
4262 |
Gene strand |
+ |
+ |
+ |
+ |
+ |
+ |
Codon substitution |
GCC/ACC |
GCC/CCC |
GCC/TCC |
GCC/GAC |
GCC/GGC |
GCC/GTC |
AA position |
64 |
64 |
64 |
64 |
64 |
64 |
AA ref |
A |
A |
A |
A |
A |
A |
AA alt |
T |
P |
S |
D |
G |
V |
Functional effect general |
missense |
missense |
missense |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
missense |
missense |
missense |
OMIM id |
516000 |
516000 |
516000 |
516000 |
516000 |
516000 |
HGVS |
NC_012920.1:g.3496G>A |
NC_012920.1:g.3496G>C |
NC_012920.1:g.3496G>T |
NC_012920.1:g.3497C>A |
NC_012920.1:g.3497C>G |
NC_012920.1:g.3497C>T |
HGNC id |
7455 |
7455 |
7455 |
7455 |
7455 |
7455 |
Respiratory Chain complex |
I |
I |
I |
I |
I |
I |
Ensembl gene id |
ENSG00000198888 |
ENSG00000198888 |
ENSG00000198888 |
ENSG00000198888 |
ENSG00000198888 |
ENSG00000198888 |
Ensembl transcript id |
ENST00000361390 |
ENST00000361390 |
ENST00000361390 |
ENST00000361390 |
ENST00000361390 |
ENST00000361390 |
Ensembl protein id |
ENSP00000354687 |
ENSP00000354687 |
ENSP00000354687 |
ENSP00000354687 |
ENSP00000354687 |
ENSP00000354687 |
Uniprot id |
P03886 |
P03886 |
P03886 |
P03886 |
P03886 |
P03886 |
Uniprot name |
NU1M_HUMAN |
NU1M_HUMAN |
NU1M_HUMAN |
NU1M_HUMAN |
NU1M_HUMAN |
NU1M_HUMAN |
Ncbi gene id |
4535 |
4535 |
4535 |
4535 |
4535 |
4535 |
Ncbi protein id |
YP_003024026.1 |
YP_003024026.1 |
YP_003024026.1 |
YP_003024026.1 |
YP_003024026.1 |
YP_003024026.1 |
PhyloP 100V |
-2.57 |
-2.57 |
-2.57 |
-0.864 |
-0.864 |
-0.864 |
PhyloP 470Way |
0.458 |
0.458 |
0.458 |
0.353 |
0.353 |
0.353 |
PhastCons 100V |
0 |
0 |
0 |
0 |
0 |
0 |
PhastCons 470Way |
0.043 |
0.043 |
0.043 |
0.049 |
0.049 |
0.049 |
PolyPhen2 |
benign |
benign |
benign |
benign |
benign |
benign |
PolyPhen2 score |
0.0 |
0.11 |
0.0 |
0.06 |
0.04 |
0.01 |
SIFT |
neutral |
neutral |
neutral |
neutral |
neutral |
neutral |
SIFT score |
0.72 |
0.35 |
0.81 |
0.61 |
0.47 |
0.49 |
SIFT4G |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
SIFT4G score |
0.23 |
0.051 |
1.0 |
0.05 |
0.078 |
0.14 |
VEST |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.34 |
0.17 |
0.42 |
0.15 |
0.39 |
0.27 |
VEST FDR |
0.5 |
0.45 |
0.55 |
0.4 |
0.5 |
0.45 |
Mitoclass.1 |
neutral |
neutral |
neutral |
neutral |
neutral |
neutral |
SNPDryad |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
SNPDryad score |
0.34 |
0.74 |
0.07 |
0.54 |
0.49 |
0.45 |
MutationTaster |
Polymorphism |
Polymorphism |
Polymorphism |
Polymorphism |
Polymorphism |
Polymorphism |
MutationTaster score |
1 |
1 |
1 |
1 |
1 |
1 |
MutationTaster converted rankscore |
0.08975 |
0.08975 |
0.08975 |
0.08975 |
0.08975 |
0.08975 |
MutationTaster model |
complex_aae |
complex_aae |
