Chr |
chrM |
chrM |
chrM |
Start |
3736 |
3736 |
3736 |
End |
3736 |
3736 |
3736 |
Ref |
G |
G |
G |
Alt |
A |
T |
C |
MitImpact id |
MI.11645 |
MI.11646 |
MI.11644 |
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 |
430 |
430 |
430 |
AA position |
144 |
144 |
144 |
AA ref |
V |
V |
V |
AA alt |
I |
F |
L |
Codon substitution |
Gtc/Atc |
Gtc/Ttc |
Gtc/Ctc |
PhyloP 100V |
7.42339 |
7.42339 |
7.42339 |
PhastCons 100V |
1 |
1 |
1 |
PolyPhen2 |
benign |
benign |
benign |
PolyPhen2 score |
0.05 |
0.11 |
0.39 |
SIFT |
neutral |
neutral |
neutral |
SIFT score |
0.47 |
0.54 |
0.61 |
SIFT4G |
Damaging |
Damaging |
Damaging |
SIFT4G score |
0.029 |
0.004 |
0.001 |
FatHmm |
neutral |
deleterious |
neutral |
FatHmm score |
-0.5 |
-4.24 |
-1.51 |
FatHmmW |
neutral |
neutral |
neutral |
FatHmmW score |
2.66 |
2.25 |
2.45 |
PROVEAN |
neutral |
deleterious |
deleterious |
PROVEAN score |
-0.89 |
-4.54 |
-2.71 |
MutationAssessor |
low impact |
high impact |
medium impact |
MutationAssessor score |
1.92 |
4.74 |
2.62 |
EFIN SP |
neutral |
neutral |
neutral |
EFIN SP score |
0.68 |
0.71 |
0.72 |
EFIN HD |
neutral |
neutral |
neutral |
EFIN HD score |
0.6 |
0.5 |
0.49 |
CADD |
neutral |
deleterious |
neutral |
CADD score |
1.68 |
1.99 |
1.62 |
CADD phred |
14.29 |
16.13 |
13.94 |
VEST pvalue |
0.41 |
0.03 |
0.26 |
VEST FDR |
0.5 |
0.35 |
0.45 |
PANTHER |
neutral |
neutral |
neutral |
PANTHER score |
0.18 |
0.48 |
0.18 |
PhD-SNP |
disease |
disease |
disease |
PhD-SNP score |
0.58 |
0.93 |
0.82 |
SNAP |
neutral |
disease |
disease |
SNAP score |
0.31 |
0.65 |
0.57 |
Meta-SNP |
neutral |
disease |
disease |
Meta-SNP score |
0.2 |
0.75 |
0.66 |
Meta-SNP RI |
6 |
5 |
3 |
CAROL |
neutral |
neutral |
neutral |
CAROL score |
0.48 |
0.37 |
0.35 |
Condel |
deleterious |
deleterious |
deleterious |
Condel score |
0.71 |
0.72 |
0.61 |
COVEC WMV |
neutral |
neutral |
neutral |
COVEC WMV score |
-6 |
-2 |
-3 |
MtoolBox |
neutral |
neutral |
neutral |
MtoolBox DS |
0.19 |
0.33 |
0.34 |
PolyPhen2 transf |
medium impact |
medium impact |
medium impact |
PolyPhen2 transf score |
0.45 |
0.1 |
-0.57 |
SIFT_transf |
medium impact |
medium impact |
medium impact |
SIFT transf score |
0.25 |
0.31 |
0.38 |
MutationAssessor transf |
medium impact |
high impact |
medium impact |
MutationAssessor transf score |
0.49 |
2.95 |
1.1 |
CHASM pvalue |
0.72 |
0.28 |
0.32 |
CHASM FDR |
0.85 |
0.8 |
0.8 |
APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
APOGEE1 score |
0.7 |
0.66 |
0.52 |
APOGEE2 |
Likely-benign |
VUS+ |
VUS+ |
APOGEE2 score |
0.202153519417109 |
0.698312049612463 |
0.577378868852128 |
SNPDryad score |
0.08 |
0.98 |
0.69 |
MutationTaster |
polymorphism |
polymorphism |
polymorphism |
MutationTaster score |
1 |
1 |
1 |
DEOGEN2 score |
0.03 |
0.15 |
0.12 |
Mitoclass.1 |
damaging |
damaging |
damaging |
dbSNP 155 id |
rs201513497 |
. |
rs201513497 |
ClinVar July2022 Variation id |
. |
. |
. |
ClinVar July2022 CLNSIG |
. |
. |
. |
ClinVar July2022 CLNDN |
. |
. |
. |
ClinVar July2022 CLNDISDB |
. |
. |
. |
COSMIC 90 |
COSM6716702 |
. |
. |
MITOMAP Allele |
G3736A |
. |
. |
MITOMAP Disease Het/Hom |
nr/nr |
. |
. |
MITOMAP Disease Clinical info |
LHON |
. |
. |
MITOMAP Disease Status |
Reported |
. |
. |
MITOMAP Disease GenBank Freq |
0.182%(0.000%) |
. |
. |
MITOMAP Disease GenBank Seqs |
108 (0) |
. |
. |
MITOMAP Disease GenBank Curated refs |
2 |
. |
. |
MITOMAP General GenBank Freq |
0.00182 |
. |
. |
MITOMAP General GenBank Seqs |
108 |
. |
. |
MITOMAP General Curated refs |
