~ | 12811 (T/C) | 12811 (T/A) | 12811 (T/G) |
---|---|---|---|
~ | 12811 (TAC/CAC) | 12811 (TAC/AAC) | 12811 (TAC/GAC) |
MitImpact id | MI.20263 | MI.20262 | MI.20261 |
Chr | chrM | chrM | chrM |
Start | 12811 | 12811 | 12811 |
Ref | T | T | T |
Alt | C | A | G |
Gene symbol | MT-ND5 | MT-ND5 | MT-ND5 |
Extended annotation | mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 | mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 | mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 5 |
Gene position | 475 | 475 | 475 |
Gene start | 12337 | 12337 | 12337 |
Gene end | 14148 | 14148 | 14148 |
Gene strand | + | + | + |
Codon substitution | TAC/CAC | TAC/AAC | TAC/GAC |
AA position | 159 | 159 | 159 |
AA ref | Y | Y | Y |
AA alt | H | N | D |
Functional effect general | missense | missense | missense |
Functional effect detailed | missense | missense | missense |
OMIM id | 516005 | 516005 | 516005 |
HGVS | NC_012920.1:g.12811T>C | NC_012920.1:g.12811T>A | NC_012920.1:g.12811T>G |
HGNC id | 7461 | 7461 | 7461 |
Respiratory Chain complex | I | I | I |
Ensembl gene id | ENSG00000198786 | ENSG00000198786 | ENSG00000198786 |
Ensembl transcript id | ENST00000361567 | ENST00000361567 | ENST00000361567 |
Ensembl protein id | ENSP00000354813 | ENSP00000354813 | ENSP00000354813 |
Uniprot id | P03915 | P03915 | P03915 |
Uniprot name | NU5M_HUMAN | NU5M_HUMAN | NU5M_HUMAN |
Ncbi gene id | 4540 | 4540 | 4540 |
Ncbi protein id | YP_003024036.1 | YP_003024036.1 | YP_003024036.1 |
PhyloP 100V | -1.369 | -1.369 | -1.369 |
PhyloP 470Way | 0.666 | 0.666 | 0.666 |
PhastCons 100V | 0 | 0 | 0 |
PhastCons 470Way | 0.785 | 0.785 | 0.785 |
PolyPhen2 | benign | possibly_damaging | possibly_damaging |
PolyPhen2 score | 0.01 | 0.48 | 0.75 |
SIFT | neutral | neutral | neutral |
SIFT score | 0.52 | 0.31 | 0.22 |
SIFT4G | Tolerated | Damaging | Damaging |
SIFT4G score | 0.349 | 0.005 | 0.001 |
VEST | Neutral | Neutral | Neutral |
VEST pvalue | 0.62 | 0.46 | 0.41 |
VEST FDR | 0.65 | 0.55 | 0.5 |
Mitoclass.1 | neutral | damaging | damaging |
SNPDryad | Pathogenic | Pathogenic | Pathogenic |
SNPDryad score | 0.98 | 0.99 | 0.96 |
MutationTaster | Disease automatic | Polymorphism | Polymorphism |
MutationTaster score | 0.000140357 | 0.998428 | 0.998863 |
MutationTaster converted rankscore | 0.20048 | 0.22162 | 0.21844 |
MutationTaster model | simple_aae | simple_aae | simple_aae |
MutationTaster AAE | Y159H | Y159N | Y159D |
fathmm | Tolerated | Tolerated | Tolerated |
fathmm score | 4.62 | 4.7 | 4.66 |
fathmm converted rankscore | 0.01834 | 0.01673 | 0.01756 |
AlphaMissense | likely_benign | likely_benign | ambiguous |
AlphaMissense score | 0.123 | 0.1595 | 0.3605 |
CADD | Neutral | Neutral | Deleterious |
CADD score | 0.043467 | 2.254487 | 3.535134 |
CADD phred | 3.016 | 17.87 | 23.1 |
PROVEAN | Tolerated | Damaging | Damaging |
PROVEAN score | -1.81 | -6.07 | -7.26 |
MutationAssessor | neutral | low | medium |
MutationAssessor score | 0.68 | 1.27 | 2.165 |
EFIN SP | Neutral | Neutral | Neutral |
EFIN SP score | 0.828 | 0.788 | 0.75 |
EFIN HD | Neutral | Neutral | Neutral |
