MitImpact id |
MI.12561 |
MI.12560 |
Chr |
chrM |
chrM |
Start |
4171 |
4171 |
Ref |
C |
C |
Alt |
A |
G |
Gene symbol |
MT-ND1 |
MT-ND1 |
Extended annotation |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
Gene position |
865 |
865 |
Gene start |
3307 |
3307 |
Gene end |
4262 |
4262 |
Gene strand |
+ |
+ |
Codon substitution |
CTA/ATA |
CTA/GTA |
AA position |
289 |
289 |
AA ref |
L |
L |
AA alt |
M |
V |
Functional effect general |
missense |
missense |
Functional effect detailed |
missense |
missense |
OMIM id |
516000 |
516000 |
HGVS |
NC_012920.1:g.4171C>A |
NC_012920.1:g.4171C>G |
HGNC id |
7455 |
7455 |
Respiratory Chain complex |
I |
I |
Ensembl gene id |
ENSG00000198888 |
ENSG00000198888 |
Ensembl transcript id |
ENST00000361390 |
ENST00000361390 |
Ensembl protein id |
ENSP00000354687 |
ENSP00000354687 |
Uniprot id |
P03886 |
P03886 |
Uniprot name |
NU1M_HUMAN |
NU1M_HUMAN |
Ncbi gene id |
4535 |
4535 |
Ncbi protein id |
YP_003024026.1 |
YP_003024026.1 |
PhyloP 100V |
-0.734 |
-0.734 |
PhyloP 470Way |
-0.473 |
-0.473 |
PhastCons 100V |
0 |
0 |
PhastCons 470Way |
0.093 |
0.093 |
PolyPhen2 |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1.0 |
1.0 |
SIFT |
neutral |
neutral |
SIFT score |
0.24 |
0.49 |
SIFT4G |
Damaging |
Tolerated |
SIFT4G score |
0.029 |
0.278 |
VEST |
Neutral |
Neutral |
VEST pvalue |
0.22 |
0.22 |
VEST FDR |
0.45 |
0.45 |
Mitoclass.1 |
damaging |
neutral |
SNPDryad |
Neutral |
Neutral |
SNPDryad score |
0.89 |
0.84 |
MutationTaster |
. |
Polymorphism |
MutationTaster score |
. |
1.0 |
MutationTaster converted rankscore |
. |
0.08975 |
MutationTaster model |
. |
complex_aae |
MutationTaster AAE |
. |
L289V |
fathmm |
. |
Tolerated |
fathmm score |
. |
2.79 |
fathmm converted rankscore |
. |
0.11189 |
AlphaMissense |
ambiguous |
ambiguous |
AlphaMissense score |
0.5038 |
0.3676 |
CADD |
Deleterious |
Neutral |
CADD score |
3.806027 |
1.769332 |
CADD phred |
23.4 |
14.81 |
PROVEAN |
Tolerated |
Tolerated |
PROVEAN score |
-0.98 |
-0.29 |
MutationAssessor |
. |
low |
MutationAssessor score |
. |
1.565 |
EFIN SP |
Neutral |
Neutral |
EFIN SP score |
0.752 |
0.876 |
EFIN HD |
Neutral |
Neutral |
EFIN HD score |
0.56 |
0.714 |
MLC |
Neutral |
Neutral |
MLC score |
0.47069829 |
0.47069829 |
PANTHER score |
. |
. |
PhD-SNP score |
. |
. |
APOGEE1 |
Pathogenic |
Neutral |
APOGEE1 score |
0.6 |
0.47 |
APOGEE2 |
Likely-pathogenic |
Likely-benign |
APOGEE2 score |
0.804645407958101 |
0.151989972386368 |
CAROL |
deleterious |
deleterious |
CAROL score |
1.0 |
1.0 |
Condel |
neutral |
neutral |
Condel score |
0.12 |
0.25 |
COVEC WMV |
neutral |
neutral |
COVEC WMV score |
-2 |
-2 |
MtoolBox |
deleterious |
deleterious |
MtoolBox DS |
0.68 |
0.65 |
DEOGEN2 |
. |
Tolerated |
DEOGEN2 score |
. |
0.020471 |
DEOGEN2 converted rankscore |
. |
0.16112 |
Meta-SNP |
. |
. |
Meta-SNP score |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
PolyPhen2 transf score |
-3.57 |
-3.57 |
SIFT_transf |
medium impact |
medium impact |
SIFT transf score |
-0.01 |
0.27 |
MutationAssessor transf |
medium impact |
medium impact |
MutationAssessor transf score |
0.35 |
-0.79 |
CHASM |
Neutral |
Neutral |
CHASM pvalue |
0.44 |
0.52 |
CHASM FDR |
0.8 |
0.8 |
ClinVar id |
9732.0 |
. |
ClinVar Allele id |
24771.0 |
. |
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 |
Uncertain_significance |
. |
MITOMAP Disease Clinical info |
LHON / Leigh-like phenotype |
. |
MITOMAP Disease Status |
Cfrm [VUS*] |
. |
MITOMAP Disease Hom/Het |
+/+ |
./. |
MITOMAP General GenBank Freq |
0.0033% |
. |
MITOMAP General GenBank Seqs |
2 |
. |
MITOMAP General Curated refs |
22879922;35104579;19616643;19555656;20491810;15972314;29987491;20301353;12112111;24884847;34670133;21457906;32652755;29253894;32045392 |
. |
MITOMAP Variant Class |
disease |
. |
gnomAD 3.1 AN |
. |
. |
gnomAD 3.1 AC Homo |
. |
. |
gnomAD 3.1 AF Hom |
. |
. |
gnomAD 3.1 AC Het |
. |
. |
gnomAD 3.1 AF Het |
. |
. |
gnomAD 3.1 filter |
. |
. |
HelixMTdb AC Hom |
0.0 |
. |
HelixMTdb AF Hom |
0.0 |
. |
HelixMTdb AC Het |
1.0 |
. |
HelixMTdb AF Het |
5.1024836e-06 |
. |
HelixMTdb mean ARF |
0.16872 |
. |
HelixMTdb max ARF |
0.16872 |
. |
ToMMo 54KJPN AC |
. |
. |
ToMMo 54KJPN AF |
. |
. |
ToMMo 54KJPN AN |
. |
. |
COSMIC 90 |
. |
. |
dbSNP 156 id |
. |
. |