MitImpact id |
MI.23813 |
MI.23812 |
Chr |
chrM |
chrM |
Start |
14495 |
14495 |
Ref |
A |
A |
Alt |
G |
C |
Gene symbol |
MT-ND6 |
MT-ND6 |
Extended annotation |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 |
Gene position |
179 |
179 |
Gene start |
14149 |
14149 |
Gene end |
14673 |
14673 |
Gene strand |
- |
- |
Codon substitution |
TTA/TCA |
TTA/TGA |
AA position |
60 |
60 |
AA ref |
L |
L |
AA alt |
S |
W |
Functional effect general |
missense |
missense |
Functional effect detailed |
missense |
missense |
OMIM id |
516006 |
516006 |
HGVS |
NC_012920.1:g.14495A>G |
NC_012920.1:g.14495A>C |
HGNC id |
7462 |
7462 |
Respiratory Chain complex |
I |
I |
Ensembl gene id |
ENSG00000198695 |
ENSG00000198695 |
Ensembl transcript id |
ENST00000361681 |
ENST00000361681 |
Ensembl protein id |
ENSP00000354665 |
ENSP00000354665 |
Uniprot id |
P03923 |
P03923 |
Uniprot name |
NU6M_HUMAN |
NU6M_HUMAN |
Ncbi gene id |
4541 |
4541 |
Ncbi protein id |
YP_003024037.1 |
YP_003024037.1 |
PhyloP 100V |
6.872 |
6.872 |
PhyloP 470Way |
0.819 |
0.819 |
PhastCons 100V |
1 |
1 |
PhastCons 470Way |
0.994 |
0.994 |
PolyPhen2 |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1 |
1 |
SIFT |
neutral |
neutral |
SIFT score |
0.29 |
0.12 |
SIFT4G |
Damaging |
Damaging |
SIFT4G score |
0.0 |
0.0 |
VEST |
Neutral |
Neutral |
VEST pvalue |
0.19 |
0.15 |
VEST FDR |
0.45 |
0.45 |
Mitoclass.1 |
damaging |
damaging |
SNPDryad |
Pathogenic |
Pathogenic |
SNPDryad score |
0.97 |
0.98 |
MutationTaster |
Disease |
. |
MutationTaster score |
1 |
. |
MutationTaster converted rankscore |
0.81001 |
. |
MutationTaster model |
without_aae |
. |
MutationTaster AAE |
. |
. |
fathmm |
Tolerated |
. |
fathmm score |
2.17 |
. |
fathmm converted rankscore |
0.19020 |
. |
AlphaMissense |
likely_pathogenic |
likely_pathogenic |
AlphaMissense score |
0.9348 |
0.9219 |
CADD |
Deleterious |
Deleterious |
CADD score |
3.774913 |
3.292697 |
CADD phred |
23.4 |
22.8 |
PROVEAN |
Damaging |
Damaging |
PROVEAN score |
-5.99 |
-5.99 |
MutationAssessor |
high |
. |
MutationAssessor score |
3.52 |
. |
EFIN SP |
Damaging |
Damaging |
EFIN SP score |
0.232 |
0.502 |
EFIN HD |
Damaging |
Damaging |
EFIN HD score |
0.166 |
0.252 |
MLC |
Neutral |
Neutral |
MLC score |
0.40364536 |
0.40364536 |
PANTHER score |
0.815 |
. |
PhD-SNP score |
0.813 |
. |
APOGEE1 |
Pathogenic |
Neutral |
APOGEE1 score |
0.87 |
0.42 |
APOGEE2 |
Pathogenic |
Likely-pathogenic |
APOGEE2 score |
0.930438486242685 |
0.856900756978538 |
CAROL |
deleterious |
deleterious |
CAROL score |
1.0 |
1.0 |
Condel |
neutral |
neutral |
Condel score |
0.15 |
0.06 |
COVEC WMV |
deleterious |
deleterious |
COVEC WMV score |
2 |
2 |
MtoolBox |
deleterious |
deleterious |
MtoolBox DS |
0.86 |
0.87 |
DEOGEN2 |
Damaging |
. |
DEOGEN2 score |
0.844405 |
. |
DEOGEN2 converted rankscore |
0.96400 |
. |
Meta-SNP |
Disease |
. |
Meta-SNP score |
0.907 |
. |
PolyPhen2 transf |
low impact |
low impact |
PolyPhen2 transf score |
-3.55 |
-3.55 |
SIFT_transf |
medium impact |
medium impact |
SIFT transf score |
-0.01 |
-0.27 |
MutationAssessor transf |
medium impact |
high impact |
MutationAssessor transf score |
1.93 |
2.21 |
CHASM |
Neutral |
Neutral |
CHASM pvalue |
0.64 |
0.68 |
CHASM FDR |
0.8 |
0.85 |
ClinVar id |
9691.0 |
. |
ClinVar Allele id |
24730.0 |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 |
. |
ClinVar CLNDN |
Mitochondrial_disease|Leber_optic_atrophy |
. |
ClinVar CLNSIG |
Likely_pathogenic |
. |
MITOMAP Disease Clinical info |
LHON |
. |
MITOMAP Disease Status |
Cfrm [LP] |
. |
MITOMAP Disease Hom/Het |
-/+ |
./. |
MITOMAP General GenBank Freq |
0.0033% |
. |
MITOMAP General GenBank Seqs |
2 |
. |
MITOMAP General Curated refs |
22879922;11133798;33779865;16380918;15972314;17122117;20301353;21457906;29253894;21397051 |
. |
MITOMAP Variant Class |
disease |
. |
gnomAD 3.1 AN |
. |
. |
gnomAD 3.1 AC Homo |
. |
. |
gnomAD 3.1 AF Hom |
. |
. |
gnomAD 3.1 AC Het |
. |
. |
gnomAD 3.1 AF Het |
. |
. |
gnomAD 3.1 filter |
. |
. |
HelixMTdb AC Hom |
. |
. |
HelixMTdb AF Hom |
. |
. |
HelixMTdb AC Het |
. |
. |
HelixMTdb AF Het |
. |
. |
HelixMTdb mean ARF |
. |
. |
HelixMTdb max ARF |
. |
. |
ToMMo 54KJPN AC |
. |
. |
ToMMo 54KJPN AF |
. |
. |
ToMMo 54KJPN AN |
. |
. |
COSMIC 90 |
. |
. |
dbSNP 156 id |
rs199476106 |
. |