news model
license
| ~ | 3635 (G/A) | 3635 (G/C) | 3635 (G/T) |
|---|---|---|---|
| ~ | 3635 (aGc/aAc) | 3635 (aGc/aCc) | 3635 (aGc/aTc) |
| 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 |
