Chr |
chrM |
chrM |
chrM |
Start |
3635 |
3635 |
3635 |
End |
3635 |
3635 |
3635 |
Ref |
G |
G |
G |
Alt |
A |
C |
T |
MitImpact id |
MI.11443 |
MI.11442 |
MI.11444 |
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 |
329 |
329 |
329 |
AA position |
110 |
110 |
110 |
AA ref |
S |
S |
S |
AA alt |
N |
T |
I |
Codon substitution |
aGc/aAc |
aGc/aCc |
aGc/aTc |
PhyloP 100V |
5.5 |
5.5 |
5.5 |
PhastCons 100V |
1 |
1 |
1 |
PolyPhen2 |
probably_damaging |
probably_damaging |
probably_damaging |
PolyPhen2 score |
1 |
1 |
1 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.19 |
0.12 |
0.36 |
FatHmm |
deleterious |
deleterious |
deleterious |
FatHmm score |
-4.17 |
-3.37 |
-5.15 |
FatHmmW |
neutral |
neutral |
neutral |
FatHmmW score |
2.16 |
2.2 |
2.14 |
PROVEAN |
deleterious |
deleterious |
deleterious |
PROVEAN score |
-2.68 |
-2.74 |
-5.49 |
MutationAssessor |
high impact |
medium impact |
high impact |
MutationAssessor score |
4.41 |
2.92 |
4.76 |
EFIN SP |
neutral |
neutral |
neutral |
EFIN SP score |
0.66 |
0.63 |
0.69 |
EFIN HD |
neutral |
neutral |
neutral |
EFIN HD score |
0.45 |
0.41 |
0.51 |
CADD |
deleterious |
deleterious |
deleterious |
CADD score |
3.52 |
3.27 |
4.04 |
CADD phred |
23.1 |
22.8 |
23.7 |
VEST pvalue |
0.29 |
0.24 |
0.05 |
VEST FDR |
0.45 |
0.45 |
0.35 |
PANTHER |
disease |
neutral |
disease |
PANTHER score |
0.62 |
0.38 |
0.51 |
PhD-SNP |
disease |
disease |
disease |
PhD-SNP score |
0.81 |
0.67 |
0.92 |
SNAP |
disease |
disease |
disease |
SNAP score |
0.72 |
0.67 |
0.73 |
Meta-SNP |
disease |
disease |
disease |
Meta-SNP score |
0.72 |
0.65 |
0.76 |
Meta-SNP RI |
4 |
3 |
5 |
CAROL |
deleterious |
deleterious |
deleterious |
CAROL score |
1 |
1 |
1 |
Condel |
neutral |
neutral |
neutral |
Condel score |
0.1 |
0.06 |
0.18 |
COVEC WMV |
deleterious |
deleterious |
deleterious |
COVEC WMV score |
2 |
1 |
2 |
MtoolBox |
deleterious |
deleterious |
deleterious |
MtoolBox DS |
0.8 |
0.75 |
0.82 |
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 |
-0.08 |
-0.21 |
0.14 |
MutationAssessor transf |
high impact |
medium impact |
high impact |
MutationAssessor transf score |
2.66 |
1.36 |
2.97 |
CHASM pvalue |
0.31 |
0.36 |
0.23 |
CHASM FDR |
0.8 |
0.8 |
0.8 |
APOGEE |
Likely-pathogenic |
VUS |
Likely-pathogenic |
APOGEE score |
0.9014272289889737 |
0.6625525142761969 |
0.8445299801075525 |