complex_aae |
complex_aae |
complex_aae |
complex_aae |
MutationTaster AAE |
A64T |
A64P |
A64S |
A64D |
A64G |
A64V |
fathmm |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
2.71 |
2.65 |
2.79 |
2.7 |
2.67 |
2.71 |
fathmm converted rankscore |
0.12055 |
0.12676 |
0.11189 |
0.12162 |
0.12473 |
0.12055 |
AlphaMissense |
likely_benign |
ambiguous |
likely_benign |
ambiguous |
likely_benign |
likely_benign |
AlphaMissense score |
0.1106 |
0.4732 |
0.0943 |
0.4515 |
0.2246 |
0.1862 |
CADD |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
CADD score |
0.895687 |
0.764189 |
-1.028131 |
1.416584 |
0.820337 |
1.246741 |
CADD phred |
10.05 |
9.241 |
0.014 |
12.87 |
9.589 |
11.99 |
PROVEAN |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
PROVEAN score |
0.01 |
-1.97 |
1.31 |
-1.71 |
-1.65 |
-1.41 |
MutationAssessor |
neutral |
neutral |
neutral |
low |
low |
low |
MutationAssessor score |
-0.68 |
0.58 |
-0.9 |
1.275 |
1.305 |
1.275 |
EFIN SP |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
EFIN SP score |
0.764 |
0.672 |
0.676 |
0.726 |
0.68 |
0.746 |
EFIN HD |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
EFIN HD score |
0.738 |
0.368 |
0.952 |
0.406 |
0.544 |
0.712 |
MLC |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
MLC score |
0.27222524 |
0.27222524 |
0.27222524 |
0.2596415 |
0.2596415 |
0.2596415 |
PANTHER score |
. |
. |
. |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
. |
. |
. |
APOGEE1 |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
APOGEE1 score |
0.46 |
0.38 |
0.44 |
0.29 |
0.44 |
0.44 |
APOGEE2 |
Benign |
VUS |
Benign |
VUS |
VUS- |
Likely-benign |
APOGEE2 score |
0.0252991649228041 |
0.483325502098256 |
0.0300959733751049 |
0.405279884876124 |
0.271502508453901 |
0.125252764204327 |
CAROL |
neutral |
neutral |
neutral |
neutral |
neutral |
neutral |
CAROL score |
0.28 |
0.6 |
0.19 |
0.32 |
0.49 |
0.49 |
Condel |
deleterious |
deleterious |
deleterious |
deleterious |
deleterious |
deleterious |
Condel score |
0.86 |
0.62 |
0.91 |
0.78 |
0.72 |
0.74 |
COVEC WMV |
neutral |
neutral |
neutral |
neutral |
neutral |
neutral |
COVEC WMV score |
-6 |
-6 |
-6 |
-6 |
-6 |
-6 |
MtoolBox |
neutral |
neutral |
neutral |
neutral |
neutral |
neutral |
MtoolBox DS |
0.09 |
0.26 |
0.08 |
0.18 |
0.14 |
0.12 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.005796 |
0.026009 |
0.004019 |
0.02448 |
0.026021 |
0.024318 |
DEOGEN2 converted rankscore |
0.05248 |
0.19333 |
0.03433 |
0.18487 |
0.19344 |
0.18398 |
Meta-SNP |
. |
. |
. |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
. |
. |
. |
PolyPhen2 transf |
high impact |
medium impact |
high impact |
medium impact |
medium impact |
