| Chr |
chrM |
chrM |
chrM |
chrM |
chrM |
chrM |
| Start |
3736 |
3736 |
3736 |
3737 |
3737 |
3737 |
| End |
3736 |
3736 |
3736 |
3737 |
3737 |
3737 |
| Ref |
G |
G |
G |
T |
T |
T |
| Alt |
T |
A |
C |
C |
G |
A |
| MitImpact id |
MI.11646 |
MI.11645 |
MI.11644 |
MI.11647 |
MI.11648 |
MI.11649 |
| Gene symbol |
MT-ND1 |
MT-ND1 |
MT-ND1 |
MT-ND1 |
MT-ND1 |
MT-ND1 |
| Respiratory Chain complex |
I |
I |
I |
I |
I |
I |
| Ensembl gene id |
ENSG00000198888 |
ENSG00000198888 |
ENSG00000198888 |
ENSG00000198888 |
ENSG00000198888 |
ENSG00000198888 |
| Ensembl protein id |
ENSP00000354687 |
ENSP00000354687 |
ENSP00000354687 |
ENSP00000354687 |
ENSP00000354687 |
ENSP00000354687 |
| Ensembl transcript id |
ENST00000361390 |
ENST00000361390 |
ENST00000361390 |
ENST00000361390 |
ENST00000361390 |
ENST00000361390 |
| Uniprot name |
NU1M_HUMAN |
NU1M_HUMAN |
NU1M_HUMAN |
NU1M_HUMAN |
NU1M_HUMAN |
NU1M_HUMAN |
| Uniprot id |
P03886 |
P03886 |
P03886 |
P03886 |
P03886 |
P03886 |
| Ncbi gene id |
4535 |
4535 |
4535 |
4535 |
4535 |
4535 |
| Ncbi protein id |
YP_003024026.1 |
YP_003024026.1 |
YP_003024026.1 |
YP_003024026.1 |
YP_003024026.1 |
YP_003024026.1 |
| Gene position |
430 |
430 |
430 |
431 |
431 |
431 |
| AA position |
144 |
144 |
144 |
144 |
144 |
144 |
| AA ref |
V |
V |
V |
V |
V |
V |
| AA alt |
F |
I |
L |
A |
G |
D |
| Codon substitution |
Gtc/Ttc |
Gtc/Atc |
Gtc/Ctc |
gTc/gCc |
gTc/gGc |
gTc/gAc |
| PhyloP 100V |
7.42339 |
7.42339 |
7.42339 |
7.42339 |
7.42339 |
7.42339 |
| PhastCons 100V |
1 |
1 |
1 |
1 |
1 |
1 |
| PolyPhen2 |
benign |
benign |
benign |
possibly_damaging |
probably_damaging |
probably_damaging |
| PolyPhen2 score |
0.11 |
0.05 |
0.39 |
0.64 |
0.93 |
0.95 |
| SIFT |
neutral |
neutral |
neutral |
neutral |
neutral |
neutral |
| SIFT score |
0.54 |
0.47 |
0.61 |
0.65 |
0.28 |
0.16 |
| SIFT4G |
Damaging |
Damaging |
Damaging |
Damaging |
Damaging |
Damaging |
| SIFT4G score |
0.004 |
0.029 |
0.001 |
0 |
0 |
0 |
| FatHmm |
deleterious |
neutral |
neutral |
deleterious |
deleterious |
deleterious |
| FatHmm score |
-4.24 |
-0.5 |
-1.51 |
-3.66 |
-5.79 |
-6.38 |
| FatHmmW |
neutral |
neutral |
neutral |
neutral |
neutral |
neutral |
| FatHmmW score |
2.25 |
2.66 |
2.45 |
2.27 |
2.23 |
2.22 |
| PROVEAN |
deleterious |
neutral |
deleterious |
deleterious |
deleterious |
deleterious |
| PROVEAN score |
-4.54 |
-0.89 |
-2.71 |
-3.63 |
-6.36 |
-6.36 |
| MutationAssessor |
high impact |
low impact |
medium impact |
medium impact |
high impact |
high impact |
| MutationAssessor score |
4.74 |
1.92 |
2.62 |
3.1 |
4.18 |
4.74 |
| EFIN SP |
neutral |
neutral |
neutral |
neutral |
neutral |
neutral |
| EFIN SP score |
0.71 |
0.68 |
0.72 |
0.7 |
0.79 |
0.73 |
| EFIN HD |
neutral |
neutral |
neutral |
neutral |
neutral |
neutral |
| EFIN HD score |
0.5 |
0.6 |
0.49 |
0.57 |
0.57 |
0.49 |
| CADD |
deleterious |
neutral |
neutral |
neutral |
deleterious |
deleterious |
| CADD score |
1.99 |
1.68 |
1.62 |
1.73 |
2.22 |
4.21 |
| CADD phred |
16.13 |
14.29 |
13.94 |
14.6 |
17.61 |
23.9 |
| VEST pvalue |
0.03 |
0.41 |
0.26 |
0.08 |
0.01 |
0.01 |
| VEST FDR |
0.35 |
0.5 |
0.45 |
0.35 |
0.35 |
0.35 |
| PANTHER |
neutral |
neutral |
neutral |
neutral |
disease |
disease |
| PANTHER score |
0.48 |
0.18 |
0.18 |
0.37 |
0.62 |
0.73 |
| PhD-SNP |
disease |
disease |
disease |
disease |
disease |
disease |
| PhD-SNP score |
0.93 |
0.58 |
0.82 |
0.65 |
0.87 |
0.92 |
| SNAP |
disease |
neutral |
disease |
disease |
disease |
disease |
| SNAP score |
0.65 |
