MitImpact id |
MI.23222 |
MI.23220 |
MI.23221 |
Chr |
chrM |
chrM |
chrM |
Start |
14207 |
14207 |
14207 |
Ref |
G |
G |
G |
Alt |
A |
C |
T |
Gene symbol |
MT-ND6 |
MT-ND6 |
MT-ND6 |
Extended annotation |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 |
mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 6 |
Gene position |
467 |
467 |
467 |
Gene start |
14149 |
14149 |
14149 |
Gene end |
14673 |
14673 |
14673 |
Gene strand |
- |
- |
- |
Codon substitution |
ACT/ATT |
ACT/AGT |
ACT/AAT |
AA position |
156 |
156 |
156 |
AA ref |
T |
T |
T |
AA alt |
I |
S |
N |
Functional effect general |
missense |
missense |
missense |
Functional effect detailed |
missense |
missense |
missense |
OMIM id |
516006 |
516006 |
516006 |
HGVS |
NC_012920.1:g.14207G>A |
NC_012920.1:g.14207G>C |
NC_012920.1:g.14207G>T |
HGNC id |
7462 |
7462 |
7462 |
Respiratory Chain complex |
I |
I |
I |
Ensembl gene id |
ENSG00000198695 |
ENSG00000198695 |
ENSG00000198695 |
Ensembl transcript id |
ENST00000361681 |
ENST00000361681 |
ENST00000361681 |
Ensembl protein id |
ENSP00000354665 |
ENSP00000354665 |
ENSP00000354665 |
Uniprot id |
P03923 |
P03923 |
P03923 |
Uniprot name |
NU6M_HUMAN |
NU6M_HUMAN |
NU6M_HUMAN |
Ncbi gene id |
4541 |
4541 |
4541 |
Ncbi protein id |
YP_003024037.1 |
YP_003024037.1 |
YP_003024037.1 |
PhyloP 100V |
0.922 |
0.922 |
0.922 |
PhyloP 470Way |
0.848 |
0.848 |
0.848 |
PhastCons 100V |
0 |
0 |
0 |
PhastCons 470Way |
0.006 |
0.006 |
0.006 |
PolyPhen2 |
benign |
benign |
possibly_damaging |
PolyPhen2 score |
0.36 |
0.37 |
0.82 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.49 |
0.21 |
0.23 |
SIFT4G |
Tolerated |
Tolerated |
Tolerated |
SIFT4G score |
0.05 |
0.861 |
0.091 |
VEST |
Neutral |
Neutral |
Neutral |
VEST pvalue |
0.45 |
0.47 |
0.44 |
VEST FDR |
0.55 |
0.55 |
0.55 |
Mitoclass.1 |
damaging |
neutral |
damaging |
SNPDryad |
Neutral |
Neutral |
Neutral |
SNPDryad score |
0.67 |
0.47 |
0.71 |
MutationTaster |
. |
. |
. |
MutationTaster score |
. |
. |
. |
MutationTaster converted rankscore |
. |
. |
. |
MutationTaster model |
. |
. |
. |
MutationTaster AAE |
. |
. |
. |
fathmm |
Tolerated |
Tolerated |
Tolerated |
fathmm score |
1.7 |
1.74 |
1.69 |
fathmm converted rankscore |
0.26885 |
0.26301 |
0.27032 |
AlphaMissense |
likely_pathogenic |
likely_benign |
likely_pathogenic |
AlphaMissense score |
0.6366 |
0.2038 |
0.6781 |
CADD |
Neutral |
Neutral |
Deleterious |
CADD score |
1.981134 |
-0.402184 |
3.112293 |
CADD phred |
16.09 |
0.382 |
22.5 |
PROVEAN |
Damaging |
Tolerated |
Damaging |
PROVEAN score |
-3.26 |
-1.01 |
-3.12 |
MutationAssessor |
low |
neutral |
medium |
MutationAssessor score |
1.53 |
-0.28 |
