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PubMed:19394258 JSONTXT

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LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-101 Sentence denotes The first founder DGUOK mutation associated with hepatocerebral mitochondrial DNA depletion syndrome.
T2 102-235 Sentence denotes Deoxyguanosine kinase (dGK) deficiency is a frequent cause of mitochondrial DNA depletion associated with a hepatocerebral phenotype.
T3 236-383 Sentence denotes In this study, we describe a new splice site mutation in the DGUOK gene and the clinical, radiologic, and genetic features of these DGUOK patients.
T4 384-603 Sentence denotes This new DGUOK homozygous mutation (c.444-62C>A) was identified in three patients from two North-African consanguineous families with combined respiratory chain deficiencies and mitochondrial DNA depletion in the liver.
T5 604-662 Sentence denotes Brain MRIs are normal in DGUOK patients in the literature.
T6 663-790 Sentence denotes Interestingly, we found subtentorial abnormal myelination and moderate hyperintensity in the bilateral pallidi in our patients.
T7 791-961 Sentence denotes This new mutation creates a cryptic splice site in intron 3 (in position -62) and is predicted to result in a larger protein with an in-frame insertion of 20 amino acids.
T8 962-1200 Sentence denotes In silico analysis of the putative impact of the insertion shows serious clashes in protein conformation: this insertion disrupts the alpha5 helix of the dGK kinase domain, rendering the protein unable to bind purine deoxyribonucleosides.
T9 1201-1418 Sentence denotes In addition, a common haplotype that segregated with the disease in both families was detected by haplotype reconstruction with 10 markers (microsatellites and SNPs), which span 4.6 Mb of DNA covering the DGUOK locus.
T10 1419-1610 Sentence denotes In conclusion, we report a new DGUOK splice site mutation that provide insight into a critical protein domain (dGK kinase domain) and the first founder mutation in a North-African population.

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
6019 18-23 GeneOrGeneProduct denotes DGUOK NCBIGene:1716
6020 49-100 DiseaseOrPhenotypicFeature denotes hepatocerebral mitochondrial DNA depletion syndrome MESH:C580039
6021 102-140 DiseaseOrPhenotypicFeature denotes Deoxyguanosine kinase (dGK) deficiency MESH:C580039
6022 164-191 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion MESH:C580039
6023 297-302 GeneOrGeneProduct denotes DGUOK NCBIGene:1716
6024 368-373 GeneOrGeneProduct denotes DGUOK NCBIGene:1716
6025 374-382 OrganismTaxon denotes patients NCBITaxon:9606
6026 393-398 GeneOrGeneProduct denotes DGUOK NCBIGene:1716
6027 420-431 SequenceVariant denotes c.444-62C>A c|SUB|C|444-62|A
6028 457-465 OrganismTaxon denotes patients NCBITaxon:9606
6029 527-557 DiseaseOrPhenotypicFeature denotes respiratory chain deficiencies MESH:D028361
6030 562-589 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion MESH:C580039
6031 629-634 GeneOrGeneProduct denotes DGUOK NCBIGene:1716
6032 635-643 OrganismTaxon denotes patients NCBITaxon:9606
6033 687-720 DiseaseOrPhenotypicFeature denotes subtentorial abnormal myelination
6034 725-748 DiseaseOrPhenotypicFeature denotes moderate hyperintensity MESH:D006973
6035 781-789 OrganismTaxon denotes patients NCBITaxon:9606
6036 1116-1119 GeneOrGeneProduct denotes dGK NCBIGene:1716
6037 1179-1199 ChemicalEntity denotes deoxyribonucleosides MESH:D003853
6038 1406-1411 GeneOrGeneProduct denotes DGUOK NCBIGene:1716
6039 1450-1455 GeneOrGeneProduct denotes DGUOK NCBIGene:1716
6040 1530-1533 GeneOrGeneProduct denotes dGK NCBIGene:1716

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 64-100 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion syndrome 0018158

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 420-431 SequenceVariant denotes c.444-62C>A