SNPDryad score |
0.6 |
0.66 |
0.98 |
MutationTaster |
disease_causing_automatic |
polymorphism |
polymorphism |
MutationTaster score |
0 |
1 |
1 |
DEOGEN2 score |
0.44 |
0.22 |
0.32 |
Mitoclass.1 |
damaging |
damaging |
damaging |
dbSNP 155 id |
rs397515507 |
. |
. |
ClinVar October2021 Variation id |
. |
. |
. |
ClinVar October2021 CLNSIG |
. |
. |
. |
ClinVar October2021 CLNDN |
. |
. |
. |
ClinVar October2021 CLNDISDB |
. |
. |
. |
COSMIC 90 |
. |
. |
. |
MITOMAP Allele |
G3635A |
. |
. |
MITOMAP Disease Het/Hom |
+/- |
. |
. |
MITOMAP Disease Clinical info |
LHON |
. |
. |
MITOMAP Disease Status |
Cfrm |
. |
. |
MITOMAP Disease GenBank Freq |
0.000% |
. |
. |
MITOMAP Disease GenBank Seqs |
9 (0) |
. |
. |
MITOMAP Disease GenBank Curated refs |
16 |
. |
. |
MITOMAP General GenBank Freq |
. |
. |
. |
MITOMAP General GenBank Seqs |
. |
. |
. |
MITOMAP General Curated refs |
. |
. |
. |
gnomAD 3.1 filter |
PASS |
. |
. |
gnomAD 3.1 AC Homo |
1 |
. |
. |
gnomAD 3.1 AC Het |
2 |
. |
. |
gnomAD 3.1 AF Hom |
1.7721699e-05 |
. |
. |
gnomAD 3.1 AF Het |
3.5443398e-05 |
. |
. |
gnomAD 3.1 AN |
56428 |
. |
. |
HelixMTdb AC Hom |
0 |
. |
. |
HelixMTdb AF Hom |
0 |
. |
. |
HelixMTdb AC Het |
2 |
. |
. |
HelixMTdb AF Het |
1.0204967e-05 |
. |
. |
HelixMTdb mean ARF |
0.16005 |
. |
. |
HelixMTdb max ARF |
0.2 |
. |
. |
EVmutation |
MT-ND1_110S|143E:0.08754;220F:0.081652;128A:0.080139;150L:0.07081;138Q:0.070111;140I:0.069596;112A:0.065162;113V:0.06453;195R:0.063676 |
MT-ND1_110S|143E:0.08754;220F:0.081652;128A:0.080139;150L:0.07081;138Q:0.070111;140I:0.069596;112A:0.065162;113V:0.06453;195R:0.063676 |
MT-ND1_110S|143E:0.08754;220F:0.081652;128A:0.080139;150L:0.07081;138Q:0.070111;140I:0.069596;112A:0.065162;113V:0.06453;195R:0.063676 |
Site A InterP |
ND1_110 |
ND1_110 |
ND1_110 |
Site B InterP |
ND2_301;ND3_92;ND3_88;ND4_182;ND4_162;ND6_152 |
ND2_301;ND3_92;ND3_88;ND4_182;ND4_162;ND6_152 |
ND2_301;ND3_92;ND3_88;ND4_182;ND4_162;ND6_152 |
Covariation Score InterP |
mfDCA_26.47;mfDCA_21.81;mfDCA_21.51;mfDCA_25.17;mfDCA_24.64;mfDCA_36.37 |
mfDCA_26.47;mfDCA_21.81;mfDCA_21.51;mfDCA_25.17;mfDCA_24.64;mfDCA_36.37 |
mfDCA_26.47;mfDCA_21.81;mfDCA_21.51;mfDCA_25.17;mfDCA_24.64;mfDCA_36.37 |
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 |
