MitImpact id |
MI.11964 |
MI.11965 |
MI.11966 |
Chr |
chrM |
chrM |
chrM |
Start |
3890 |
3890 |
3890 |
Ref |
G |
G |
G |
Alt |
A |
C |
T |
Gene symbol |
MT-ND1 |
MT-ND1 |
MT-ND1 |
Extended annotation |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 |
Gene position |
584 |
584 |
584 |
Gene start |
3307 |
3307 |
3307 |
Gene end |
4262 |
4262 |
4262 |
Gene strand |
+ |
+ |
+ |
Codon substitution |
CGA/CAA |
CGA/CCA |
CGA/CTA |
AA position |
195 |
195 |
195 |
AA ref |
R |
R |
R |
AA alt |
Q |
P |
L |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516000 |
516000 |
516000 |
HGVS |
NC_012920.1:g.3890G>A |
NC_012920.1:g.3890G>C |
NC_012920.1:g.3890G>T |
HGNC id |
7455 |
7455 |
7455 |
Respiratory Chain complex |
I |
I |
I |
Ensembl gene id |
ENSG00000198888 |
ENSG00000198888 |
ENSG00000198888 |
Ensembl transcript id |
ENST00000361390 |
ENST00000361390 |
ENST00000361390 |
Ensembl protein id |
ENSP00000354687 |
ENSP00000354687 |
ENSP00000354687 |
Uniprot id |
P03886 |
P03886 |
P03886 |
Uniprot name |
NU1M_HUMAN |
NU1M_HUMAN |
NU1M_HUMAN |
Ncbi gene id |
4535 |
4535 |
4535 |
Ncbi protein id |
YP_003024026.1 |
YP_003024026.1 |
YP_003024026.1 |
PhyloP 100V |
3.884 |
3.884 |
3.884 |
PhyloP 470Way |
0.602 |
0.602 |
0.602 |
PhastCons 100V |
0.996 |
0.996 |
0.996 |
PhastCons 470Way |
0.05 |
0.05 |
0.05 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1.0 |
1.0 |
1.0 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.49 |
0.31 |
0.99 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.0 |
0.001 |
0.006 |
VEST |
Neutral |
Pathogenic |
Pathogenic |
VEST pvalue |
0.17 |
0.02 |
0.04 |
VEST FDR |
0.45 |
0.35 |
0.35 |
Mitoclass.1 |
damaging |
damaging |
damaging |
SNPDryad |
Pathogenic |
Pathogenic |
Pathogenic |
SNPDryad score |
1.0 |
1.0 |
1.0 |
MutationTaster |
Disease automatic |
Polymorphism |
Polymorphism |
MutationTaster score |
0.00265266 |
0.999805 |
0.999939 |
MutationTaster converted rankscore |
0.22697 |
0.20292 |
0.19363 |
MutationTaster model |
complex_aae |
complex_aae |
complex_aae |
MutationTaster AAE |
R195Q |
R195P |
R195L |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
1.65 |
1.61 |
1.63 |
fathmm converted rankscore |
0.27650 |
0.28391 |
0.28002 |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.8496 |
0.9926 |
0.9581 |
CADD |
Deleterious |
Deleterious |
Deleterious |
CADD score |
4.555087 |
4.301042 |
4.31195 |
CADD phred |
24.4 |
24.0 |
24.0 |
PROVEAN |
Damaging |
Damaging |
Damaging |
PROVEAN score |
-3.8 |
-6.66 |
-6.66 |
MutationAssessor |
high |
high |
high |
MutationAssessor score |
4.975 |
4.63 |
4.975 |
EFIN SP |
Neutral |
Neutral |
Neutral |
EFIN SP score |
0.724 |
0.628 |
0.754 |
EFIN HD |
Damaging |
Damaging |
Damaging |
EFIN HD score |
0.096 |
0.056 |
0.09 |
MLC |
Deleterious |
Deleterious |
Deleterious |
MLC score |
0.93228318 |
0.93228318 |
0.93228318 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.73 |
0.71 |
0.72 |
APOGEE2 |
Pathogenic |
Likely-pathogenic |
Likely-pathogenic |
APOGEE2 score |
0.930881313582521 |
0.858072953352285 |
0.840449308382027 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1.0 |
1.0 |
1.0 |
Condel |
neutral |
neutral |
deleterious |
Condel score |
0.25 |
0.16 |
0.5 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
2 |
2 |
2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.82 |
0.89 |
0.88 |
DEOGEN2 |
Tolerated |
Tolerated |
Tolerated |
DEOGEN2 score |
0.480654 |
0.497571 |
0.360861 |
DEOGEN2 converted rankscore |
0.80955 |
0.81938 |
0.72703 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-3.57 |
-3.57 |
-3.57 |
SIFT_transf |
medium impact |
medium impact |
medium impact |
SIFT transf score |
0.27 |
0.08 |
1.39 |
MutationAssessor transf |
high impact |
high impact |
high impact |
MutationAssessor transf score |
2.79 |
3.1 |
3.1 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.81 |
0.1 |
0.02 |
CHASM FDR |
0.85 |
0.8 |
0.8 |
ClinVar id |
155881.0 |
. |
. |
ClinVar Allele id |
165630.0 |
. |
. |
ClinVar CLNDISDB |
MedGen:CN169374|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380 |
. |
. |
ClinVar CLNDN |
not_specified|Leigh_syndrome|Mitochondrial_disease |
. |
. |
ClinVar CLNSIG |
Likely_pathogenic |
. |
. |
MITOMAP Disease Clinical info |
Progressive Encephalomyopathy / Leigh Syndrome / Optic Atrophy |
. |
. |
MITOMAP Disease Status |
Cfrm [LP] |
. |
. |
MITOMAP Disease Hom/Het |
-/+ |
./. |
./. |
MITOMAP General GenBank Freq |
0.0016% |
. |
. |
MITOMAP General GenBank Seqs |
1 |
. |
. |
MITOMAP General Curated refs |
27798429;34390870;29987491;23847141;30095618;18504678;23246842;29253894 |
. |
. |
MITOMAP Variant Class |
disease |
. |
. |
gnomAD 3.1 AN |
56433.0 |
. |
. |
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 |
. |
. |
. |
dbSNP 156 id |
rs587776434 |
. |
. |