| ~ | 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 | 3.70496 | 3.70496 | 3.70496 |
| PhastCons 100V | 0.992126 | 0.992126 | 0.992126 |
| 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 | 0.001 | 0.006 |
| 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 | 1.0 | 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 |
| 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 |
| 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 |
| SNPDryad score | 1.0 | 1.0 | 1.0 |
| 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 July2022 Variation id | . | . | . |
| ClinVar July2022 CLNSIG | . | . | . |
| ClinVar July2022 CLNDN | . | . | . |
| ClinVar July2022 CLNDISDB | . | . | . |
| COSMIC 90 | . | . | . |
| MITOMAP Allele | G3890A | . | . |
| MITOMAP Disease Het/Hom | -/+ | . | . |
| MITOMAP Disease Clinical info | Progressive Encephalomyopathy / Leigh Syndrome / Optic Atrophy | . | . |
| MITOMAP Disease Status | Cfrm [LP] | . | . |
| MITOMAP Disease GenBank Freq | 0.002%(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 | . | . | . |