2.08 |
EFIN SP |
Neutral |
Neutral |
Neutral |
EFIN SP score |
0.772 |
0.888 |
0.764 |
EFIN HD |
Neutral |
Neutral |
Neutral |
EFIN HD score |
0.48 |
0.976 |
0.518 |
MLC |
Neutral |
Neutral |
Neutral |
MLC score |
0.22937413 |
0.22937413 |
0.22937413 |
PANTHER score |
. |
. |
. |
PhD-SNP score |
. |
. |
. |
APOGEE1 |
Neutral |
Pathogenic |
Neutral |
APOGEE1 score |
0.36 |
0.59 |
0.45 |
APOGEE2 |
VUS- |
Benign |
VUS |
APOGEE2 score |
0.27823764923054 |
0.0547578554035591 |
0.418443805789245 |
CAROL |
neutral |
neutral |
neutral |
CAROL score |
0.43 |
0.75 |
0.88 |
Condel |
deleterious |
neutral |
neutral |
Condel score |
0.57 |
0.42 |
0.21 |
COVEC WMV |
neutral |
neutral |
. |
COVEC WMV score |
-3 |
-6 |
0 |
MtoolBox |
neutral |
neutral |
deleterious |
MtoolBox DS |
0.39 |
0.33 |
0.73 |
DEOGEN2 |
Damaging |
Tolerated |
Damaging |
DEOGEN2 score |
0.537662 |
0.198639 |
0.568479 |
DEOGEN2 converted rankscore |
0.84112 |
0.55568 |
0.85673 |
Meta-SNP |
. |
. |
. |
Meta-SNP score |
. |
. |
. |
PolyPhen2 transf |
medium impact |
medium impact |
low impact |
PolyPhen2 transf score |
-0.57 |
-0.58 |
-1.4 |
SIFT_transf |
medium impact |
medium impact |
medium impact |
SIFT transf score |
0.2 |
-0.11 |
-0.09 |
MutationAssessor transf |
medium impact |
medium impact |
medium impact |
MutationAssessor transf score |
0.83 |
-0.86 |
0.83 |
CHASM |
Neutral |
Neutral |
Neutral |
CHASM pvalue |
0.84 |
0.74 |
0.85 |
CHASM FDR |
0.9 |
0.85 |
0.9 |
ClinVar id |
693690.0 |
. |
. |
ClinVar Allele id |
680580.0 |
. |
. |
ClinVar CLNDISDB |
MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506 |
. |
. |
ClinVar CLNDN |
Leigh_syndrome |
. |
. |
ClinVar CLNSIG |
Benign |
. |
. |
MITOMAP Disease Clinical info |
. |
. |
. |
MITOMAP Disease Status |
. |
. |
. |
MITOMAP Disease Hom/Het |
./. |
./. |
./. |
MITOMAP General GenBank Freq |
0.0654% |
0.0049% |
. |
MITOMAP General GenBank Seqs |
40 |
3 |
. |
MITOMAP General Curated refs |
21978175;22487888;20151402 |
. |
. |
MITOMAP Variant Class |
polymorphism |
polymorphism |
. |
gnomAD 3.1 AN |
56400.0 |
. |
. |
gnomAD 3.1 AC Homo |
21.0 |
. |
. |
gnomAD 3.1 AF Hom |
0.00037234 |
. |
. |
gnomAD 3.1 AC Het |
16.0 |
. |
. |
gnomAD 3.1 AF Het |
0.000283688 |
. |
. |
gnomAD 3.1 filter |
PASS |
. |
. |
HelixMTdb AC Hom |
62.0 |
1.0 |
. |
HelixMTdb AF Hom |
0.00031635398 |
5.1024836e-06 |
. |
HelixMTdb AC Het |
46.0 |
0.0 |
. |
HelixMTdb AF Het |
0.00023471423 |
0.0 |
. |
HelixMTdb mean ARF |
0.35853 |
. |
. |
HelixMTdb max ARF |
0.90566 |
. |
. |
ToMMo 54KJPN AC |
33 |
. |
. |
ToMMo 54KJPN AF |
0.000608 |
. |
. |
ToMMo 54KJPN AN |
54302 |
. |
. |
COSMIC 90 |
. |
. |
. |
dbSNP 156 id |
rs879217937 |
. |
. |