| ~ | 3460 (G/A) | 3460 (G/C) | 3460 (G/T) |
|---|---|---|---|
| ~ | 3460 (Gcc/Acc) | 3460 (Gcc/Ccc) | 3460 (Gcc/Tcc) |
| Chr | chrM | chrM | chrM |
| Start | 3460 | 3460 | 3460 |
| End | 3460 | 3460 | 3460 |
| Ref | G | G | G |
| Alt | A | C | T |
| MitImpact id | MI.11080 | MI.11079 | MI.11078 |
| 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 | P | S |
| Codon substitution | Gcc/Acc | Gcc/Ccc | Gcc/Tcc |
| PhyloP 100V | 6.26138 | 6.26138 | 6.26138 |
| PhastCons 100V | 1 | 1 | 1 |
| PolyPhen2 | probably_damaging | probably_damaging | probably_damaging |
| PolyPhen2 score | 1.0 | 1.0 | 1.0 |
| SIFT | neutral | neutral | neutral |
| SIFT score | 0.54 | 0.31 | 0.6 |
| SIFT4G | Damaging | Damaging | Damaging |
| SIFT4G score | 0.001 | 0.001 | 0.008 |
| FatHmm | neutral | deleterious | neutral |
| FatHmm score | -1.54 | -3.8 | -2.08 |
| FatHmmW | neutral | neutral | neutral |
| FatHmmW score | 2.62 | 2.56 | 2.64 |
| PROVEAN | neutral | deleterious | neutral |
| PROVEAN score | -2.36 | -2.62 | -0.79 |
| MutationAssessor | medium impact | high impact | medium impact |
| MutationAssessor score | 3.08 | 4.05 | 3.36 |
| EFIN SP | damaging | damaging | neutral |
| EFIN SP score | 0.29 | 0.52 | 0.75 |
| EFIN HD | neutral | damaging | neutral |
| EFIN HD score | 0.45 | 0.27 | 0.49 |
| CADD | deleterious | deleterious | deleterious |
| CADD score | 4.24 | 3.77 | 3.6 |
| CADD phred | 23.9 | 23.4 | 23.2 |
| VEST pvalue | 0.13 | 0.02 | 0.2 |
| VEST FDR | 0.4 | 0.35 | 0.45 |
| PANTHER | neutral | disease | neutral |
| PANTHER score | 0.26 | 0.6 | 0.35 |
| PhD-SNP | disease | disease | disease |
| PhD-SNP score | 0.72 | 0.93 | 0.75 |
| SNAP | disease | disease | disease |
| SNAP score | 0.65 | 0.76 | 0.65 |
| Meta-SNP | disease | disease | disease |
| Meta-SNP score | 0.7 | 0.83 | 0.7 |
| Meta-SNP RI | 4 | 7 | 4 |
| CAROL | deleterious | deleterious | deleterious |
| CAROL score | 1.0 | 1.0 | 1.0 |
| Condel | neutral | neutral | neutral |
| Condel score | 0.27 | 0.16 | 0.3 |
| COVEC WMV | deleterious | deleterious | deleterious |
| COVEC WMV score | 1 | 2 | 1 |
| MtoolBox | deleterious | deleterious | deleterious |
| MtoolBox DS | 0.76 | 0.9 | 0.8 |
| 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 | 0.08 | 0.37 |
| MutationAssessor transf | medium impact | high impact | medium impact |
| MutationAssessor transf score | 1.5 | 2.35 | 1.75 |
| CHASM pvalue | 0.78 | 0.56 | 0.48 |
| CHASM FDR | 0.85 | 0.8 | 0.8 |
| APOGEE1 | Pathogenic | Neutral | Neutral |
| APOGEE1 score | 0.86 | 0.46 | 0.37 |
| APOGEE2 | Likely-pathogenic | Likely-pathogenic | VUS |
| APOGEE2 score | 0.869393471058617 | 0.781113234821376 | 0.52821895292228 |
| SNPDryad score | 0.7 | 0.96 | 0.93 |
| MutationTaster | disease_causing_automatic | polymorphism | polymorphism |
| MutationTaster score | 0 | 1 | 1 |
| DEOGEN2 score | 0.13 | 0.23 | 0.09 |
| Mitoclass.1 | damaging | damaging | damaging |
| dbSNP 155 id | rs199476118 | . | . |
| ClinVar July2022 Variation id | . | . | . |
| ClinVar July2022 CLNSIG | . | . | . |
| ClinVar July2022 CLNDN | . | . | . |
| ClinVar July2022 CLNDISDB | . | . | . |
| COSMIC 90 | COSM6716713 | . | . |
| MITOMAP Allele | G3460A | . | . |
| MITOMAP Disease Het/Hom | +/+ | . | . |
| MITOMAP Disease Clinical info | LHON | . | . |
| MITOMAP Disease Status | Cfrm [P] | . | . |
| MITOMAP Disease GenBank Freq | 0.052%(0.000%) | . | . |
| MITOMAP Disease GenBank Seqs | 31 (0) | . | . |
| MITOMAP Disease GenBank Curated refs | 221 | . | . |
| 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 | 0.000017722326 | . | . |
| gnomAD 3.1 AN | 56426 | . | . |
| HelixMTdb AC Hom | 0.0 | . | . |
| HelixMTdb AF Hom | 0.0 | . | . |
| HelixMTdb AC Het | 14.0 | . | . |
| 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 | . | . | . |
