~ | 3890 (G/A) | 3890 (G/C) | 3890 (G/T) |
---|---|---|---|
~ | 3890 (cGa/cAa) | 3890 (cGa/cCa) | 3890 (cGa/cTa) |
Chr | chrM | chrM | chrM |
Start | 3890 | 3890 | 3890 |
End | 3890 | 3890 | 3890 |
Ref | G | G | G |
Alt | A | C | T |
MitImpact id | MI.11964 | MI.11965 | MI.11966 |
Gene symbol | MT-ND1 | MT-ND1 | MT-ND1 |
Respiratory Chain complex | I | I | I |
Ensembl gene id | ENSG00000198888 | ENSG00000198888 | ENSG00000198888 |
Ensembl protein id | ENSP00000354687 | ENSP00000354687 | ENSP00000354687 |
Ensembl transcript id | ENST00000361390 | ENST00000361390 | ENST00000361390 |
Uniprot name | NU1M_HUMAN | NU1M_HUMAN | NU1M_HUMAN |
Uniprot id | P03886 | P03886 | P03886 |
Ncbi gene id | 4535 | 4535 | 4535 |
Ncbi protein id | YP_003024026.1 | YP_003024026.1 | YP_003024026.1 |
Gene position | 584 | 584 | 584 |
AA position | 195 | 195 | 195 |
AA ref | R | R | R |
AA alt | Q | P | L |
Codon substitution | cGa/cAa | cGa/cCa | cGa/cTa |
PhyloP 100V | 2.75 | 2.75 | 2.75 |
PhastCons 100V | 0.98 | 0.98 | 0.98 |
PolyPhen2 | probably_damaging | probably_damaging | probably_damaging |
PolyPhen2 score | 1 | 1 | 1 |
SIFT | neutral | neutral | neutral |
SIFT score | 0.49 | 0.31 | 0.99 |
FatHmm | deleterious | deleterious | deleterious |
FatHmm score | -5.17 | -6.63 | -5.7 |
FatHmmW | neutral | neutral | neutral |
FatHmmW score | 1.65 | 1.61 | 1.63 |
PROVEAN | deleterious | deleterious | deleterious |
PROVEAN score | -3.8 | -6.66 | -6.66 |
MutationAssessor | high impact | high impact | high impact |
MutationAssessor score | 4.56 | 4.91 | 4.91 |
EFIN SP | neutral | neutral | neutral |
EFIN SP score | 0.72 | 0.63 | 0.75 |
EFIN HD | damaging | damaging | damaging |
EFIN HD score | 0.1 | 0.06 | 0.09 |
CADD | deleterious | deleterious | deleterious |
CADD score | 4.56 | 4.3 | 4.31 |
CADD phred | 24.4 | 24 | 24 |
VEST pvalue | 0.17 | 0.02 | 0.04 |
VEST FDR | 0.45 | 0.35 | 0.35 |
PANTHER | disease | disease | disease |
PANTHER score | 0.58 | 0.84 | 0.75 |
PhD-SNP | disease | disease | disease |
PhD-SNP score | 0.84 | 0.87 | 0.9 |
SNAP | disease | disease | disease |
SNAP score | 0.74 | 0.75 | 0.77 |
Meta-SNP | disease | disease | disease |
Meta-SNP score | 0.7 | 0.64 | 0.7 |
Meta-SNP RI | 4 | 3 | 4 |
CAROL | deleterious | deleterious | deleterious |
CAROL score | 1 | 1 | 1 |
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 |
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 pvalue | 0.81 | 0.1 | 0.02 |
CHASM FDR | 0.85 | 0.8 | 0.8 |
APOGEE | Pathogenic | Likely-pathogenic | Likely-pathogenic |
APOGEE score | 0.9308813135825208 | 0.8580729533522852 | 0.8404493083820274 |
SNPDryad score | 1 | 1 | 1 |
MutationTaster | disease_causing_automatic | polymorphism | polymorphism |
MutationTaster score | 0 | 1 | 1 |
DEOGEN2 score | 0.48 | 0.5 | 0.36 |
Mitoclass.1 | damaging | damaging | damaging |
dbSNP 155 id | rs587776434 | . | . |
ClinVar October2021 Variation id | . | . | . |
ClinVar October2021 CLNSIG | . | . | . |
ClinVar October2021 CLNDN | . | . | . |
ClinVar October2021 CLNDISDB | . | . | . |
COSMIC 90 | . | . | . |
MITOMAP Allele | G3890A | . | . |
MITOMAP Disease Het/Hom | -/+ | . | . |
MITOMAP Disease Clinical info | Progressive Encephalomyopathy / Leigh Syndrome / Optic Atrophy | . | . |
MITOMAP Disease Status | Cfrm | . | . |
MITOMAP Disease GenBank Freq | 0.000% | . | . |
MITOMAP Disease GenBank Seqs | 1 (0) | . | . |
MITOMAP Disease GenBank Curated refs | 8 | . | . |
MITOMAP General GenBank Freq | . | . | . |
MITOMAP General GenBank Seqs | . | . | . |
MITOMAP General Curated refs | . | . | . |
gnomAD 3.1 filter | npg | . | . |
gnomAD 3.1 AC Homo | 0 | . | . |
gnomAD 3.1 AC Het | 0 | . | . |
gnomAD 3.1 AF Hom | 0 | . | . |
gnomAD 3.1 AF Het | 0 | . | . |
gnomAD 3.1 AN | 56433 | . | . |
HelixMTdb AC Hom | . | . | . |
HelixMTdb AF Hom | . | . | . |
HelixMTdb AC Het | . | . | . |
HelixMTdb AF Het | . | . | . |
HelixMTdb mean ARF | . | . | . | HelixMTdb max ARF | . | . | . |
EVmutation | MT-ND1_195R|228Y:0.148397;274R:0.131203;227E:0.111292;202E:0.094825;207L:0.086625;199D:0.08047 | MT-ND1_195R|228Y:0.148397;274R:0.131203;227E:0.111292;202E:0.094825;207L:0.086625;199D:0.08047 | MT-ND1_195R|228Y:0.148397;274R:0.131203;227E:0.111292;202E:0.094825;207L:0.086625;199D:0.08047 |
Site A InterP | . | . | . |
Site B InterP | . | . | . |
Covariation Score InterP | . | . | . |
Site A IntraP | . | . | . |
Site B IntraP | . | . | . |
Covariation Score IntraP | . | . | . |
CPD AA ref | . | . | . |
CPD AA alt | . | . | . |
CPD Aln pos | . | . | . |
CPD Frequency | . | . | . |
CPD Species name | . | . | . |
CPD RefSeq Protein ID | . | . | . |
CPD Ncbi Taxon id | . | . | . |
DDG intra | . | . | . |
DDG intra interface | . | . | . |
DDG inter | . | . | . |