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 18-23 GeneOrGeneProduct denotes DGUOK
T2 24-32 GeneOrGeneProduct denotes mutation
T3 64-77 GeneOrGeneProduct denotes mitochondrial
T4 82-91 GeneOrGeneProduct denotes depletion
T5 92-100 GeneOrGeneProduct denotes syndrome
T6 102-123 GeneOrGeneProduct denotes Deoxyguanosine kinase
T7 125-128 GeneOrGeneProduct denotes dGK
T8 164-177 GeneOrGeneProduct denotes mitochondrial
T9 182-191 GeneOrGeneProduct denotes depletion
T10 269-275 GeneOrGeneProduct denotes splice
T11 281-289 GeneOrGeneProduct denotes mutation
T12 297-302 GeneOrGeneProduct denotes DGUOK
T13 368-373 GeneOrGeneProduct denotes DGUOK
T14 393-398 GeneOrGeneProduct denotes DGUOK
T15 410-418 GeneOrGeneProduct denotes mutation
T16 539-544 GeneOrGeneProduct denotes chain
T17 562-575 GeneOrGeneProduct denotes mitochondrial
T18 580-589 GeneOrGeneProduct denotes depletion
T19 597-602 GeneOrGeneProduct denotes liver
T20 604-609 GeneOrGeneProduct denotes Brain
T21 629-634 GeneOrGeneProduct denotes DGUOK
T22 800-808 GeneOrGeneProduct denotes mutation
T23 809-816 GeneOrGeneProduct denotes creates
T24 819-826 GeneOrGeneProduct denotes cryptic
T25 827-833 GeneOrGeneProduct denotes splice
T26 876-885 GeneOrGeneProduct denotes predicted
T27 896-900 GeneOrGeneProduct denotes in a
T28 908-915 GeneOrGeneProduct denotes protein
T29 949-960 GeneOrGeneProduct denotes amino acids
T30 988-996 GeneOrGeneProduct denotes putative
T31 997-1003 GeneOrGeneProduct denotes impact
T32 1046-1053 GeneOrGeneProduct denotes protein
T33 1083-1091 GeneOrGeneProduct denotes disrupts
T34 1096-1102 GeneOrGeneProduct denotes alpha5
T35 1103-1108 GeneOrGeneProduct denotes helix
T36 1116-1119 GeneOrGeneProduct denotes dGK
T37 1120-1126 GeneOrGeneProduct denotes kinase
T38 1149-1156 GeneOrGeneProduct denotes protein
T39 1167-1171 GeneOrGeneProduct denotes bind
T40 1179-1199 GeneOrGeneProduct denotes deoxyribonucleosides
T41 1374-1378 GeneOrGeneProduct denotes span
T42 1383-1385 GeneOrGeneProduct denotes Mb
T43 1406-1411 GeneOrGeneProduct denotes DGUOK
T44 1450-1455 GeneOrGeneProduct denotes DGUOK
T45 1456-1462 GeneOrGeneProduct denotes splice
T46 1468-1481 GeneOrGeneProduct denotes mutation that
T47 1514-1521 GeneOrGeneProduct denotes protein
T48 1530-1533 GeneOrGeneProduct denotes dGK
T49 1534-1540 GeneOrGeneProduct denotes kinase
T50 1571-1579 GeneOrGeneProduct denotes mutation

