MitImpact id |
MI.21487 |
MI.21486 |
MI.21485 |
Chr |
chrM |
chrM |
chrM |
Start |
13379 |
13379 |
13379 |
Ref |
A |
A |
A |
Alt |
C |
G |
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 |
1043 |
1043 |
1043 |
Gene start |
12337 |
12337 |
12337 |
Gene end |
14148 |
14148 |
14148 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
CAC/CCC |
CAC/CGC |
CAC/CTC |
AA position |
348 |
348 |
348 |
AA ref |
H |
H |
H |
AA alt |
P |
R |
L |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516005 |
516005 |
516005 |
HGVS |
NC_012920.1:g.13379A>C |
NC_012920.1:g.13379A>G |
NC_012920.1:g.13379A>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 |
8.666 |
8.666 |
8.666 |
PhyloP 470Way |
0.819 |
0.819 |
0.819 |
PhastCons 100V |
1 |
1 |
1 |
PhastCons 470Way |
0.973 |
0.973 |
0.973 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1 |
1 |
1 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.21 |
0.35 |
0.78 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.001 |
0.0 |
0.0 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.15 |
0.39 |
0.17 |
VEST FDR |
0.4 |
0.5 |
0.45 |
Mitoclass.1 |
damaging |
damaging |
damaging |
SNPDryad |
Pathogenic |
Pathogenic |
Pathogenic |
SNPDryad score |
0.97 |
0.99 |
0.97 |
MutationTaster |
Disease |
Disease |
Disease |
MutationTaster score |
0.999974 |
0.999885 |
0.999976 |
MutationTaster converted rankscore |
0.53665 |
0.50402 |
0.53665 |
MutationTaster model |
simple_aae |
simple_aae |
simple_aae |
MutationTaster AAE |
H348P |
H348R |
H348L |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
4.49 |
4.54 |
4.55 |
fathmm converted rankscore |
0.02049 |
0.01963 |
0.01948 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.9749 |
0.91 |
0.9211 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
3.279813 |
3.048053 |
3.963319 |
CADD phred |
22.8 |
22.4 |
23.6 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-9.01 |
-7.21 |
-9.91 |
MutationAssessor |
high |
medium |
medium |
MutationAssessor score |
4.4 |
3.36 |
3.18 |
EFIN SP |
Damaging |
Damaging |
Damaging |
EFIN SP score |
0.41 |
0.478 |
0.346 |
EFIN HD |
Damaging |
Damaging |
Damaging |
EFIN HD score |
0.112 |
0.104 |
0.09 |
MLC |
Deleterious |
Deleterious |
Deleterious |
MLC score |
0.6671495 |
0.6671495 |
0.6671495 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.8 |
0.56 |
0.67 |
APOGEE2 |
Pathogenic |
Likely-pathogenic |
Likely-pathogenic |
APOGEE2 score |
0.954332812574913 |
0.803494086069945 |
0.838527101496156 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1.0 |
1.0 |
1.0 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.11 |
0.18 |
0.39 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
2 |
2 |
2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.9 |
0.87 |
0.86 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.395585 |
0.206409 |
0.203386 |
DEOGEN2 converted rankscore |
0.75443 |
0.56575 |
0.56184 |
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 |
-0.09 |
0.08 |
0.54 |
MutationAssessor transf |
high impact |
high impact |
high impact |
MutationAssessor transf score |
2.97 |
2.27 |
2.03 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.28 |
0.54 |
0.35 |
CHASM FDR |
0.8 |
0.8 |
0.8 |
ClinVar id |
986501.0 |
1693553.0 |
. |
ClinVar Allele id |
974652.0 |
1685987.0 |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380 |
MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380 |
. |
ClinVar CLNDN |
Mitochondrial_disease |
Mitochondrial_disease |
. |
ClinVar CLNSIG |
Uncertain_significance |
Uncertain_significance |
. |
MITOMAP Disease Clinical info |
LHON |
LHON |
. |
MITOMAP Disease Status |
Reported [VUS] |
Cfrm [VUS*] |
. |
MITOMAP Disease Hom/Het |
+/- |
+/- |
./. |
MITOMAP General GenBank Freq |
0.0% |
0.0% |
. |
MITOMAP General GenBank Seqs |
0 |
0 |
. |
MITOMAP General Curated refs |
17003408 |
31669237;34177762 |
. |
MITOMAP Variant Class |
disease |
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 |
rs2124597679 |
rs2124597679 |
. |