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| ~ | 3460 (G/A) | 3460 (G/T) | 3460 (G/C) |
|---|---|---|---|
| ~ | 3460 (Gcc/Acc) | 3460 (Gcc/Tcc) | 3460 (Gcc/Ccc) |
| Chr | chrM | chrM | chrM |
| Start | 3460 | 3460 | 3460 |
| End | 3460 | 3460 | 3460 |
| Ref | G | G | G |
| Alt | A | T | C |
| MitImpact id | MI.11080 | MI.11078 | MI.11079 |
| 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 | 154 | 154 | 154 |
| AA position | 52 | 52 | 52 |
| AA ref | A | A | A |
| AA alt | T | S | P |
| Codon substitution | Gcc/Acc | Gcc/Tcc | Gcc/Ccc |
| PhyloP 100V | -7.82 | -7.82 | -7.82 |
| PhastCons 100V | 0 | 0 | 0 |
| PolyPhen2 | probably_damaging | probably_damaging | probably_damaging |
| PolyPhen2 score | 1 | 1 | 1 |
| SIFT | neutral | neutral | neutral |
| SIFT score | 0.54 | 0.6 | 0.31 |
| FatHmm | neutral | neutral | deleterious |
| FatHmm score | -1.54 | -2.08 | -3.8 |
| FatHmmW | neutral | neutral | neutral |
| FatHmmW score | 2.62 | 2.64 | 2.56 |
| PROVEAN | neutral | neutral | deleterious |
| PROVEAN score | -2.36 | -0.79 | -2.62 |
| MutationAssessor | medium impact | medium impact | high impact |
| MutationAssessor score | 3.08 | 3.36 | 4.05 |
| EFIN SP | damaging | neutral | damaging |
| EFIN SP score | 0.29 | 0.75 | 0.52 |
| EFIN HD | neutral | neutral | damaging |
| EFIN HD score | 0.45 | 0.49 | 0.27 |
| CADD | deleterious | deleterious | deleterious |
| CADD score | 4.24 | 3.6 | 3.77 |
| CADD phred | 23.9 | 23.2 | 23.4 |
| VEST pvalue | 0.13 | 0.2 | 0.02 |
| VEST FDR | 0.4 | 0.45 | 0.35 |
| PANTHER | neutral | neutral | disease |
| PANTHER score | 0.26 | 0.35 | 0.6 |
| PhD-SNP | disease | disease | disease |
| PhD-SNP score | 0.72 | 0.75 | 0.93 |
| SNAP | disease | disease | disease |
| SNAP score | 0.65 | 0.65 | 0.76 |
| Meta-SNP | disease | disease | disease |
| Meta-SNP score | 0.7 | 0.7 | 0.83 |
| Meta-SNP RI | 4 | 4 | 7 |
| CAROL | deleterious | deleterious | deleterious |
| CAROL score | 1 | 1 | 1 |
| Condel | neutral | neutral | neutral |
| Condel score | 0.27 | 0.3 | 0.16 |
| COVEC WMV | deleterious | deleterious | deleterious |
| COVEC WMV score | 1 | 1 | 2 |
| MtoolBox | deleterious | deleterious | deleterious |
| MtoolBox DS | 0.76 | 0.8 | 0.9 |
| 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 | 0.31 | 0.37 | 0.08 |
| MutationAssessor transf | medium impact | medium impact | high impact |
| MutationAssessor transf score | 1.5 | 1.75 | 2.35 |
| CHASM pvalue | 0.78 | 0.48 | 0.56 |
| CHASM FDR | 0.85 | 0.8 | 0.8 |
| APOGEE | Likely-pathogenic | VUS | Likely-pathogenic |
| APOGEE score | 0.8693934710586168 | 0.52821895292228 | 0.7811132348213756 |
| SNPDryad score | 0.7 | 0.93 | 0.96 |
| MutationTaster | disease_causing_automatic | polymorphism | polymorphism |
| MutationTaster score | 0 | 1 | 1 |
| DEOGEN2 score | 0.13 | 0.09 | 0.23 |
| Mitoclass.1 | damaging | damaging | damaging |
| dbSNP 155 id | rs199476118 | . | . |
| ClinVar October2021 Variation id | . | . | . |
| ClinVar October2021 CLNSIG | . | . | . |
| ClinVar October2021 CLNDN | . | . | . |
| ClinVar October2021 CLNDISDB | . | . | . |
| COSMIC 90 | COSM6716713 | . | . |
| MITOMAP Allele | G3460A | . | . |
| MITOMAP Disease Het/Hom | +/+ | . | . |
| MITOMAP Disease Clinical info | LHON | . | . |
| MITOMAP Disease Status | Cfrm | . | . |
| MITOMAP Disease GenBank Freq | 0.000% | . | . |
| MITOMAP Disease GenBank Seqs | 31 (0) | . | . |
| MITOMAP Disease GenBank Curated refs | 206 | . | . |
| MITOMAP General GenBank Freq | . | . | . |
| MITOMAP General GenBank Seqs | . | . | . |
| MITOMAP General Curated refs | . | . | . |
| gnomAD 3.1 filter | PASS | . | . |
| gnomAD 3.1 AC Homo | 0 | . | . |
| gnomAD 3.1 AC Het | 1 | . | . |
| gnomAD 3.1 AF Hom | 0 | . | . |
| gnomAD 3.1 AF Het | 1.7722326e-05 | . | . |
| gnomAD 3.1 AN | 56426 | . | . |
| HelixMTdb AC Hom | 0 | . | . |
| HelixMTdb AF Hom | 0 | . | . |
| HelixMTdb AC Het | 14 | . | . |
| HelixMTdb AF Het | 7.143477e-05 | . | . |
| HelixMTdb mean ARF | 0.29635 | . | . | HelixMTdb max ARF | 0.88333 | . | . |
| EVmutation | MT-ND1_52A|56F:0.158649;221A:0.15824;57T:0.151346;225M:0.115603;119S:0.100308;55L:0.094289;81I:0.086307;83L:0.083706;110S:0.075964;218G:0.065091 | MT-ND1_52A|56F:0.158649;221A:0.15824;57T:0.151346;225M:0.115603;119S:0.100308;55L:0.094289;81I:0.086307;83L:0.083706;110S:0.075964;218G:0.065091 | MT-ND1_52A|56F:0.158649;221A:0.15824;57T:0.151346;225M:0.115603;119S:0.100308;55L:0.094289;81I:0.086307;83L:0.083706;110S:0.075964;218G:0.065091 |
| Site A InterP | ND1_52 | ND1_52 | ND1_52 |
| Site B InterP | ND5_194 | ND5_194 | ND5_194 |
| Covariation Score InterP | mfDCA_26.26 | mfDCA_26.26 | mfDCA_26.26 |
| 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 | . | . | . |
