MitImpact id |
MI.16535 |
MI.16534 |
MI.16533 |
Chr |
chrM |
chrM |
chrM |
Start |
10863 |
10863 |
10863 |
Ref |
G |
G |
G |
Alt |
A |
C |
T |
Gene symbol |
MT-ND4 |
MT-ND4 |
MT-ND4 |
Extended annotation |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 |
Gene position |
104 |
104 |
104 |
Gene start |
10760 |
10760 |
10760 |
Gene end |
12137 |
12137 |
12137 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
AGC/AAC |
AGC/ACC |
AGC/ATC |
AA position |
35 |
35 |
35 |
AA ref |
S |
S |
S |
AA alt |
N |
T |
I |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516003 |
516003 |
516003 |
HGVS |
NC_012920.1:g.10863G>A |
NC_012920.1:g.10863G>C |
NC_012920.1:g.10863G>T |
HGNC id |
7459 |
7459 |
7459 |
Respiratory Chain complex |
I |
I |
I |
Ensembl gene id |
ENSG00000198886 |
ENSG00000198886 |
ENSG00000198886 |
Ensembl transcript id |
ENST00000361381 |
ENST00000361381 |
ENST00000361381 |
Ensembl protein id |
ENSP00000354961 |
ENSP00000354961 |
ENSP00000354961 |
Uniprot id |
P03905 |
P03905 |
P03905 |
Uniprot name |
NU4M_HUMAN |
NU4M_HUMAN |
NU4M_HUMAN |
Ncbi gene id |
4538 |
4538 |
4538 |
Ncbi protein id |
YP_003024035.1 |
YP_003024035.1 |
YP_003024035.1 |
PhyloP 100V |
1.422 |
1.422 |
1.422 |
PhyloP 470Way |
0.848 |
0.848 |
0.848 |
PhastCons 100V |
0.002 |
0.002 |
0.002 |
PhastCons 470Way |
0.141 |
0.141 |
0.141 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1.0 |
1.0 |
1.0 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.22 |
0.34 |
0.41 |
SIFT4G |
Tolerated |
Tolerated |
Damaging |
SIFT4G score |
0.061 |
0.06 |
0.001 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.52 |
0.32 |
0.19 |
VEST FDR |
0.6 |
0.5 |
0.45 |
Mitoclass.1 |
damaging |
neutral |
neutral |
SNPDryad |
Neutral |
Neutral |
Pathogenic |
SNPDryad score |
0.52 |
0.2 |
0.96 |
MutationTaster |
Polymorphism |
Polymorphism |
Polymorphism |
MutationTaster score |
1 |
1 |
1 |
MutationTaster converted rankscore |
0.08975 |
0.08975 |
0.08975 |
MutationTaster model |
complex_aae |
complex_aae |
complex_aae |
MutationTaster AAE |
S35N |
S35T |
S35I |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
1.46 |
1.53 |
1.59 |
fathmm converted rankscore |
0.32238 |
0.30401 |
0.28836 |
AlphaMissense |
likely_pathogenic |
likely_benign |
likely_pathogenic |
AlphaMissense score |
0.7779 |
0.215 |
0.7611 |
CADD |
Neutral |
Deleterious |
Deleterious |
CADD score |
2.282881 |
3.092398 |
3.904103 |
CADD phred |
18.05 |
22.5 |
23.5 |
PROVEAN |
Tolerated |
Tolerated |
Damaging |
PROVEAN score |
-2.0 |
-1.32 |
-3.07 |
MutationAssessor |
medium |
medium |
medium |
MutationAssessor score |
2.185 |
2.23 |
2.835 |
EFIN SP |
Neutral |
Neutral |
Neutral |
EFIN SP score |
0.732 |
0.744 |
0.644 |
EFIN HD |
Neutral |
Neutral |
Neutral |
EFIN HD score |
0.864 |
0.928 |
0.626 |
MLC |
Deleterious |
Deleterious |
Deleterious |
MLC score |
0.75079969 |
0.75079969 |
0.75079969 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Neutral |
Neutral |
Neutral |
APOGEE1 score |
0.39 |
0.47 |
0.33 |
APOGEE2 |
Likely-benign |
Likely-benign |
VUS- |
APOGEE2 score |
0.198443713928335 |
0.126734424260455 |
0.364778231760783 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1.0 |
1.0 |
1.0 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.11 |
0.17 |
0.21 |
COVEC WMV |
neutral |
deleterious |
neutral |
COVEC WMV score |
-2 |
1 |
-2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.76 |
0.72 |
0.79 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.035208 |
0.031866 |
0.091578 |
DEOGEN2 converted rankscore |
0.23629 |
0.22232 |
0.38824 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-3.54 |
-3.54 |
-3.54 |
SIFT_transf |
medium impact |
medium impact |
medium impact |
SIFT transf score |
-0.11 |
0.04 |
0.11 |
MutationAssessor transf |
medium impact |
medium impact |
medium impact |
MutationAssessor transf score |
0.34 |
1.33 |
0.73 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.41 |
0.49 |
0.28 |
CHASM FDR |
0.8 |
0.8 |
0.8 |
ClinVar id |
693321.0 |
. |
. |
ClinVar Allele id |
680211.0 |
. |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 |
. |
. |
ClinVar CLNDN |
Leigh_syndrome |
. |
. |
ClinVar CLNSIG |
Uncertain_significance |
. |
. |
MITOMAP Disease Clinical info |
. |
. |
. |
MITOMAP Disease Status |
. |
. |
. |
MITOMAP Disease Hom/Het |
./. |
./. |
./. |
MITOMAP General GenBank Freq |
0.0049% |
. |
. |
MITOMAP General GenBank Seqs |
3 |
. |
. |
MITOMAP General Curated refs |
24448545 |
. |
. |
MITOMAP Variant Class |
polymorphism |
. |
. |
gnomAD 3.1 AN |
56430.0 |
. |
. |
gnomAD 3.1 AC Homo |
5.0 |
. |
. |
gnomAD 3.1 AF Hom |
8.860540000000001e-05 |
. |
. |
gnomAD 3.1 AC Het |
0.0 |
. |
. |
gnomAD 3.1 AF Het |
0.0 |
. |
. |
gnomAD 3.1 filter |
PASS |
. |
. |
HelixMTdb AC Hom |
67.0 |
. |
. |
HelixMTdb AF Hom |
0.0003418664 |
. |
. |
HelixMTdb AC Het |
1.0 |
. |
. |
HelixMTdb AF Het |
5.1024836e-06 |
. |
. |
HelixMTdb mean ARF |
0.09 |
. |
. |
HelixMTdb max ARF |
0.09 |
. |
. |
ToMMo 54KJPN AC |
. |
. |
. |
ToMMo 54KJPN AF |
. |
. |
. |
ToMMo 54KJPN AN |
. |
. |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs1603222992 |
. |
. |