4 |
. |
. |
gnomAD 3.1 filter |
PASS |
. |
. |
gnomAD 3.1 AC Homo |
115 |
. |
. |
gnomAD 3.1 AC Het |
8 |
. |
. |
gnomAD 3.1 AF Hom |
0.0020383927 |
. |
. |
gnomAD 3.1 AF Het |
0.00014180123 |
. |
. |
gnomAD 3.1 AN |
56417 |
. |
. |
HelixMTdb AC Hom |
149.0 |
. |
. |
HelixMTdb AF Hom |
0.00076027005 |
. |
. |
HelixMTdb AC Het |
24.0 |
. |
. |
HelixMTdb AF Het |
0.0001224596 |
. |
. |
HelixMTdb mean ARF |
0.39152 |
. |
. |
HelixMTdb max ARF |
0.72 |
. |
. |
EVmutation |
MT-ND1_144V|145T:0.199006;294L:0.154717;301L:0.09302;148I:0.084539;278P:0.069915;191A:0.065596 |
MT-ND1_144V|145T:0.199006;294L:0.154717;301L:0.09302;148I:0.084539;278P:0.069915;191A:0.065596 |
MT-ND1_144V|145T:0.199006;294L:0.154717;301L:0.09302;148I:0.084539;278P:0.069915;191A:0.065596 |
Site A InterP |
ND1_144 |
ND1_144 |
ND1_144 |
Site B InterP |
ND3_10;ND6_116;ND6_109 |
ND3_10;ND6_116;ND6_109 |
ND3_10;ND6_116;ND6_109 |
Covariation Score InterP |
mfDCA_23.8;mfDCA_24.26;mfDCA_22.08 |
mfDCA_23.8;mfDCA_24.26;mfDCA_22.08 |
mfDCA_23.8;mfDCA_24.26;mfDCA_22.08 |
Site A IntraP |
. |
. |
. |
Site B IntraP |
. |
. |
. |
Covariation Score IntraP |
. |
. |
. |
CPD AA ref |
V |
. |
. |
CPD AA alt |
I |
. |
. |
CPD Aln pos |
145 |
. |
. |
CPD Frequency |
0.89 |
. |
. |
CPD Species name |
Lepilemur hubbardorum,Lepilemur ruficaudatus,Pongo pygmaeus,Macaca sylvanus,Pongo abelii,Nomascus gabriellae |
. |
. |
CPD RefSeq Protein ID |
YP_003856721,YP_008379047,NP_008225,NP_114334,NP_007835,YP_006883018 |
. |
. |
CPD Ncbi Taxon id |
756882,78866,9600,9546,9601,61852 |
. |
. |
DDG intra |
. |
. |
. |
DDG intra interface |
. |
. |
. |
DDG inter |
MT-ND1:MT-ND3:5lc5:H:A:V144I:N10H:-0.84139:-0.425349414:-0.468639374;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10K:-0.16116:-0.425349414:0.559670269;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10S:0.5813:-0.425349414:1.00994909;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10I:-0.54679:-0.425349414:-0.200120538;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10T:-1.33442:-0.425349414:-0.845690131;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10D:1.4578:-0.425349414:1.9348892;MT-ND1:MT-ND3:5lc5:H:A:V144I:N10Y:-0.55928:-0.425349414:-1.04049873;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10H:-2.16077:-0.742519736:-1.41110837;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10K:-1.24705:-0.742519736:-0.557247937;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10S:-0.02027:-0.742519736:0.722851157;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10I:-2.80958:-0.742519736:-1.98465884;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10T:-1.76381:-0.742519736:-0.944197059;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10D:0.76455:-0.742519736:1.56138194;MT-ND1:MT-ND3:5ldw:H:A:V144I:N10Y:-2.80113:-0.742519736:-1.868029;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10H:-1.89614:-0.622790158:-1.23474002;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10K:-1.46186:-0.622790158:-0.983650565;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10S:0.27821:-0.622790158:0.834559619;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10I:-2.35861:-0.622790158:-1.75487101;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10T:-1.25017:-0.622790158:-0.727460086;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10D:1.20721:-0.622790158:1.77093887;MT-ND1:MT-ND3:5ldx:H:A:V144I:N10Y:-2.90714:-0.622790158:-1.7146492 |