EFIN HD score | 0.97 | 0.686 | 0.368 |
MLC | Deleterious | Deleterious | Deleterious |
MLC score | 0.63974893 | 0.63974893 | 0.63974893 |
PANTHER score | . | . | . |
PhD-SNP score | . | . | . |
APOGEE1 | Neutral | Neutral | Neutral |
APOGEE1 score | 0.32 | 0.28 | 0.36 |
APOGEE2 | Benign | VUS- | VUS+ |
APOGEE2 score | 0.011745441687242 | 0.321958989354946 | 0.571234760296309 |
CAROL | neutral | neutral | neutral |
CAROL score | 0.46 | 0.66 | 0.85 |
Condel | deleterious | neutral | neutral |
Condel score | 0.76 | 0.42 | 0.24 |
COVEC WMV | neutral | neutral | . |
COVEC WMV score | -6 | -3 | 0 |
MtoolBox | neutral | deleterious | deleterious |
MtoolBox DS | 0.17 | 0.43 | 0.56 |
DEOGEN2 | Tolerated | Tolerated | Tolerated |
DEOGEN2 score | 0.029089 | 0.091686 | 0.09079 |
DEOGEN2 converted rankscore | 0.20925 | 0.38848 | 0.38659 |
Meta-SNP | . | . | . |
Meta-SNP score | . | . | . |
PolyPhen2 transf | medium impact | medium impact | low impact |
PolyPhen2 transf score | 1.15 | -0.71 | -1.2 |
SIFT_transf | medium impact | medium impact | medium impact |
SIFT transf score | 0.25 | 0.04 | -0.07 |
MutationAssessor transf | medium impact | medium impact | medium impact |
MutationAssessor transf score | -0.36 | 0.48 | 1.96 |
CHASM | Neutral | Neutral | Neutral |
CHASM pvalue | 0.4 | 0.35 | 0.37 |
CHASM FDR | 0.8 | 0.8 | 0.8 |
ClinVar id | 65510.0 | . | . |
ClinVar Allele id | 76418.0 | . | . |
ClinVar CLNDISDB | MedGen:CN517202|MONDO:MONDO:0044970,MedGen:C0751651,Orphanet:68380|MONDO:MONDO:0009723,MedGen:C0023264,OMIM:256000,Orphanet:506|Human_Phenotype_Ontology:HP:0001086,Human_Phenotype_Ontology:HP:0001112,MONDO:MONDO:0010788,MedGen:C0917796,OMIM:535000,Orphanet:104 | . | . |
ClinVar CLNDN | not_provided|Mitochondrial_disease|Leigh_syndrome|Leber_optic_atrophy | . | . |
ClinVar CLNSIG | Benign | . | . |
MITOMAP Disease Clinical info | Possible LHON factor | . | . |
MITOMAP Disease Status | Reported [B] | . | . |
MITOMAP Disease Hom/Het | +/- | ./. | ./. |
MITOMAP General GenBank Freq | 1.1139% | . | . |
MITOMAP General GenBank Seqs | 681 | . | . |
MITOMAP General Curated refs | 21978175;21281460;31478599;22110754;19022198;18545700;19818876;32094358;17434142;21099167;17072496;23304069;7901141;8600429;11938495;19026397;17406640;15638829;16404693;19527690;29253894;16714301;16895436;20301353;24667788;19167085;7599218;12436196;33493461;29387390;17259400;29987491;31797714;17257906;20067846;30446962 | . | . |
MITOMAP Variant Class | polymorphism;disease | . | . |
gnomAD 3.1 AN | 56431.0 | . | . |
gnomAD 3.1 AC Homo | 328.0 | . | . |
gnomAD 3.1 AF Hom | 0.00581241 | . | . |
gnomAD 3.1 AC Het | 1.0 | . | . |
gnomAD 3.1 AF Het | 1.77208e-05 | . | . |
gnomAD 3.1 filter | PASS | . | . |
HelixMTdb AC Hom | 1274.0 | . | . |
HelixMTdb AF Hom | 0.006500564 | . | . |
HelixMTdb AC Het | 14.0 | . | . |
HelixMTdb AF Het | 7.143477e-05 | . | . |
HelixMTdb mean ARF | 0.76333 | . | . |
HelixMTdb max ARF | 0.91667 | . | . |
ToMMo 54KJPN AC | 2645 | . | . |
ToMMo 54KJPN AF | 0.048709 | . | . |
ToMMo 54KJPN AN | 54302 | . | . |
COSMIC 90 | . | . | . |
dbSNP 156 id | rs199974018 | . | . |