Chr |
chrM |
chrM |
chrM |
Start |
14484 |
14484 |
14484 |
End |
14484 |
14484 |
14484 |
Ref |
T |
T |
T |
Alt |
C |
G |
A |
MitImpact id |
MI.23790 |
MI.23792 |
MI.23791 |
Gene symbol |
MT-ND6 |
MT-ND6 |
MT-ND6 |
Respiratory Chain complex |
I |
I |
I |
Ensembl gene id |
ENSG00000198695 |
ENSG00000198695 |
ENSG00000198695 |
Ensembl protein id |
ENSP00000354665 |
ENSP00000354665 |
ENSP00000354665 |
Ensembl transcript id |
ENST00000361681 |
ENST00000361681 |
ENST00000361681 |
Uniprot name |
NU6M_HUMAN |
NU6M_HUMAN |
NU6M_HUMAN |
Uniprot id |
P03923 |
P03923 |
P03923 |
Ncbi gene id |
4541 |
4541 |
4541 |
Ncbi protein id |
YP_003024037.1 |
YP_003024037.1 |
YP_003024037.1 |
Gene position |
190 |
190 |
190 |
AA position |
64 |
64 |
64 |
AA ref |
M |
M |
M |
AA alt |
V |
L |
L |
Codon substitution |
Atg/Gtg |
Atg/Ctg |
Atg/Ttg |
PhyloP 100V |
-1.56032 |
-1.56032 |
-1.56032 |
PhastCons 100V |
0 |
0 |
0 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
0.99 |
0.98 |
0.98 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.49 |
1.0 |
1.0 |
SIFT4G |
Damaging |
Tolerated |
Tolerated |
SIFT4G score |
0.002 |
1 |
1 |
FatHmm |
neutral |
neutral |
neutral |
FatHmm score |
-0.49 |
0.6 |
0.6 |
FatHmmW |
neutral |
neutral |
neutral |
FatHmmW score |
2.26 |
2.42 |
2.42 |
PROVEAN |
neutral |
neutral |
neutral |
PROVEAN score |
-1.97 |
0.36 |
0.36 |
MutationAssessor |
medium impact |
neutral impact |
neutral impact |
MutationAssessor score |
3.06 |
0 |
0 |
EFIN SP |
damaging |
neutral |
neutral |
EFIN SP score |
0.24 |
0.84 |
0.84 |
EFIN HD |
neutral |
neutral |
neutral |
EFIN HD score |
0.47 |
0.98 |
0.98 |
CADD |
neutral |
neutral |
neutral |
CADD score |
0.89 |
-1.1 |
-0.99 |
CADD phred |
10.02 |
0.01 |
0.02 |
VEST pvalue |
0.39 |
0.33 |
0.33 |
VEST FDR |
0.5 |
0.5 |
0.5 |
PANTHER |
neutral |
neutral |
neutral |
PANTHER score |
0.23 |
0.17 |
0.17 |
PhD-SNP |
disease |
disease |
disease |
PhD-SNP score |
0.92 |
0.54 |
0.54 |
SNAP |
disease |
neutral |
neutral |
SNAP score |
0.61 |
0.38 |
0.38 |
Meta-SNP |
disease |
neutral |
neutral |
Meta-SNP score |
0.81 |
0.42 |
0.42 |
Meta-SNP RI |
6 |
2 |
2 |
CAROL |
deleterious |
neutral |
neutral |
CAROL score |
0.99 |
0.98 |
0.98 |
Condel |
neutral |
deleterious |
deleterious |
Condel score |
0.25 |
0.51 |
0.51 |
COVEC WMV |
deleterious |
neutral |
neutral |
COVEC WMV score |
1 |
-2 |
-2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.8 |
0.66 |
0.66 |
PolyPhen2 transf |
low impact |
low impact |
low impact |
PolyPhen2 transf score |
-2.63 |
-2.35 |
-2.35 |
SIFT_transf |
medium impact |
high impact |
high impact |
SIFT transf score |
0.2 |
1.87 |
1.87 |
MutationAssessor transf |
medium impact |
low impact |
low impact |
MutationAssessor transf score |
1.42 |
-1.14 |
-1.14 |
CHASM pvalue |
0.58 |
0.64 |
0.64 |
CHASM FDR |
0.8 |
0.8 |
0.8 |
APOGEE1 |
Pathogenic |
Neutral |
Neutral |
APOGEE1 score |
0.95 |
0.41 |
0.42 |
APOGEE2 |
Likely-pathogenic |
Likely-benign |
Likely-benign |
APOGEE2 score |
0.897187271374113 |
0.080828708259613 |
0.080828708259613 |
SNPDryad score |