medium impact |
PolyPhen2 transf score |
2.07 |
0.1 |
2.07 |
0.37 |
0.55 |
1.12 |
SIFT_transf |
medium impact |
medium impact |
medium impact |
medium impact |
medium impact |
medium impact |
SIFT transf score |
0.51 |
0.12 |
0.63 |
0.38 |
0.25 |
0.27 |
MutationAssessor transf |
low impact |
medium impact |
low impact |
medium impact |
medium impact |
medium impact |
MutationAssessor transf score |
-1.63 |
-0.2 |
-1.92 |
-0.02 |
0.07 |
0 |
CHASM |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.55 |
0.37 |
0.39 |
0.17 |
0.52 |
0.47 |
CHASM FDR |
0.8 |
0.8 |
0.8 |
0.8 |
0.8 |
0.8 |
ClinVar id |
692359.0 |
. |
. |
. |
. |
692360.0 |
ClinVar Allele id |
680895.0 |
. |
. |
. |
. |
680896.0 |
ClinVar CLNDISDB |
MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 |
. |
. |
. |
. |
MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 |
ClinVar CLNDN |
Leigh_syndrome |
. |
. |
. |
. |
Leigh_syndrome |
ClinVar CLNSIG |
Uncertain_significance |
. |
. |
. |
. |
Benign |
MITOMAP Disease Clinical info |
. |
. |
LHON |
. |
. |
LHON |
MITOMAP Disease Status |
. |
. |
Reported / Secondary |
. |
. |
Reported / Secondary |
MITOMAP Disease Hom/Het |
./. |
./. |
+/- |
./. |
./. |
+/- |
MITOMAP General GenBank Freq |
0.0131% |
. |
0.018% |
. |
. |
0.3435% |
MITOMAP General GenBank Seqs |
8 |
. |
11 |
. |
. |
210 |
MITOMAP General Curated refs |
24448545 |
. |
10520236;16060290;15466285;15972314;29987491;16714301 |
. |
. |
19370763;21281460;10520236;16060290;22475488;16714301;15466285;29387390;20151402;15972314;29987491;11853713;18545700;16477364;29343773;17341440;12870132 |
MITOMAP Variant Class |
polymorphism |
. |
polymorphism;disease |
. |
. |
polymorphism;disease |
gnomAD 3.1 AN |
56428.0 |
56431.0 |
56429.0 |
. |
. |
56433.0 |
gnomAD 3.1 AC Homo |
3.0 |
0.0 |
0.0 |
. |
. |
28.0 |
gnomAD 3.1 AF Hom |
5.31651e-05 |
0.0 |
0.0 |
. |
. |
0.000496164 |
gnomAD 3.1 AC Het |
1.0 |
0.0 |
0.0 |
. |
. |
1.0 |
gnomAD 3.1 AF Het |
1.77217e-05 |
0.0 |
0.0 |
. |
. |
1.77201e-05 |
gnomAD 3.1 filter |
PASS |
npg |
npg |
. |
. |
PASS |
HelixMTdb AC Hom |
6.0 |
. |
16.0 |
. |
. |
238.0 |
HelixMTdb AF Hom |
3.06149e-05 |
. |
8.163974e-05 |
. |
. |
0.0012143911 |
HelixMTdb AC Het |
1.0 |
. |
0.0 |
. |
. |
2.0 |
HelixMTdb AF Het |
5.1024836e-06 |
. |
0.0 |
. |
. |
1.0204967e-05 |
HelixMTdb mean ARF |
0.86726 |
. |
. |
. |
. |
0.20944 |
HelixMTdb max ARF |
0.86726 |
. |
. |
. |
. |
0.28986 |
ToMMo 54KJPN AC |
. |
. |
610 |
. |
. |
1756 |
ToMMo 54KJPN AF |
. |
. |
0.011233 |
. |
. |
0.032338 |
ToMMo 54KJPN AN |
. |
. |
54302 |
. |
. |
54302 |
COSMIC 90 |
COSM5653110 |
. |
. |
. |
. |
. |
dbSNP 156 id |
rs1603218984 |
. |
rs1603218984 |
. |
. |
rs200319905 |