0.31 |
0.57 |
0.61 |
0.65 |
0.74 |
| Meta-SNP |
disease |
neutral |
disease |
disease |
disease |
disease |
| Meta-SNP score |
0.75 |
0.2 |
0.66 |
0.65 |
0.71 |
0.73 |
| Meta-SNP RI |
5 |
6 |
3 |
3 |
4 |
5 |
| CAROL |
neutral |
neutral |
neutral |
neutral |
neutral |
neutral |
| CAROL score |
0.37 |
0.48 |
0.35 |
0.57 |
0.94 |
0.97 |
| Condel |
deleterious |
deleterious |
deleterious |
deleterious |
neutral |
neutral |
| Condel score |
0.72 |
0.71 |
0.61 |
0.51 |
0.18 |
0.11 |
| COVEC WMV |
neutral |
neutral |
neutral |
. |
deleterious |
deleterious |
| COVEC WMV score |
-2 |
-6 |
-3 |
0 |
2 |
2 |
| MtoolBox |
neutral |
neutral |
neutral |
deleterious |
deleterious |
deleterious |
| MtoolBox DS |
0.33 |
0.19 |
0.34 |
0.54 |
0.76 |
0.85 |
| PolyPhen2 transf |
medium impact |
medium impact |
medium impact |
medium impact |
low impact |
low impact |
| PolyPhen2 transf score |
0.1 |
0.45 |
-0.57 |
-0.99 |
-1.81 |
-1.95 |
| SIFT_transf |
medium impact |
medium impact |
medium impact |
medium impact |
medium impact |
medium impact |
| SIFT transf score |
0.31 |
0.25 |
0.38 |
0.43 |
0.05 |
-0.13 |
| MutationAssessor transf |
high impact |
medium impact |
medium impact |
medium impact |
high impact |
high impact |
| MutationAssessor transf score |
2.95 |
0.49 |
1.1 |
1.52 |
2.46 |
2.95 |
| CHASM pvalue |
0.28 |
0.72 |
0.32 |
0.11 |
0.31 |
0.14 |
| CHASM FDR |
0.8 |
0.85 |
0.8 |
0.8 |
0.8 |
0.8 |
| APOGEE1 |
Pathogenic |
Pathogenic |
Pathogenic |
Pathogenic |
Pathogenic |
Pathogenic |
| APOGEE1 score |
0.66 |
0.7 |
0.52 |
0.59 |
0.63 |
0.71 |
| APOGEE2 |
VUS+ |
Likely-benign |
VUS+ |
VUS |
Likely-pathogenic |
Likely-pathogenic |
| APOGEE2 score |
0.698312049612463 |
0.202153519417109 |
0.577378868852128 |
0.541663004275382 |
0.730491888263469 |
0.813317475589399 |
| SNPDryad score |
0.98 |
0.08 |
0.69 |
0.87 |
0.96 |
0.99 |
| MutationTaster |
polymorphism |
polymorphism |
polymorphism |
polymorphism |
polymorphism |
polymorphism |
| MutationTaster score |
1 |
1 |
1 |
1 |
1 |
1 |
| DEOGEN2 score |
0.15 |
0.03 |
0.12 |
0.13 |
0.2 |
0.37 |
| Mitoclass.1 |
damaging |
damaging |
damaging |
damaging |
damaging |
damaging |
| dbSNP 155 id |
. |
rs201513497 |
rs201513497 |
rs1603219109 |
. |
. |
| 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 |
. |
0 |
. |
. |
| MITOMAP General GenBank Seqs |
. |
108 |
. |
0 |
. |
. |
| MITOMAP General Curated refs |
. |
4 |
. |
1 |
. |
. |
| gnomAD 3.1 filter |
. |
PASS |
. |
npg |
. |
. |
| gnomAD 3.1 AC Homo |
. |
115 |
. |
0 |
. |
. |
| gnomAD 3.1 AC Het |
. |
8 |
. |
0 |
. |
. |
| gnomAD 3.1 AF Hom |
. |
0.0020383927 |
. |
0 |
. |
. |
| gnomAD 3.1 AF Het |
. |
0.00014180123 |
. |
0 |
. |
. |
| gnomAD 3.1 AN |
. |
56417 |
. |
56431 |
. |
. |
| HelixMTdb AC Hom |
. |
149.0 |
. |
0.0 |
. |
. |
| HelixMTdb AF Hom |
. |
0.00076027005 |
. |
0.0 |
. |
. |
| HelixMTdb AC Het |
. |
24.0 |
. |
1.0 |
. |
. |
| HelixMTdb AF Het |
. |
0.0001224596 |
. |
5.1024836e-06 |
. |
. |
| HelixMTdb mean ARF |
. |
0.39152 |
. |
0.10309 |
. |
. |
HelixMTdb max ARF |
. |
0.72 |
. |
0.10309 |
. |
. |
| 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 |
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 |
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 |
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 |
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: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: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 |
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