| ~ | 10197 (G/A) | 10197 (G/C) | 10197 (G/T) |
|---|---|---|---|
| ~ | 10197 (Gcc/Acc) | 10197 (Gcc/Ccc) | 10197 (Gcc/Tcc) |
| Chr | chrM | chrM | chrM |
| Start | 10197 | 10197 | 10197 |
| End | 10197 | 10197 | 10197 |
| Ref | G | G | G |
| Alt | A | C | T |
| MitImpact id | MI.15259 | MI.15260 | MI.15258 |
| Gene symbol | MT-ND3 | MT-ND3 | MT-ND3 |
| Respiratory Chain complex | I | I | I |
| Ensembl gene id | ENSG00000198840 | ENSG00000198840 | ENSG00000198840 |
| Ensembl protein id | ENSP00000355206 | ENSP00000355206 | ENSP00000355206 |
| Ensembl transcript id | ENST00000361227 | ENST00000361227 | ENST00000361227 |
| Uniprot name | NU3M_HUMAN | NU3M_HUMAN | NU3M_HUMAN |
| Uniprot id | P03897 | P03897 | P03897 |
| Ncbi gene id | 4537 | 4537 | 4537 |
| Ncbi protein id | YP_003024033.1 | YP_003024033.1 | YP_003024033.1 |
| Gene position | 139 | 139 | 139 |
| AA position | 47 | 47 | 47 |
| AA ref | A | A | A |
| AA alt | T | P | S |
| Codon substitution | Gcc/Acc | Gcc/Ccc | Gcc/Tcc |
| PhyloP 100V | 4.49807 | 4.49807 | 4.49807 |
| 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 | 0.52 | 0.32 | 1.0 |
| SIFT4G | Damaging | Damaging | Damaging |
| SIFT4G score | 0 | 0.001 | 0.007 |
| FatHmm | neutral | deleterious | neutral |
| FatHmm score | -1.8 | -3.08 | -1.42 |
| FatHmmW | neutral | neutral | neutral |
| FatHmmW score | 0.89 | 0.82 | 0.98 |
| PROVEAN | deleterious | deleterious | deleterious |
| PROVEAN score | -3.52 | -4.73 | -2.76 |
| MutationAssessor | medium impact | medium impact | low impact |
| MutationAssessor score | 2.54 | 2.73 | 1.77 |
| EFIN SP | damaging | damaging | damaging |
| EFIN SP score | 0.09 | 0.39 | 0.46 |
| EFIN HD | neutral | damaging | neutral |
| EFIN HD score | 0.38 | 0.24 | 0.37 |
| CADD | deleterious | deleterious | deleterious |
| CADD score | 4.2 | 3.87 | 3.72 |
| CADD phred | 23.9 | 23.5 | 23.3 |
| VEST pvalue | 0.17 | 0.04 | 0.26 |
| VEST FDR | 0.45 | 0.35 | 0.45 |
| PANTHER | neutral | disease | neutral |
| PANTHER score | 0.31 | 0.58 | 0.17 |
| PhD-SNP | disease | disease | disease |
| PhD-SNP score | 0.74 | 0.77 | 0.69 |
| SNAP | disease | disease | disease |
| SNAP score | 0.74 | 0.74 | 0.71 |
| Meta-SNP | disease | disease | neutral |
| Meta-SNP score | 0.58 | 0.7 | 0.36 |
| Meta-SNP RI | 2 | 4 | 3 |
| CAROL | deleterious | deleterious | deleterious |
| CAROL score | 1.0 | 1.0 | 1.0 |
| Condel | neutral | neutral | deleterious |
| Condel score | 0.26 | 0.16 | 0.5 |
| COVEC WMV | deleterious | deleterious | neutral |
| COVEC WMV score | 1 | 1 | -2 |
| MtoolBox | deleterious | deleterious | deleterious |
| MtoolBox DS | 0.79 | 0.84 | 0.75 |
| PolyPhen2 transf | low impact | low impact | low impact |