MT-ND1:MT-ND3:5ldw:H:A:S110N:L92I:0.09732:-0.065448761:0.16793099;MT-ND1:MT-ND3:5ldw:H:A:S110N:L92H:1.6902:-0.065448761:1.3556602;MT-ND1:MT-ND3:5ldw:H:A:S110N:L92V:0.59927:-0.065448761:0.702309787;MT-ND1:MT-ND3:5ldw:H:A:S110N:L92P:1.50351:-0.065448761:1.50191998;MT-ND1:MT-ND3:5ldw:H:A:S110N:L92R:0.42064:-0.065448761:0.488179773;MT-ND1:MT-ND3:5ldw:H:A:S110N:L92F:1.2334:-0.065448761:1.34787941;MT-ND1:MT-ND3:5ldw:H:A:S110N:V88L:-0.82686:-0.065448761:-0.735748291;MT-ND1:MT-ND3:5ldw:H:A:S110N:V88A:1.05173:-0.065448761:1.03500056;MT-ND1:MT-ND3:5ldw:H:A:S110N:V88F:1.16857:-0.065448761:1.28829992;MT-ND1:MT-ND3:5ldw:H:A:S110N:V88D:2.02358:-0.065448761:2.07409167;MT-ND1:MT-ND3:5ldw:H:A:S110N:V88G:1.21653:-0.065448761:1.25951159;MT-ND1:MT-ND3:5ldw:H:A:S110N:V88I:-0.43739:-0.065448761:-0.326898187;MT-ND1:MT-ND3:5ldx:H:A:S110N:L92I:0.12733:0.0408100113:0.0743099228;MT-ND1:MT-ND3:5ldx:H:A:S110N:L92H:1.38491:0.0408100113:0.948080838;MT-ND1:MT-ND3:5ldx:H:A:S110N:L92V:0.73549:0.0408100113:0.683309913;MT-ND1:MT-ND3:5ldx:H:A:S110N:L92P:1.58808:0.0408100113:1.50272024;MT-ND1:MT-ND3:5ldx:H:A:S110N:L92R:0.30507:0.0408100113:0.361429989;MT-ND1:MT-ND3:5ldx:H:A:S110N:L92F:1.11695:0.0408100113:0.761830509;MT-ND1:MT-ND3:5ldx:H:A:S110N:V88L:-0.71435:0.0408100113:-0.704050064;MT-ND1:MT-ND3:5ldx:H:A:S110N:V88A:0.8689:0.0408100113:0.87761879;MT-ND1:MT-ND3:5ldx:H:A:S110N:V88F:1.55018:0.0408100113:1.55911982;MT-ND1:MT-ND3:5ldx:H:A:S110N:V88D:1.71795:0.0408100113:1.69415927;MT-ND1:MT-ND3:5ldx:H:A:S110N:V88G:1.06067:0.0408100113:1.0098598;MT-ND1:MT-ND3:5ldx:H:A:S110N:V88I:-0.25495:0.0408100113:-0.256721109 |
MT-ND1:MT-ND3:5ldw:H:A:S110T:L92V:0.74797:0.0389705673:0.702309787;MT-ND1:MT-ND3:5ldw:H:A:S110T:L92P:1.5274:0.0389705673:1.50191998;MT-ND1:MT-ND3:5ldw:H:A:S110T:L92I:0.19537:0.0389705673:0.16793099;MT-ND1:MT-ND3:5ldw:H:A:S110T:L92R:0.5067:0.0389705673:0.488179773;MT-ND1:MT-ND3:5ldw:H:A:S110T:L92F:1.34728:0.0389705673:1.34787941;MT-ND1:MT-ND3:5ldw:H:A:S110T:L92H:1.80532:0.0389705673:1.3556602;MT-ND1:MT-ND3:5ldw:H:A:S110T:V88D:2.14781:0.0389705673:2.07409167;MT-ND1:MT-ND3:5ldw:H:A:S110T:V88F:1.81814:0.0389705673:1.28829992;MT-ND1:MT-ND3:5ldw:H:A:S110T:V88I:-0.29214:0.0389705673:-0.326898187;MT-ND1:MT-ND3:5ldw:H:A:S110T:V88G:1.31525:0.0389705673:1.25951159;MT-ND1:MT-ND3:5ldw:H:A:S110T:V88L:-0.69363:0.0389705673:-0.735748291;MT-ND1:MT-ND3:5ldw:H:A:S110T:V88A:1.07805:0.0389705673:1.03500056;MT-ND1:MT-ND3:5ldx:H:A:S110T:L92V:0.7277:0.0469390862:0.683