0.71 |
0.25 |
0.25 |
MutationTaster |
. |
. |
. |
MutationTaster score |
. |
. |
. |
DEOGEN2 score |
0.39 |
0.2 |
0.2 |
Mitoclass.1 |
neutral |
neutral |
neutral |
dbSNP 155 id |
. |
. |
. |
ClinVar July2022 Variation id |
. |
. |
. |
ClinVar July2022 CLNSIG |
. |
. |
. |
ClinVar July2022 CLNDN |
. |
. |
. |
ClinVar July2022 CLNDISDB |
. |
. |
. |
COSMIC 90 |
. |
. |
. |
MITOMAP Allele |
T14484C |
. |
. |
MITOMAP Disease Het/Hom |
+/+ |
. |
. |
MITOMAP Disease Clinical info |
LHON |
. |
. |
MITOMAP Disease Status |
Cfrm [P] |
. |
. |
MITOMAP Disease GenBank Freq |
0.114%(0.000%) |
. |
. |
MITOMAP Disease GenBank Seqs |
68 (0) |
. |
. |
MITOMAP Disease GenBank Curated refs |
262 |
. |
. |
MITOMAP General GenBank Freq |
. |
0 |
0 |
MITOMAP General GenBank Seqs |
. |
0 |
0 |
MITOMAP General Curated refs |
. |
1 |
1 |
gnomAD 3.1 filter |
PASS |
. |
PASS |
gnomAD 3.1 AC Homo |
30 |
. |
1 |
gnomAD 3.1 AC Het |
7 |
. |
0 |
gnomAD 3.1 AF Hom |
0.0005316604 |
. |
0.000017719814 |
gnomAD 3.1 AF Het |
0.00012405409 |
. |
0 |
gnomAD 3.1 AN |
56427 |
. |
56434 |
HelixMTdb AC Hom |
144.0 |
1.0 |
3.0 |
HelixMTdb AF Hom |
0.00073475763 |
5.1024836e-06 |
1.530745e-05 |
HelixMTdb AC Het |
26.0 |
0.0 |
0.0 |
HelixMTdb AF Het |
0.00013266457 |
0.0 |
0.0 |
HelixMTdb mean ARF |
0.34311 |
. |
. |
HelixMTdb max ARF |
0.82803 |
. |
. |
EVmutation |
MT-ND6_64M|140I:0.138042;171A:0.090933;170I:0.08143;157G:0.076795;75I:0.070908;101G:0.064738 |
MT-ND6_64M|140I:0.138042;171A:0.090933;170I:0.08143;157G:0.076795;75I:0.070908;101G:0.064738 |
MT-ND6_64M|140I:0.138042;171A:0.090933;170I:0.08143;157G:0.076795;75I:0.070908;101G:0.064738 |
Site A InterP |
ND6_64 |
ND6_64 |
ND6_64 |
Site B InterP |
ND1_225;ND3_24 |
ND1_225;ND3_24 |
ND1_225;ND3_24 |
Covariation Score InterP |
mfDCA_26.74;mfDCA_19.8 |
mfDCA_26.74;mfDCA_19.8 |
mfDCA_26.74;mfDCA_19.8 |
Site A IntraP |
ND6_64 |
ND6_64 |
ND6_64 |
Site B IntraP |
ND6_15 |
ND6_15 |
ND6_15 |
Covariation Score IntraP |
mfDCA_15.0909 |
mfDCA_15.0909 |
mfDCA_15.0909 |
CPD AA ref |
M |
. |
. |
CPD AA alt |
V |
. |
. |
CPD Aln pos |
66 |
. |
. |
CPD Frequency |
0.15 |
. |
. |
CPD Species name |
Meriones unguiculatus |
. |
. |
CPD RefSeq Protein ID |
YP_008994666 |
. |
. |
CPD Ncbi Taxon id |
10047 |
. |
. |
DDG intra |
MT-ND6:M64V:G15V:7.0165:1.88842:5.16697;MT-ND6:M64V:G15R:5.23277:1.88842:3.49027;MT-ND6:M64V:G15E:6.93709:1.88842:5.18405;MT-ND6:M64V:G15W:11.1379:1.88842:9.69947;MT-ND6:M64V:G15A:1.48748:1.88842:-0.423829 |
MT-ND6:M64L:G15A:-0.53137:-0.0980552:-0.423829;MT-ND6:M64L:G15V:5.08609:-0.0980552:5.16697;MT-ND6:M64L:G15W:9.27804:-0.0980552:9.69947;MT-ND6:M64L:G15R:3.52763:-0.0980552:3.49027;MT-ND6:M64L:G15E:5.07221:-0.0980552:5.18405;MT-ND6:M64L:G15E:5.07221:-0.0980552:5.18405 |
MT-ND6:M64L:G15A:-0.53137:-0.0980552:-0.423829;MT-ND6:M64L:G15V:5.08609:-0.0980552:5.16697;MT-ND6:M64L:G15W:9.27804:-0.0980552:9.69947;MT-ND6:M64L:G15R:3.52763:-0.0980552:3.49027;MT-ND6:M64L:G15E:5.07221:-0.0980552:5.18405;MT-ND6:M64L:G15E:5.07221:-0.0980552:5.18405 |
DDG intra interface |
. |
. |
. |
DDG inter |
. |
. |
. |