| ~ | 13513 (G/A) | 13513 (G/C) | 13513 (G/T) |
|---|---|---|---|
| ~ | 13513 (Gac/Aac) | 13513 (Gac/Cac) | 13513 (Gac/Tac) |
| Chr | chrM | chrM | chrM |
| Start | 13513 | 13513 | 13513 |
| End | 13513 | 13513 | 13513 |
| Ref | G | G | G |
| Alt | A | C | T |
| MitImpact id | MI.21768 | MI.21769 | MI.21767 |
| Gene symbol | MT-ND5 | MT-ND5 | MT-ND5 |
| Respiratory Chain complex | I | I | I |
| Ensembl gene id | ENSG00000198786 | ENSG00000198786 | ENSG00000198786 |
| Ensembl protein id | ENSP00000354813 | ENSP00000354813 | ENSP00000354813 |
| Ensembl transcript id | ENST00000361567 | ENST00000361567 | ENST00000361567 |
| Uniprot name | NU5M_HUMAN | NU5M_HUMAN | NU5M_HUMAN |
| Uniprot id | P03915 | P03915 | P03915 |
| Ncbi gene id | 4540 | 4540 | 4540 |
| Ncbi protein id | YP_003024036.1 | YP_003024036.1 | YP_003024036.1 |
| Gene position | 1177 | 1177 | 1177 |
| AA position | 393 | 393 | 393 |
| AA ref | D | D | D |
| AA alt | N | H | Y |
| Codon substitution | Gac/Aac | Gac/Cac | Gac/Tac |
| PhyloP 100V | 4.52 | 4.52 | 4.52 |
| PhastCons 100V | 1 | 1 | 1 |
| PolyPhen2 | probably_damaging | probably_damaging | probably_damaging |
| PolyPhen2 score | 1 | 1 | 1 |
| SIFT | neutral | neutral | neutral |
| SIFT score | 0.32 | 0.53 | 1 |
| FatHmm | deleterious | deleterious | neutral |
| FatHmm score | -3.73 | -4.65 | -2.85 |
| FatHmmW | neutral | neutral | neutral |
| FatHmmW score | 4.5 | 4.51 | 4.56 |
| PROVEAN | deleterious | deleterious | deleterious |
| PROVEAN score | -4.5 | -6.29 | -8.09 |
| MutationAssessor | high impact | medium impact | high impact |
| MutationAssessor score | 4.7 | 3.42 | 4.7 |
| EFIN SP | damaging | damaging | damaging |
| EFIN SP score | 0.03 | 0.25 | 0.24 |
| EFIN HD | neutral | neutral | neutral |
| EFIN HD score | 0.44 | 0.31 | 0.32 |
| CADD | deleterious | deleterious | deleterious |
| CADD score | 4.36 | 3.69 | 4 |
| CADD phred | 24.1 | 23.3 | 23.6 |
| VEST pvalue | 0.45 | 0.28 | 0.25 |
| VEST FDR | 0.55 | 0.45 | 0.45 |
| PANTHER | disease | disease | disease |
| PANTHER score | 0.82 | 0.87 | 0.85 |
| PhD-SNP | disease | disease | disease |
| PhD-SNP score | 0.85 | 0.87 | 0.94 |
| SNAP | disease | disease | disease |
| SNAP score | 0.76 | 0.79 | 0.79 |
| Meta-SNP | disease | disease | disease |
| Meta-SNP score | 0.81 | 0.85 | 0.88 |
| Meta-SNP RI | 6 | 7 | 8 |
| CAROL | deleterious | deleterious | deleterious |
| CAROL score | 1 | 1 | 1 |
| Condel | neutral | neutral | deleterious |
| Condel score | 0.16 | 0.27 | 0.5 |
| COVEC WMV | deleterious | deleterious | deleterious |
| COVEC WMV score | 2 | 1 | 2 |
| MtoolBox | deleterious | deleterious | deleterious |
| MtoolBox DS | 0.87 | 0.89 | 0.91 |
| PolyPhen2 transf | low impact | low impact | low impact |
| PolyPhen2 transf score | -3.6 | -3.6 | -3.6 |
| SIFT_transf | medium impact | medium impact | high impact |
| SIFT transf score | 0.05 | 0.26 | 1.89 |
| MutationAssessor transf | high impact | medium impact | high impact |
| MutationAssessor transf score | 3.09 | 1.92 | 3.09 |
| CHASM pvalue | 0.8 | 0.44 | 0.33 |
| CHASM FDR | 0.85 | 0.8 | 0.8 |
| APOGEE | Pathogenic | Pathogenic | Pathogenic |
| APOGEE score | 0.97 | 0.89 | 0.82 |
| SNPDryad score | 0.98 | 0.99 | 0.99 |
| MutationTaster | disease_causing_automatic | disease_causing | disease_causing |
| MutationTaster score | 1 | 1 | 1 |
| DEOGEN2 score | 0.41 | 0.24 | 0.22 |
| Mitoclass.1 | damaging | damaging | damaging |
| dbSNP 155 id | . | . | . |
| ClinVar October2021 Variation id | 9702 | . | . |
| ClinVar October2021 CLNSIG | Pathogenic | . | . |
| ClinVar October2021 CLNDN | Leigh_syndrome|Juvenile_myopathy,_encephalopathy,_lactic_acidosis_AND_stroke|Mitochondrial_diseases|Leigh_syndrome_due_to_mitochondrial_complex_I_deficiency|not_provided | . | . |
| ClinVar October2021 CLNDISDB | MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:ORPHA506,SNOMED_CT:29570005|MONDO:MONDO:0010789,MedGen:C0162671,OMIM:540000,Orphanet:ORPHA550,SNOMED_CT:39925003|MedGen:C0751651,Orphanet:ORPHA68380|MedGen:C1838951|MedGen:CN517202 | . | . |
| COSMIC 90 | . | . | . |
| MITOMAP Allele | G13513A | . | . |
| MITOMAP Disease Het/Hom | -/+ | . | . |
| MITOMAP Disease Clinical info | Leigh Disease / MELAS / LHON-MELAS Overlap Syndrome / negative association w Carotid Atherosclerosis | . | . |
| MITOMAP Disease Status | Cfrm | . | . |
| MITOMAP Disease GenBank Freq | 0.000% | . | . |
| MITOMAP Disease GenBank Seqs | 1 (0) | . | . |
| MITOMAP Disease GenBank Curated refs | 50 | . | . |
| 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 | 56431 | . | . |
| EVmutation | MT-ND5_393D|397E:0.304998;394H:0.100091;396I:0.064101 | MT-ND5_393D|397E:0.304998;394H:0.100091;396I:0.064101 | MT-ND5_393D|397E:0.304998;394H:0.100091;396I:0.064101 |
| 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 | . | . | . |
