MitImpact id |
MI.20030 |
MI.20032 |
MI.20031 |
Chr |
chrM |
chrM |
chrM |
Start |
12706 |
12706 |
12706 |
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 |
370 |
370 |
370 |
Gene start |
12337 |
12337 |
12337 |
Gene end |
14148 |
14148 |
14148 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
TTC/CTC |
TTC/ATC |
TTC/GTC |
AA position |
124 |
124 |
124 |
AA ref |
F |
F |
F |
AA alt |
L |
I |
V |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516005 |
516005 |
516005 |
HGVS |
NC_012920.1:g.12706T>C |
NC_012920.1:g.12706T>A |
NC_012920.1:g.12706T>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 |
5.789 |
5.789 |
5.789 |
PhyloP 470Way |
0.666 |
0.666 |
0.666 |
PhastCons 100V |
1 |
1 |
1 |
PhastCons 470Way |
0.022 |
0.022 |
0.022 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1 |
1 |
1 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
1.0 |
0.56 |
0.61 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.0 |
0.0 |
0.0 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.35 |
0.19 |
0.28 |
VEST FDR |
0.5 |
0.45 |
0.45 |
Mitoclass.1 |
damaging |
damaging |
damaging |
SNPDryad |
Pathogenic |
Pathogenic |
Pathogenic |
SNPDryad score |
0.91 |
0.95 |
0.94 |
MutationTaster |
Disease automatic |
Polymorphism |
Polymorphism |
MutationTaster score |
0.0248107 |
0.977447 |
0.953052 |
MutationTaster converted rankscore |
0.25448 |
0.25312 |
0.26417 |
MutationTaster model |
simple_aae |
simple_aae |
simple_aae |
MutationTaster AAE |
F124L |
F124I |
F124V |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
3.29 |
3.15 |
3.16 |
fathmm converted rankscore |
0.06445 |
0.07820 |
0.07711 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.9989 |
0.994 |
0.9927 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
3.923715 |
4.251539 |
3.933452 |
CADD phred |
23.5 |
23.9 |
23.5 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-5.92 |
-5.92 |
-6.9 |
MutationAssessor |
high |
high |
high |
MutationAssessor score |
5.065 |
5.41 |
5.065 |
EFIN SP |
Damaging |
Damaging |
Damaging |
EFIN SP score |
0.07 |
0.294 |
0.206 |
EFIN HD |
Neutral |
Neutral |
Neutral |
EFIN HD score |
0.5 |
0.582 |
0.428 |
MLC |
Deleterious |
Deleterious |
Deleterious |
MLC score |
0.8221679 |
0.8221679 |
0.8221679 |
PANTHER score |
0.637 |
. |
. |
PhD-SNP score |
0.661 |
. |
. |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.9 |
0.87 |
0.87 |
APOGEE2 |
Likely-pathogenic |
Likely-pathogenic |
Likely-pathogenic |
APOGEE2 score |
0.899085861129664 |
0.813430831797395 |
0.835390380090944 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
0.99 |
1.0 |
1.0 |
Condel |
deleterious |
neutral |
neutral |
Condel score |
0.5 |
0.28 |
0.31 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
2 |
2 |
2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.78 |
0.82 |
0.82 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.272972 |
0.302463 |
0.297859 |
DEOGEN2 converted rankscore |
0.64539 |
0.67486 |
0.67044 |
Meta-SNP |
Disease |
. |
. |
Meta-SNP score |
0.819 |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-3.6 |
-3.6 |
-3.6 |
SIFT_transf |
high impact |
medium impact |
medium impact |
SIFT transf score |
1.89 |
0.29 |
0.34 |
MutationAssessor transf |
high impact |
high impact |
high impact |
MutationAssessor transf score |
3.36 |
3.36 |
3.36 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.56 |
0.56 |
0.63 |
CHASM FDR |
0.8 |
0.8 |
0.8 |
ClinVar id |
9698.0 |
. |
. |
ClinVar Allele id |
24737.0 |
. |
. |
ClinVar CLNDISDB |
MedGen:C1838951|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 |
Leigh_syndrome_due_to_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 |
31996177;17317336;14684687;20064630;18402672;11938446;15972314;23847141;21364701;30095618;21457906;32652755 |
. |
. |
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 |
0.093023 |
. |
. |
HelixMTdb max ARF |
0.093023 |
. |
. |
ToMMo 54KJPN AC |
. |
. |
. |
ToMMo 54KJPN AF |
. |
. |
. |
ToMMo 54KJPN AN |
. |
. |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs267606893 |
. |
. |