news model
license
| ~ | 3736 (G/C) | 3736 (G/A) | 3736 (G/T) | 3737 (T/C) | 3737 (T/G) | 3737 (T/A) |
|---|---|---|---|---|---|---|
| ~ | 3736 (Gtc/Ctc) | 3736 (Gtc/Atc) | 3736 (Gtc/Ttc) | 3737 (gTc/gCc) | 3737 (gTc/gGc) | 3737 (gTc/gAc) |
| 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 | C | A | T | C | G | A |
| MitImpact id | MI.11644 | MI.11645 | MI.11646 | 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 | L | I | F | A | G | D |
| Codon substitution | Gtc/Ctc | Gtc/Atc | Gtc/Ttc | gTc/gCc | gTc/gGc | gTc/gAc |
| PhyloP 100V | 4.58 | 4.58 | 4.58 | 7.11 | 7.11 | 7.11 |
| PhastCons 100V | 1 | 1 | 1 | 1 | 1 | 1 |
| PolyPhen2 | benign | benign | benign | possibly_damaging | probably_damaging | probably_damaging |
| PolyPhen2 score | 0.39 | 0.05 | 0.11 | 0.64 | 0.93 | 0.95 |
| SIFT | neutral | neutral | neutral | neutral | neutral | neutral |
| SIFT score | 0.61 | 0.47 | 0.54 | 0.65 | 0.28 | 0.16 |
| FatHmm | neutral | neutral | deleterious | deleterious | deleterious | deleterious |
| FatHmm score | -1.51 | -0.5 | -4.24 | -3.66 | -5.79 | -6.38 |
| FatHmmW | neutral | neutral | neutral | neutral | neutral | neutral |
| FatHmmW score | 2.45 | 2.66 | 2.25 | 2.27 | 2.23 | 2.22 |
| PROVEAN | deleterious | neutral | deleterious | deleterious | deleterious | deleterious |
| PROVEAN score | -2.71 | -0.89 | -4.54 | -3.63 | -6.36 | -6.36 |
| MutationAssessor | medium impact | low impact | high impact | medium impact | high impact | high impact |
| MutationAssessor score | 2.62 | 1.92 | 4.74 | 3.1 | 4.18 | 4.74 |
| EFIN SP | neutral | neutral | neutral | neutral | neutral | neutral |
| EFIN SP score | 0.72 | 0.68 | 0.71 | 0.7 | 0.79 | 0.73 |
| EFIN HD | neutral | neutral | neutral | neutral | neutral | neutral |
| EFIN HD score | 0.49 | 0.6 | 0.5 | 0.57 | 0.57 | 0.49 |
| CADD | neutral | neutral | deleterious | neutral | deleterious | deleterious |
| CADD score | 1.62 | 1.68 | 1.99 | 1.73 | 2.22 | 4.21 |
| CADD phred | 13.94 | 14.29 | 16.13 | 14.6 | 17.61 | 23.9 |
| VEST pvalue | 0.26 | 0.41 | 0.03 | 0.08 | 0.01 | 0.01 |
| VEST FDR | 0.45 | 0.5 | 0.35 | 0.35 | 0.35 | 0.35 |
| PANTHER | neutral | neutral | neutral | neutral | disease | disease |
| PANTHER score | 0.18 | 0.18 | 0.48 | 0.37 | 0.62 | 0.73 |
| PhD-SNP | disease | disease | disease | disease | disease | disease |
| PhD-SNP score | 0.82 | 0.58 | 0.93 | 0.65 | 0.87 | 0.92 |
| SNAP | disease | neutral | disease | disease | disease | disease |
| SNAP score | 0.57 | 0.31 | 0.65 | 0.61 | 0.65 | 0.74 |
| Meta-SNP | disease | neutral | disease | disease | disease | disease |
| Meta-SNP score | 0.66 | 0.2 | 0.75 | 0.65 | 0.71 | 0.73 |
| Meta-SNP RI | 3 | 6 | 5 | 3 | 4 | 5 |
| CAROL | neutral | neutral | neutral | neutral | neutral | neutral |
| CAROL score | 0.35 | 0.48 | 0.37 | 0.57 | 0.94 | 0.97 |
| Condel | deleterious | deleterious | deleterious | deleterious | neutral | neutral |
| Condel score | 0.61 | 0.71 | 0.72 | 0.51 | 0.18 | 0.11 |
| COVEC WMV | neutral | neutral | neutral | . | deleterious | deleterious |
| COVEC WMV score | -3 | -6 | -2 | 0 | 2 | 2 |
| MtoolBox | neutral | neutral | neutral | deleterious | deleterious | deleterious |
| MtoolBox DS | 0.34 | 0.19 | 0.33 | 0.54 | 0.76 | 0.85 |
| PolyPhen2 transf | medium impact | medium impact | medium impact | medium impact | low impact | low impact |
| PolyPhen2 transf score | -0.57 | 0.45 | 0.1 | -0.99 | -1.81 | -1.95 |
| SIFT_transf | medium impact | medium impact | medium impact | medium impact | medium impact | medium impact |
| SIFT transf score | 0.38 | 0.25 | 0.31 | 0.43 | 0.05 | -0.13 |
