MitImpact id |
MI.11443 |
MI.11442 |
MI.11444 |
Chr |
chrM |
chrM |
chrM |
Start |
3635 |
3635 |
3635 |
Ref |
G |
G |
G |
Alt |
A |
C |
T |
Gene symbol |
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 |
Gene position |
329 |
329 |
329 |
Gene start |
3307 |
3307 |
3307 |
Gene end |
4262 |
4262 |
4262 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
AGC/AAC |
AGC/ACC |
AGC/ATC |
AA position |
110 |
110 |
110 |
AA ref |
S |
S |
S |
AA alt |
N |
T |
I |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516000 |
516000 |
516000 |
HGVS |
NC_012920.1:g.3635G>A |
NC_012920.1:g.3635G>C |
NC_012920.1:g.3635G>T |
HGNC id |
7455 |
7455 |
7455 |
Respiratory Chain complex |
I |
I |
I |
Ensembl gene id |
ENSG00000198888 |
ENSG00000198888 |
ENSG00000198888 |
Ensembl transcript id |
ENST00000361390 |
ENST00000361390 |
ENST00000361390 |
Ensembl protein id |
ENSP00000354687 |
ENSP00000354687 |
ENSP00000354687 |
Uniprot id |
P03886 |
P03886 |
P03886 |
Uniprot name |
NU1M_HUMAN |
NU1M_HUMAN |
NU1M_HUMAN |
Ncbi gene id |
4535 |
4535 |
4535 |
Ncbi protein id |
YP_003024026.1 |
YP_003024026.1 |
YP_003024026.1 |
PhyloP 100V |
6.353 |
6.353 |
6.353 |
PhyloP 470Way |
0.602 |
0.602 |
0.602 |
PhastCons 100V |
1 |
1 |
1 |
PhastCons 470Way |
0.018 |
0.018 |
0.018 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1.0 |
1.0 |
1.0 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.19 |
0.12 |
0.36 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.0 |
0.0 |
0.0 |
VEST |
Neutral |
Neutral |
Pathogenic |
VEST pvalue |
0.29 |
0.24 |
0.05 |
VEST FDR |
0.45 |
0.45 |
0.35 |
Mitoclass.1 |
damaging |
damaging |
damaging |
SNPDryad |
Neutral |
Neutral |
Pathogenic |
SNPDryad score |
0.6 |
0.66 |
0.98 |
MutationTaster |
Disease automatic |
Polymorphism |
Polymorphism |
MutationTaster score |
1.69163e-06 |
0.999997 |
1 |
MutationTaster converted rankscore |
0.08975 |
0.08975 |
0.08975 |
MutationTaster model |
complex_aae |
complex_aae |
complex_aae |
MutationTaster AAE |
S110N |
S110T |
S110I |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
2.16 |
2.2 |
2.14 |
fathmm converted rankscore |
0.19166 |
0.18570 |
0.19450 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.9149 |
0.6119 |
0.9242 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
3.523494 |
3.274846 |
4.043755 |
CADD phred |
23.1 |
22.8 |
23.7 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-2.68 |
-2.74 |
-5.49 |
MutationAssessor |
high |
high |
high |
MutationAssessor score |
4.775 |
3.875 |
4.775 |
EFIN SP |
Neutral |
Neutral |
Neutral |
EFIN SP score |
0.658 |
0.626 |
0.688 |
EFIN HD |
Neutral |
Neutral |
Neutral |
EFIN HD score |
0.446 |
0.412 |
0.508 |
MLC |
Deleterious |
Deleterious |
Deleterious |
MLC score |
0.58509868 |
0.58509868 |
0.58509868 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.75 |
0.62 |
0.74 |
APOGEE2 |
Likely-pathogenic |
VUS+ |
Likely-pathogenic |
APOGEE2 score |
0.901427228988974 |
0.662552514276197 |
0.844529980107552 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1.0 |
1.0 |
1.0 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.1 |
0.06 |
0.18 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
2 |
1 |
2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.8 |
0.75 |
0.82 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.443841 |
0.216878 |
0.317791 |
DEOGEN2 converted rankscore |
0.78747 |
0.57916 |
0.68921 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-3.57 |
-3.57 |
-3.57 |
SIFT_transf |
medium impact |
medium impact |
medium impact |
SIFT transf score |
-0.08 |
-0.21 |
0.14 |
MutationAssessor transf |
high impact |
medium impact |
high impact |
MutationAssessor transf score |
2.66 |
1.36 |
2.97 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.31 |
0.36 |
0.23 |
CHASM FDR |
0.8 |
0.8 |
0.8 |
ClinVar id |
65518.0 |
. |
. |
ClinVar Allele id |
76426.0 |
. |
. |
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 |
0.0147% |
. |
. |
MITOMAP General GenBank Seqs |
9 |
. |
. |
MITOMAP General Curated refs |
34156427;31817256;35905669;38346855;27177320;23304069;29387390;25194554;15972314;20301353;39147111;33417421;11479733;19527690;19497304;29253894;21074518;32652755 |
. |
. |
MITOMAP Variant Class |
disease |
. |
. |
gnomAD 3.1 AN |
56428.0 |
. |
. |
gnomAD 3.1 AC Homo |
1.0 |
. |
. |
gnomAD 3.1 AF Hom |
1.77217e-05 |
. |
. |
gnomAD 3.1 AC Het |
2.0 |
. |
. |
gnomAD 3.1 AF Het |
3.54434e-05 |
. |
. |
gnomAD 3.1 filter |
PASS |
. |
. |
HelixMTdb AC Hom |
0.0 |
. |
. |
HelixMTdb AF Hom |
0.0 |
. |
. |
HelixMTdb AC Het |
2.0 |
. |
. |
HelixMTdb AF Het |
1.0204967e-05 |
. |
. |
HelixMTdb mean ARF |
0.16005 |
. |
. |
HelixMTdb max ARF |
0.2 |
. |
. |
ToMMo 54KJPN AC |
. |
. |
. |
ToMMo 54KJPN AF |
. |
. |
. |
ToMMo 54KJPN AN |
. |
. |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs397515507 |
. |
. |