309913;MT-ND1:MT-ND3:5ldx:H:A:S110T:L92P:1.50927:0.0469390862:1.50272024;MT-ND1:MT-ND3:5ldx:H:A:S110T:L92I:0.12756:0.0469390862:0.0743099228;MT-ND1:MT-ND3:5ldx:H:A:S110T:L92R:0.29659:0.0469390862:0.361429989;MT-ND1:MT-ND3:5ldx:H:A:S110T:L92F:0.86018:0.0469390862:0.761830509;MT-ND1:MT-ND3:5ldx:H:A:S110T:L92H:1.40112:0.0469390862:0.948080838;MT-ND1:MT-ND3:5ldx:H:A:S110T:V88D:1.74035:0.0469390862:1.69415927;MT-ND1:MT-ND3:5ldx:H:A:S110T:V88F:1.62684:0.0469390862:1.55911982;MT-ND1:MT-ND3:5ldx:H:A:S110T:V88I:-0.21785:0.0469390862:-0.256721109;MT-ND1:MT-ND3:5ldx:H:A:S110T:V88G:1.08482:0.0469390862:1.0098598;MT-ND1:MT-ND3:5ldx:H:A:S110T:V88L:-0.6969:0.0469390862:-0.704050064;MT-ND1:MT-ND3:5ldx:H:A:S110T:V88A:0.89326:0.0469390862:0.87761879 |
MT-ND1:MT-ND3:5ldw:H:A:S110I:L92H:1.72642:-0.132949829:1.3556602;MT-ND1:MT-ND3:5ldw:H:A:S110I:L92P:1.24051:-0.132949829:1.50191998;MT-ND1:MT-ND3:5ldw:H:A:S110I:L92V:0.55188:-0.132949829:0.702309787;MT-ND1:MT-ND3:5ldw:H:A:S110I:L92F:1.22293:-0.132949829:1.34787941;MT-ND1:MT-ND3:5ldw:H:A:S110I:L92I:-0.00531:-0.132949829:0.16793099;MT-ND1:MT-ND3:5ldw:H:A:S110I:L92R:0.25836:-0.132949829:0.488179773;MT-ND1:MT-ND3:5ldw:H:A:S110I:V88A:0.87451:-0.132949829:1.03500056;MT-ND1:MT-ND3:5ldw:H:A:S110I:V88L:-0.88897:-0.132949829:-0.735748291;MT-ND1:MT-ND3:5ldw:H:A:S110I:V88G:1.10355:-0.132949829:1.25951159;MT-ND1:MT-ND3:5ldw:H:A:S110I:V88F:0.91761:-0.132949829:1.28829992;MT-ND1:MT-ND3:5ldw:H:A:S110I:V88I:-0.48093:-0.132949829:-0.326898187;MT-ND1:MT-ND3:5ldw:H:A:S110I:V88D:1.94377:-0.132949829:2.07409167;MT-ND1:MT-ND3:5ldx:H:A:S110I:L92H:1.63662:0.00460014353:0.948080838;MT-ND1:MT-ND3:5ldx:H:A:S110I:L92P:1.38591:0.00460014353:1.50272024;MT-ND1:MT-ND3:5ldx:H:A:S110I:L92V:0.71864:0.00460014353:0.683309913;MT-ND1:MT-ND3:5ldx:H:A:S110I:L92F:0.56534:0.00460014353:0.761830509;MT-ND1:MT-ND3:5ldx:H:A:S110I:L92I:0.07108:0.00460014353:0.0743099228;MT-ND1:MT-ND3:5ldx:H:A:S110I:L92R:0.41893:0.00460014353:0.361429989;MT-ND1:MT-ND3:5ldx:H:A:S110I:V88A:0.88014:0.00460014353:0.87761879;MT-ND1:MT-ND3:5ldx:H:A:S110I:V88L:-0.64795:0.00460014353:-0.704050064;MT-ND1:MT-ND3:5ldx:H:A:S110I:V88G:1.00283:0.00460014353:1.0098598;MT-ND1:MT-ND3:5ldx:H:A:S110I:V88F:2.04248:0.00460014353:1.55911982;MT-ND1:MT-ND3:5ldx:H:A:S110I:V88I:-0.22589:0.00460014353:-0.256721109;MT-ND1:MT-ND3:5ldx:H:A:S110I:V88D:1.74737:0.00460014353:1.69415927 |