~ | 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 | 9.06334 | 9.06334 | 9.06334 |
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 | 1.0 |
SIFT4G | Damaging | Damaging | Damaging |
SIFT4G score | 0 | 0 | 0 |
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 | 4.0 |
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 | 1.0 | 1.0 | 1.0 |
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 |
APOGEE1 | Pathogenic | Pathogenic | Pathogenic |
APOGEE1 score | 0.97 | 0.89 | 0.82 |
APOGEE2 | Pathogenic | Likely-pathogenic | Likely-pathogenic |
APOGEE2 score | 0.917725267895409 | 0.834280803179125 | 0.844457955738889 |
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 July2022 Variation id | . | . | . |
ClinVar July2022 CLNSIG | . | . | . |
ClinVar July2022 CLNDN | . | . | . |
ClinVar July2022 CLNDISDB | . | . | . |
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 [P] | . | . |
MITOMAP Disease GenBank Freq | 0.002%(0.000%) | . | . |
MITOMAP Disease GenBank Seqs | 1 (0) | . | . |
MITOMAP Disease GenBank Curated refs | 56 | . | . |
MITOMAP General GenBank Freq | . | 0.00002 | . |
MITOMAP General GenBank Seqs | . | 1 | . |
MITOMAP General Curated refs | . | 1 | . |
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 | . | . |
HelixMTdb AC Hom | . | . | . |
HelixMTdb AF Hom | . | . | . |
HelixMTdb AC Het | . | . | . |
HelixMTdb AF Het | . | . | . |
HelixMTdb mean ARF | . | . | . | HelixMTdb max ARF | . | . | . |
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 | . | . | . |