| PolyPhen2 transf score | -3.43 | -3.43 | -3.43 |
| SIFT_transf | medium impact | medium impact | high impact |
| SIFT transf score | 0.21 | 0.01 | 1.85 |
| MutationAssessor transf | medium impact | medium impact | medium impact |
| MutationAssessor transf score | 1.22 | 1.39 | 0.51 |
| CHASM pvalue | 0.76 | 0.31 | 0.21 |
| CHASM FDR | 0.85 | 0.8 | 0.8 |
| APOGEE1 | Pathogenic | Neutral | Neutral |
| APOGEE1 score | 0.88 | 0.46 | 0.39 |
| APOGEE2 | Likely-pathogenic | VUS+ | VUS |
| APOGEE2 score | 0.843686040876126 | 0.645176820055587 | 0.498126916021381 |
| SNPDryad score | 0.93 | 0.96 | 0.98 |
| MutationTaster | disease_causing_automatic | polymorphism | polymorphism |
| MutationTaster score | 0 | 1 | 1 |
| DEOGEN2 score | 0.53 | 0.54 | 0.5 |
| Mitoclass.1 | damaging | damaging | neutral |
| dbSNP 155 id | rs267606891 | . | . |
| ClinVar July2022 Variation id | . | . | . |
| ClinVar July2022 CLNSIG | . | . | . |
| ClinVar July2022 CLNDN | . | . | . |
| ClinVar July2022 CLNDISDB | . | . | . |
| COSMIC 90 | . | . | . |
| MITOMAP Allele | G10197A | . | . |
| MITOMAP Disease Het/Hom | +/+ | . | . |
| MITOMAP Disease Clinical info | Leigh Disease / Dystonia / Stroke / LDYT | . | . |
| MITOMAP Disease Status | Cfrm [P] | . | . |
| MITOMAP Disease GenBank Freq | 0.007%(0.000%) | . | . |
| MITOMAP Disease GenBank Seqs | 4 (0) | . | . |
| MITOMAP Disease GenBank Curated refs | 25 | . | . |
| MITOMAP General GenBank Freq | . | . | . |
| MITOMAP General GenBank Seqs | . | . | . |
| MITOMAP General Curated refs | . | . | . |
| gnomAD 3.1 filter | npg | npg | . |
| gnomAD 3.1 AC Homo | 0 | 0 | . |
| gnomAD 3.1 AC Het | 0 | 0 | . |
| gnomAD 3.1 AF Hom | 0 | 0 | . |
| gnomAD 3.1 AF Het | 0 | 0 | . |
| gnomAD 3.1 AN | 56422 | 56433 | . |
| HelixMTdb AC Hom | 0.0 | . | . |
| HelixMTdb AF Hom | 0.0 | . | . |
| HelixMTdb AC Het | 7.0 | . | . |
| HelixMTdb AF Het | 3.5717385e-05 | . | . |
| HelixMTdb mean ARF | 0.15194 | . | . | HelixMTdb max ARF | 0.25 | . | . |
| EVmutation | MT-ND3_47A|48R:0.529134;51F:0.204156;60I:0.185266;70A:0.161734;49V:0.124035;64L:0.101053;57L:0.084193;50P:0.081725;52S:0.069404;73L:0.064072 | MT-ND3_47A|48R:0.529134;51F:0.204156;60I:0.185266;70A:0.161734;49V:0.124035;64L:0.101053;57L:0.084193;50P:0.081725;52S:0.069404;73L:0.064072 | MT-ND3_47A|48R:0.529134;51F:0.204156;60I:0.185266;70A:0.161734;49V:0.124035;64L:0.101053;57L:0.084193;50P:0.081725;52S:0.069404;73L:0.064072 |
| Site A InterP | ND3_47 | ND3_47 | ND3_47 |
| Site B InterP | ND6_68 | ND6_68 | ND6_68 |
| Covariation Score InterP | cMI_13.9282 | cMI_13.9282 | cMI_13.9282 |
| 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 | . | . | . |