MT-ND1:MT-ND3:5lc5:H:A:V144F:N10K:1.56466:0.667149723:0.559670269;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10T:0.04708:0.667149723:-0.845690131;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10H:-0.04231:0.667149723:-0.468639374;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10Y:-0.30979:0.667149723:-1.04049873;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10S:1.74823:0.667149723:1.00994909;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10I:0.1666:0.667149723:-0.200120538;MT-ND1:MT-ND3:5lc5:H:A:V144F:N10D:2.6989:0.667149723:1.9348892;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10K:0.30533:1.16558003:-0.557247937;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10T:0.12131:1.16558003:-0.944197059;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10H:-0.32227:1.16558003:-1.41110837;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10Y:-0.82489:1.16558003:-1.868029;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10S:1.81696:1.16558003:0.722851157;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10I:-1.08114:1.16558003:-1.98465884;MT-ND1:MT-ND3:5ldw:H:A:V144F:N10D:2.45502:1.16558003:1.56138194;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10K:0.0192:0.767220318:-0.983650565;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10T:0.0218:0.767220318:-0.727460086;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10H:-0.54073:0.767220318:-1.23474002;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10Y:-1.89816:0.767220318:-1.7146492;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10S:1.68158:0.767220318:0.834559619;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10I:-0.86444:0.767220318:-1.75487101;MT-ND1:MT-ND3:5ldx:H:A:V144F:N10D:2.41322:0.767220318:1.77093887 |
MT-ND1:MT-ND3:5lc5:H:A:V144L:N10D:-0.41196:-2.40359163:1.9348892;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10T:-3.0952:-2.40359163:-0.845690131;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10H:-3.18939:-2.40359163:-0.468639374;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10K:-2.06377:-2.40359163:0.559670269;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10Y:-2.80684:-2.40359163:-1.04049873;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10I:-2.86892:-2.40359163:-0.200120538;MT-ND1:MT-ND3:5lc5:H:A:V144L:N10S:-1.30784:-2.40359163:1.00994909;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10D:0.5791:-0.945389569:1.56138194;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10T:-1.89848:-0.945389569:-0.944197059;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10H:-2.28821:-0.945389569:-1.41110837;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10K:-1.263:-0.945389569:-0.557247937;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10Y:-2.68569:-0.945389569:-1.868029;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10I:-2.92276:-0.945389569:-1.98465884;MT-ND1:MT-ND3:5ldw:H:A:V144L:N10S:-0.19617:-0.945389569:0.722851157;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10D:0.66908:-1.05275989:1.77093887;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10T:-1.6146:-1.05275989:-0.727460086;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10H:-2.23498:-1.05275989:-1.23474002;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10K:-2.04694:-1.05275989:-0.983650565;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10Y:-3.41559:-1.05275989:-1.7146492;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10I:-2.75453:-1.05275989:-1.75487101;MT-ND1:MT-ND3:5ldx:H:A:V144L:N10S:-0.09797:-1.05275989:0.834559619 |