~ | 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 | . | . | . |