~ | 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 | 3.68488 | 3.68488 | 3.68488 |
PhastCons 100V | 1 | 1 | 1 |
PolyPhen2 | probably_damaging | probably_damaging | probably_damaging |
PolyPhen2 score | 1.0 | 1.0 | 1.0 |
SIFT | deleterious | deleterious | deleterious |
SIFT score | 0.0 | 0.0 | 0.0 |
SIFT4G | Damaging | Damaging | Damaging |
SIFT4G score | 0 | 0.001 | 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 | 1.0 | 1.0 | 1.0 |
Condel | neutral | neutral | neutral |
Condel score | 0.0 | 0.0 | 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 |
APOGEE1 | Pathogenic | Pathogenic | Pathogenic |
APOGEE1 score | 0.97 | 0.76 | 0.81 |
APOGEE2 | Pathogenic | Likely-pathogenic | Likely-pathogenic |
APOGEE2 score | 0.926042202256757 | 0.837464517623008 | 0.818322642772869 |
SNPDryad score | 1.0 | 0.99 | 1.0 |
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 July2022 Variation id | . | . | . |
ClinVar July2022 CLNSIG | . | . | . |
ClinVar July2022 CLNDN | . | . | . |
ClinVar July2022 CLNDISDB | . | . | . |
COSMIC 90 | . | . | . |
MITOMAP Allele | G11778A | . | . |
MITOMAP Disease Het/Hom | +/+ | . | . |
MITOMAP Disease Clinical info | LHON / Progressive Dystonia | . | . |
MITOMAP Disease Status | Cfrm [P] | . | . |
MITOMAP Disease GenBank Freq | 0.315%(0.000%) | . | . |
MITOMAP Disease GenBank Seqs | 187 (0) | . | . |
MITOMAP Disease GenBank Curated refs | 412 | . | . |
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 | . | . |
HelixMTdb AC Hom | 44.0 | . | . |
HelixMTdb AF Hom | 0.00022450926 | . | . |
HelixMTdb AC Het | 34.0 | . | . |
HelixMTdb AF Het | 0.00017348444 | . | . |
HelixMTdb mean ARF | 0.37469 | . | . | HelixMTdb max ARF | 0.91005 | . | . |
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 | . | . | . |