MitImpact id |
MI.18467 |
MI.18465 |
MI.18466 |
Chr |
chrM |
chrM |
chrM |
Start |
11777 |
11777 |
11777 |
Ref |
C |
C |
C |
Alt |
A |
G |
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 |
1018 |
1018 |
1018 |
Gene start |
10760 |
10760 |
10760 |
Gene end |
12137 |
12137 |
12137 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
CGC/AGC |
CGC/GGC |
CGC/TGC |
AA position |
340 |
340 |
340 |
AA ref |
R |
R |
R |
AA alt |
S |
G |
C |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516003 |
516003 |
516003 |
HGVS |
NC_012920.1:g.11777C>A |
NC_012920.1:g.11777C>G |
NC_012920.1:g.11777C>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 |
4.531 |
4.531 |
4.531 |
PhyloP 470Way |
0.65 |
0.65 |
0.65 |
PhastCons 100V |
1 |
1 |
1 |
PhastCons 470Way |
0.037 |
0.037 |
0.037 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1.0 |
1.0 |
1.0 |
SIFT |
deleterious |
deleterious |
deleterious |
SIFT score |
0.0 |
0.0 |
0.0 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.0 |
0.001 |
0.0 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.06 |
0.06 |
0.07 |
VEST FDR |
0.35 |
0.35 |
0.35 |
Mitoclass.1 |
damaging |
damaging |
damaging |
SNPDryad |
Neutral |
Pathogenic |
Pathogenic |
SNPDryad score |
0.81 |
0.98 |
1.0 |
MutationTaster |
Disease automatic |
Disease automatic |
Polymorphism |
MutationTaster score |
4.94832e-07 |
4.06166e-07 |
1.0 |
MutationTaster converted rankscore |
0.08975 |
0.08975 |
0.08975 |
MutationTaster model |
complex_aae |
complex_aae |
complex_aae |
MutationTaster AAE |
R340S |
R340G |
R340C |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
4.52 |
4.45 |
4.42 |
fathmm converted rankscore |
0.01997 |
0.02121 |
0.02177 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.9886 |
0.9705 |
0.9523 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
4.687983 |
4.320026 |
5.187938 |
CADD phred |
24.6 |
24.0 |
25.5 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-5.69 |
-6.64 |
-7.59 |
MutationAssessor |
high |
high |
high |
MutationAssessor score |
3.685 |
4.265 |
4.725 |
EFIN SP |
Damaging |
Damaging |
Damaging |
EFIN SP score |
0.438 |
0.414 |
0.416 |
EFIN HD |
Neutral |
Neutral |
Damaging |
EFIN HD score |
0.316 |
0.314 |
0.14 |
MLC |
Deleterious |
Deleterious |
Deleterious |
MLC score |
0.88985455 |
0.88985455 |
0.88985455 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.83 |
0.84 |
0.71 |
APOGEE2 |
Likely-pathogenic |
Likely-pathogenic |
Likely-pathogenic |
APOGEE2 score |
0.893048046100007 |
0.812274511916627 |
0.842545024849707 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1.0 |
1.0 |
1.0 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.0 |
0.0 |
0.0 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
6 |
6 |
6 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.84 |
0.81 |
0.84 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.213436 |
0.230901 |
0.426581 |
DEOGEN2 converted rankscore |
0.57475 |
0.59709 |
0.77633 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-3.54 |
-3.54 |
-3.54 |
SIFT_transf |
low impact |
low impact |
low impact |
SIFT transf score |
-1.48 |
-1.48 |
-1.48 |
MutationAssessor transf |
high impact |
high impact |
high impact |
MutationAssessor transf score |
2.88 |
2.75 |
3.44 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.27 |
0.27 |
0.77 |
CHASM FDR |
0.8 |
0.8 |
0.85 |
ClinVar id |
9711.0 |
. |
. |
ClinVar Allele id |
24750.0 |
. |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0100133,MedGen:C1838979,Orphanet:2609|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|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 |
. |
. |
ClinVar CLNDN |
Mitochondrial_complex_I_deficiency|Mitochondrial_disease|Leber_optic_atrophy|Leigh_syndrome |
. |
. |
ClinVar CLNSIG |
Likely_pathogenic |
. |
. |
MITOMAP Disease Clinical info |
Leigh Disease |
. |
. |
MITOMAP Disease Status |
Cfrm [LP] |
. |
. |
MITOMAP Disease Hom/Het |
-/+ |
./. |
./. |
MITOMAP General GenBank Freq |
0.0% |
. |
. |
MITOMAP General GenBank Seqs |
0 |
. |
. |
MITOMAP General Curated refs |
24642831;29428506;20502985;15576045;20064630;16120329;18402672;18977334;37038312;15972314;12707444;30095618;21457906 |
. |
. |
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 |
. |
. |
. |
HelixMTdb AF Hom |
. |
. |
. |
HelixMTdb AC Het |
. |
. |
. |
HelixMTdb AF Het |
. |
. |
. |
HelixMTdb mean ARF |
. |
. |
. |
HelixMTdb max ARF |
. |
. |
. |
ToMMo 54KJPN AC |
. |
. |
. |
ToMMo 54KJPN AF |
. |
. |
. |
ToMMo 54KJPN AN |
. |
. |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs28384199 |
rs28384199 |
. |