MitImpact id |
MI.20860 |
MI.20861 |
MI.20862 |
Chr |
chrM |
chrM |
chrM |
Start |
13094 |
13094 |
13094 |
Ref |
T |
T |
T |
Alt |
C |
A |
G |
Gene symbol |
MT-ND5 |
MT-ND5 |
MT-ND5 |
Extended annotation |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 |
Gene position |
758 |
758 |
758 |
Gene start |
12337 |
12337 |
12337 |
Gene end |
14148 |
14148 |
14148 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
GTT/GCT |
GTT/GAT |
GTT/GGT |
AA position |
253 |
253 |
253 |
AA ref |
V |
V |
V |
AA alt |
A |
D |
G |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516005 |
516005 |
516005 |
HGVS |
NC_012920.1:g.13094T>C |
NC_012920.1:g.13094T>A |
NC_012920.1:g.13094T>G |
HGNC id |
7461 |
7461 |
7461 |
Respiratory Chain complex |
I |
I |
I |
Ensembl gene id |
ENSG00000198786 |
ENSG00000198786 |
ENSG00000198786 |
Ensembl transcript id |
ENST00000361567 |
ENST00000361567 |
ENST00000361567 |
Ensembl protein id |
ENSP00000354813 |
ENSP00000354813 |
ENSP00000354813 |
Uniprot id |
P03915 |
P03915 |
P03915 |
Uniprot name |
NU5M_HUMAN |
NU5M_HUMAN |
NU5M_HUMAN |
Ncbi gene id |
4540 |
4540 |
4540 |
Ncbi protein id |
YP_003024036.1 |
YP_003024036.1 |
YP_003024036.1 |
PhyloP 100V |
5.764 |
5.764 |
5.764 |
PhyloP 470Way |
0.666 |
0.666 |
0.666 |
PhastCons 100V |
1 |
1 |
1 |
PhastCons 470Way |
0.991 |
0.991 |
0.991 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1 |
1 |
1 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.62 |
0.23 |
0.5 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.001 |
0.0 |
0.0 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.46 |
0.1 |
0.25 |
VEST FDR |
0.55 |
0.4 |
0.45 |
Mitoclass.1 |
damaging |
damaging |
damaging |
SNPDryad |
Neutral |
Pathogenic |
Neutral |
SNPDryad score |
0.52 |
0.93 |
0.89 |
MutationTaster |
Disease |
Disease |
Disease |
MutationTaster score |
1.0 |
1.0 |
1.0 |
MutationTaster converted rankscore |
0.81001 |
0.81001 |
0.81001 |
MutationTaster model |
simple_aae |
simple_aae |
simple_aae |
MutationTaster AAE |
V253A |
V253D |
V253G |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
4.23 |
4.19 |
4.2 |
fathmm converted rankscore |
0.02616 |
0.02716 |
0.02689 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.9632 |
0.9879 |
0.8552 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
3.519427 |
4.45563 |
3.79066 |
CADD phred |
23.1 |
24.2 |
23.4 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-3.61 |
-6.31 |
-6.31 |
MutationAssessor |
high |
high |
high |
MutationAssessor score |
4.12 |
4.58 |
4.925 |
EFIN SP |
Damaging |
Damaging |
Damaging |
EFIN SP score |
0.224 |
0.532 |
0.378 |
EFIN HD |
Damaging |
Damaging |
Damaging |
EFIN HD score |
0.138 |
0.104 |
0.14 |
MLC |
Deleterious |
Deleterious |
Deleterious |
MLC score |
0.9420303 |
0.9420303 |
0.9420303 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.89 |
0.67 |
0.76 |
APOGEE2 |
Likely-pathogenic |
Likely-pathogenic |
Likely-pathogenic |
APOGEE2 score |
0.904714881362999 |
0.854530909051963 |
0.882522572948442 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1.0 |
1.0 |
1.0 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.31 |
0.12 |
0.25 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
2 |
2 |
2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.81 |
0.87 |
0.83 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.299319 |
0.436572 |
0.423997 |
DEOGEN2 converted rankscore |
0.67185 |
0.78291 |
0.77457 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-3.6 |
-3.6 |
-3.6 |
SIFT_transf |
medium impact |
medium impact |
medium impact |
SIFT transf score |
0.35 |
-0.06 |
0.23 |
MutationAssessor transf |
high impact |
high impact |
high impact |
MutationAssessor transf score |
3.09 |
3.59 |
3.59 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.52 |
0.58 |
0.48 |
CHASM FDR |
0.8 |
0.8 |
0.8 |
ClinVar id |
693516.0 |
. |
. |
ClinVar Allele id |
680406.0 |
. |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MONDO:MONDO:0010789,MedGen:C0162671,OMIM:540000,Orphanet:550|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 |
. |
. |
ClinVar CLNDN |
Mitochondrial_disease|Juvenile_myopathy,_encephalopathy,_lactic_acidosis_AND_stroke|Leber_optic_atrophy |
. |
. |
ClinVar CLNSIG |
Pathogenic |
. |
. |
MITOMAP Disease Clinical info |
Ataxia+PEO / MELAS, LD, LHON, myoclonus, fatigue |
. |
. |
MITOMAP Disease Status |
Cfrm [P] |
. |
. |
MITOMAP Disease Hom/Het |
+/+ |
./. |
./. |
MITOMAP General GenBank Freq |
0.0016% |
. |
. |
MITOMAP General GenBank Seqs |
1 |
. |
. |
MITOMAP General Curated refs |
29479304;31226990;34135385;37038312;31665838;18977334;29506874;28429146;33763872;22249460;29987491;21364701;22577219 |
. |
. |
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 |
0.13986 |
. |
. |
HelixMTdb max ARF |
0.13986 |
. |
. |
ToMMo 54KJPN AC |
. |
. |
. |
ToMMo 54KJPN AF |
. |
. |
. |
ToMMo 54KJPN AN |
. |
. |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs1603224029 |
. |
. |