| MutationAssessor transf | medium impact | medium impact | high impact | medium impact | high impact | high impact |
| MutationAssessor transf score | 1.1 | 0.49 | 2.95 | 1.52 | 2.46 | 2.95 |
| CHASM pvalue | 0.32 | 0.72 | 0.28 | 0.11 | 0.31 | 0.14 |
| CHASM FDR | 0.8 | 0.85 | 0.8 | 0.8 | 0.8 | 0.8 |
| APOGEE | VUS | Likely-benign | VUS | VUS | Likely-pathogenic | Likely-pathogenic |
| APOGEE score | 0.5773788688521281 | 0.2021535194171086 | 0.6983120496124628 | 0.5416630042753822 | 0.7304918882634687 | 0.8133174755893987 |
| SNPDryad score | 0.69 | 0.08 | 0.98 | 0.87 | 0.96 | 0.99 |
| MutationTaster | polymorphism | polymorphism | polymorphism | polymorphism | polymorphism | polymorphism |
| MutationTaster score | 1 | 1 | 1 | 1 | 1 | 1 |
| DEOGEN2 score | 0.12 | 0.03 | 0.15 | 0.13 | 0.2 | 0.37 |
| Mitoclass.1 | damaging | damaging | damaging | damaging | damaging | damaging |
| dbSNP 155 id | rs201513497 | rs201513497 | . | rs1603219109 | . | . |
| ClinVar October2021 Variation id | . | . | . | . | . | . |
| ClinVar October2021 CLNSIG | . | . | . | . | . | . |
| ClinVar October2021 CLNDN | . | . | . | . | . | . |
| ClinVar October2021 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 | . | 0.000% | . | . | . | . |
| MITOMAP Disease GenBank Seqs | . | 107 (0) | . | . | . | . |
| MITOMAP Disease GenBank Curated refs | . | 2 | . | . | . | . |
| MITOMAP General GenBank Freq | . | 0.188% | . | 0.000% | . | . |
| MITOMAP General GenBank Seqs | . | 107 | . | 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 | . | . |
| HelixMTdb AF Hom | . | 0.00076027005 | . | 0 | . | . |
| HelixMTdb AC Het | . | 24 | . | 1 | . | . |
| 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: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 | 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:V144A:N10S:1.5254:0.477989584:1.00994909;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10K:0.95416:0.477989584:0.559670269;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10D:2.40856:0.477989584:1.9348892;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10Y:-0.01481:0.477989584:-1.04049873;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10T:-0.32927:0.477989584:-0.845690131;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10H:-0.34081:0.477989584:-0.468639374;MT-ND1:MT-ND3:5lc5:H:A:V144A:N10I:0.26565:0.477989584:-0.200120538;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10S:2.08637:1.37451053:0.722851157;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10K:0.80985:1.37451053:-0.557247937;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10D:2.94017:1.37451053:1.56138194;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10Y:-0.45072:1.37451053:-1.868029;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10T:0.39451:1.37451053:-0.944197059;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10H:-0.04321:1.37451053:-1.41110837;MT-ND1:MT-ND3:5ldw:H:A:V144A:N10I:-0.57641:1.37451053:-1.98465884;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10S:2.27043:1.45349884:0.834559619;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10K:0.50927:1.45349884:-0.983650565;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10D:3.18168:1.45349884:1.77093887;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10Y:-0.508:1.45349884:-1.7146492;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10T:0.7206:1.45349884:-0.727460086;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10H:0.22963:1.45349884:-1.23474002;MT-ND1:MT-ND3:5ldx:H:A:V144A:N10I:-0.33633:1.45349884:-1.75487101 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