MitImpact id |
MI.20753 |
MI.20754 |
MI.20755 |
Chr |
chrM |
chrM |
chrM |
Start |
13042 |
13042 |
13042 |
Ref |
G |
G |
G |
Alt |
A |
C |
T |
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 |
706 |
706 |
706 |
Gene start |
12337 |
12337 |
12337 |
Gene end |
14148 |
14148 |
14148 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
GCC/ACC |
GCC/CCC |
GCC/TCC |
AA position |
236 |
236 |
236 |
AA ref |
A |
A |
A |
AA alt |
T |
P |
S |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516005 |
516005 |
516005 |
HGVS |
NC_012920.1:g.13042G>A |
NC_012920.1:g.13042G>C |
NC_012920.1:g.13042G>T |
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 |
7.459 |
7.459 |
7.459 |
PhyloP 470Way |
0.848 |
0.848 |
0.848 |
PhastCons 100V |
1 |
1 |
1 |
PhastCons 470Way |
0.908 |
0.908 |
0.908 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1 |
1 |
1 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.42 |
0.24 |
0.45 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.0 |
0.0 |
0.0 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.33 |
0.24 |
0.22 |
VEST FDR |
0.5 |
0.45 |
0.45 |
Mitoclass.1 |
damaging |
damaging |
damaging |
SNPDryad |
Pathogenic |
Pathogenic |
Pathogenic |
SNPDryad score |
0.94 |
0.96 |
0.98 |
MutationTaster |
Disease automatic |
Polymorphism |
Polymorphism |
MutationTaster score |
0.0294022 |
0.90419 |
0.987052 |
MutationTaster converted rankscore |
0.25696 |
0.27641 |
0.24556 |
MutationTaster model |
simple_aae |
simple_aae |
simple_aae |
MutationTaster AAE |
A236T |
A236P |
A236S |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
4.12 |
4.02 |
4.23 |
fathmm converted rankscore |
0.02891 |
0.03178 |
0.02616 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.9637 |
0.9904 |
0.6373 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
4.204556 |
3.842942 |
3.678833 |
CADD phred |
23.9 |
23.4 |
23.3 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-3.72 |
-4.65 |
-2.79 |
MutationAssessor |
high |
high |
medium |
MutationAssessor score |
4.56 |
4.56 |
2.62 |
EFIN SP |
Damaging |
Damaging |
Damaging |
EFIN SP score |
0.254 |
0.27 |
0.324 |
EFIN HD |
Damaging |
Damaging |
Neutral |
EFIN HD score |
0.192 |
0.268 |
0.388 |
MLC |
Deleterious |
Deleterious |
Deleterious |
MLC score |
0.92896373 |
0.92896373 |
0.92896373 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.85 |
0.83 |
0.62 |
APOGEE2 |
Likely-pathogenic |
Likely-pathogenic |
Likely-pathogenic |
APOGEE2 score |
0.893732485692743 |
0.843779945642372 |
0.722186813848507 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1.0 |
1.0 |
1.0 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.21 |
0.12 |
0.23 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
2 |
2 |
2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.78 |
0.83 |
0.8 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.222964 |
0.426211 |
0.216675 |
DEOGEN2 converted rankscore |
0.58697 |
0.77607 |
0.57891 |
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 |
0.16 |
-0.04 |
0.18 |
MutationAssessor transf |
high impact |
high impact |
high impact |
MutationAssessor transf score |
3.25 |
2.83 |
2.12 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.72 |
0.6 |
0.69 |
CHASM FDR |
0.85 |
0.8 |
0.85 |
ClinVar id |
9703.0 |
. |
. |
ClinVar Allele id |
24742.0 |
. |
. |
ClinVar CLNDISDB |
MedGen:C1838951|MONDO:MONDO:0010790,MedGen:C0162672,OMIM:545000,Orphanet:551|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:0010789,MedGen:C0162671,OMIM:540000,Orphanet:550 |
. |
. |
ClinVar CLNDN |
Leigh_syndrome_due_to_mitochondrial_complex_I_deficiency|MERRF_syndrome|Mitochondrial_disease|Leber_optic_atrophy|Juvenile_myopathy,_encephalopathy,_lactic_acidosis_AND_stroke |
. |
. |
ClinVar CLNSIG |
Likely_pathogenic |
. |
. |
MITOMAP Disease Clinical info |
Optic neuropathy/ retinopathy/ LD |
. |
. |
MITOMAP Disease Status |
Cfrm [LP] |
. |
. |
MITOMAP Disease Hom/Het |
-/+ |
./. |
./. |
MITOMAP General GenBank Freq |
0.0033% |
. |
. |
MITOMAP General GenBank Seqs |
2 |
. |
. |
MITOMAP General Curated refs |
17400793;31996177;15382008;16816025;35778412;18332249;21457906;29253894;15767514 |
. |
. |
MITOMAP Variant Class |
disease |
. |
. |
gnomAD 3.1 AN |
56428.0 |
. |
. |
gnomAD 3.1 AC Homo |
0.0 |
. |
. |
gnomAD 3.1 AF Hom |
0.0 |
. |
. |
gnomAD 3.1 AC Het |
0.0 |
. |
. |
gnomAD 3.1 AF Het |
0.0 |
. |
. |
gnomAD 3.1 filter |
npg |
. |
. |
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 |
COSM5652748 |
. |
. |
dbSNP 156 id |
rs267606898 |
. |
. |