| ~ | 11778 (G/A) | 11778 (G/C) | 11778 (G/T) |
|---|---|---|---|
| ~ | 11778 (cGc/cAc) | 11778 (cGc/cCc) | 11778 (cGc/cTc) |
| Chr | chrM | chrM | chrM |
| Start | 11778 | 11778 | 11778 |
| End | 11778 | 11778 | 11778 |
| Ref | G | G | G |
| Alt | A | C | T |
| MitImpact id | MI.18470 | MI.18469 | MI.18468 |
| Gene symbol | MT-ND4 | MT-ND4 | MT-ND4 |
| Respiratory Chain complex | I | I | I |
| Ensembl gene id | ENSG00000198886 | ENSG00000198886 | ENSG00000198886 |
| Ensembl protein id | ENSP00000354961 | ENSP00000354961 | ENSP00000354961 |
| Ensembl transcript id | ENST00000361381 | ENST00000361381 | ENST00000361381 |
| Uniprot name | NU4M_HUMAN | NU4M_HUMAN | NU4M_HUMAN |
| Uniprot id | P03905 | P03905 | P03905 |
| Ncbi gene id | 4538 | 4538 | 4538 |
| Ncbi protein id | YP_003024035.1 | YP_003024035.1 | YP_003024035.1 |
| Gene position | 1019 | 1019 | 1019 |
| AA position | 340 | 340 | 340 |
| AA ref | R | R | R |
| AA alt | H | P | L |
| Codon substitution | cGc/cAc | cGc/cCc | cGc/cTc |
| PhyloP 100V | 4.4 | 4.4 | 4.4 |
| PhastCons 100V | 1 | 1 | 1 |
| PolyPhen2 | probably_damaging | probably_damaging | probably_damaging |
| PolyPhen2 score | 1 | 1 | 1 |
| SIFT | deleterious | deleterious | deleterious |
| SIFT score | 0 | 0 | 0 |
| FatHmm | deleterious | deleterious | deleterious |
| FatHmm score | -3.75 | -4.4 | -3.21 |
| FatHmmW | neutral | neutral | neutral |
| FatHmmW score | 4.44 | 4.44 | 4.45 |
| PROVEAN | deleterious | deleterious | deleterious |
| PROVEAN score | -4.74 | -6.64 | -6.64 |
| MutationAssessor | high impact | high impact | high impact |
| MutationAssessor score | 4.61 | 4.61 | 3.56 |
| EFIN SP | damaging | damaging | damaging |
| EFIN SP score | 0.18 | 0.4 | 0.39 |
| EFIN HD | damaging | damaging | damaging |
| EFIN HD score | 0.13 | 0.2 | 0.26 |
| CADD | deleterious | deleterious | deleterious |
| CADD score | 4.56 | 4.35 | 4.46 |
| CADD phred | 24.4 | 24.1 | 24.2 |
| VEST pvalue | 0.21 | 0.03 | 0.06 |
| VEST FDR | 0.45 | 0.35 | 0.35 |
| PANTHER | disease | neutral | neutral |
| PANTHER score | 0.63 | 0.28 | 0.5 |
| PhD-SNP | disease | disease | disease |
| PhD-SNP score | 0.87 | 0.91 | 0.92 |
| SNAP | disease | disease | disease |
| SNAP score | 0.8 | 0.87 | 0.8 |
| Meta-SNP | disease | disease | disease |
| Meta-SNP score | 0.72 | 0.72 | 0.75 |
| Meta-SNP RI | 4 | 4 | 5 |
| CAROL | deleterious | deleterious | deleterious |
| CAROL score | 1 | 1 | 1 |
| Condel | neutral | neutral | neutral |
| Condel score | 0 | 0 | 0 |
| COVEC WMV | deleterious | deleterious | deleterious |
| COVEC WMV score | 6 | 6 | 6 |
| MtoolBox | deleterious | deleterious | deleterious |
| MtoolBox DS | 0.85 | 0.83 | 0.84 |
| PolyPhen2 transf | low impact | low impact | low impact |
| PolyPhen2 transf score | -3.54 | -3.54 | -3.54 |
| SIFT_transf | low impact | low impact | low impact |
| SIFT transf score | -1.48 | -1.48 | -1.48 |
| MutationAssessor transf | high impact | high impact | high impact |
| MutationAssessor transf score | 3.44 | 3.44 | 2.4 |
| CHASM pvalue | 0.77 | 0.13 | 0.02 |
| CHASM FDR | 0.85 | 0.8 | 0.8 |
| APOGEE | Pathogenic | Pathogenic | Pathogenic |
| APOGEE score | 0.97 | 0.76 | 0.81 |
| SNPDryad score | 1 | 0.99 | 1 |
| MutationTaster | disease_causing_automatic | polymorphism | polymorphism |
| MutationTaster score | 0 | 1 | 1 |
| DEOGEN2 score | 0.24 | 0.4 | 0.21 |
| Mitoclass.1 | damaging | damaging | damaging |
| dbSNP 155 id | rs199476112 | . | . |
| ClinVar October2021 Variation id | 9708 | . | . |
| ClinVar October2021 CLNSIG | Pathogenic | . | . |
| ClinVar October2021 CLNDN | Leber_hereditary_optic_neuropathy|not_provided | . | . |
| ClinVar October2021 CLNDISDB | Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:ORPHA104,SNOMED_CT:58610003|MedGen:CN517202 | . | . |
| COSMIC 90 | . | . | . |
| MITOMAP Allele | G11778A | . | . |
| MITOMAP Disease Het/Hom | +/+ | . | . |
| MITOMAP Disease Clinical info | LHON / Progressive Dystonia | . | . |
| MITOMAP Disease Status | Cfrm | . | . |
| MITOMAP Disease GenBank Freq | 0.000% | . | . |
| MITOMAP Disease GenBank Seqs | 185 (0) | . | . |
| MITOMAP Disease GenBank Curated refs | 388 | . | . |
| MITOMAP General GenBank Freq | . | . | . |
| MITOMAP General GenBank Seqs | . | . | . |
| MITOMAP General Curated refs | . | . | . |
| gnomAD 3.1 filter | PASS | . | . |
| gnomAD 3.1 AC Homo | 11 | . | . |
| gnomAD 3.1 AC Het | 13 | . | . |
| gnomAD 3.1 AF Hom | 0.00019495595 | . | . |
| gnomAD 3.1 AF Het | 0.0002304025 | . | . |
| gnomAD 3.1 AN | 56423 | . | . |
| EVmutation | MT-ND4_340R|344L:0.142928;341I:0.12325;342M:0.084446;343I:0.079417 | MT-ND4_340R|344L:0.142928;341I:0.12325;342M:0.084446;343I:0.079417 | MT-ND4_340R|344L:0.142928;341I:0.12325;342M:0.084446;343I:0.079417 |
| 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 | . | . | . |