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 18-23 GeneOrGeneProduct denotes DGUOK
T2 64-77 GeneOrGeneProduct denotes mitochondrial
T3 92-100 GeneOrGeneProduct denotes syndrome
T4 102-123 GeneOrGeneProduct denotes Deoxyguanosine kinase
T5 125-128 GeneOrGeneProduct denotes dGK
T6 164-177 GeneOrGeneProduct denotes mitochondrial
T7 297-302 GeneOrGeneProduct denotes DGUOK
T8 368-373 GeneOrGeneProduct denotes DGUOK
T9 393-398 GeneOrGeneProduct denotes DGUOK
T10 539-544 GeneOrGeneProduct denotes chain
T11 562-575 GeneOrGeneProduct denotes mitochondrial
T12 597-602 GeneOrGeneProduct denotes liver
T13 604-609 GeneOrGeneProduct denotes Brain
T14 629-634 GeneOrGeneProduct denotes DGUOK
T15 819-826 GeneOrGeneProduct denotes cryptic
T16 908-915 GeneOrGeneProduct denotes protein
T17 949-960 GeneOrGeneProduct denotes amino acids
T18 988-996 GeneOrGeneProduct denotes putative
T19 997-1003 GeneOrGeneProduct denotes impact
T20 1046-1053 GeneOrGeneProduct denotes protein
T21 1096-1102 GeneOrGeneProduct denotes alpha5
T22 1103-1108 GeneOrGeneProduct denotes helix
T23 1116-1119 GeneOrGeneProduct denotes dGK
T24 1120-1126 GeneOrGeneProduct denotes kinase
T25 1149-1156 GeneOrGeneProduct denotes protein
T26 1179-1199 GeneOrGeneProduct denotes deoxyribonucleosides
T27 1374-1378 GeneOrGeneProduct denotes span
T28 1406-1411 GeneOrGeneProduct denotes DGUOK
T29 1450-1455 GeneOrGeneProduct denotes DGUOK
T30 1514-1521 GeneOrGeneProduct denotes protein
T31 1530-1533 GeneOrGeneProduct denotes dGK
T32 1534-1540 GeneOrGeneProduct denotes kinase

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 49-100 DiseaseOrPhenotypicFeature denotes hepatocerebral mitochondrial DNA depletion syndrome C580039
T2 164-191 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion DISEASE
T3 527-557 DiseaseOrPhenotypicFeature denotes respiratory chain deficiencies D028361
T4 562-589 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion DISEASE
T5 1258-1265 DiseaseOrPhenotypicFeature denotes disease D004194

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 18-23 GeneOrGeneProduct denotes DGUOK
T2 102-123 GeneOrGeneProduct denotes Deoxyguanosine kinase
T3 125-128 GeneOrGeneProduct denotes dGK
T4 297-302 GeneOrGeneProduct denotes DGUOK
T5 368-373 GeneOrGeneProduct denotes DGUOK
T6 393-398 GeneOrGeneProduct denotes DGUOK
T7 629-634 GeneOrGeneProduct denotes DGUOK
T8 988-1003 GeneOrGeneProduct denotes putative impact
T9 1096-1102 GeneOrGeneProduct denotes alpha5
T10 1116-1119 GeneOrGeneProduct denotes dGK
T11 1179-1199 GeneOrGeneProduct denotes deoxyribonucleosides
T12 1374-1378 GeneOrGeneProduct denotes span
T13 1406-1411 GeneOrGeneProduct denotes DGUOK
T14 1450-1455 GeneOrGeneProduct denotes DGUOK
T15 1530-1533 GeneOrGeneProduct denotes dGK

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 64-100 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion syndrome 0018158

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 49-100 DiseaseOrPhenotypicFeature denotes hepatocerebral mitochondrial DNA depletion syndrome C580039
T2 102-140 DiseaseOrPhenotypicFeature denotes Deoxyguanosine kinase (dGK) deficiency DISEASE
T3 164-191 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion DISEASE
T4 527-557 DiseaseOrPhenotypicFeature denotes respiratory chain deficiencies D028361
T5 562-589 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion DISEASE
T6 687-720 DiseaseOrPhenotypicFeature denotes subtentorial abnormal myelination DISEASE
T7 725-748 DiseaseOrPhenotypicFeature denotes moderate hyperintensity DISEASE
T8 1258-1265 DiseaseOrPhenotypicFeature denotes disease D004194

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 49-100 DiseaseOrPhenotypicFeature denotes hepatocerebral mitochondrial DNA depletion syndrome C580039
T2 102-140 DiseaseOrPhenotypicFeature denotes Deoxyguanosine kinase (dGK) deficiency DISEASE
T3 164-191 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion DISEASE
T4 527-557 DiseaseOrPhenotypicFeature denotes respiratory chain deficiencies D028361
T5 562-589 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion DISEASE
T6 687-720 DiseaseOrPhenotypicFeature denotes subtentorial abnormal myelination DISEASE
T7 725-748 DiseaseOrPhenotypicFeature denotes moderate hyperintensity DISEASE

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 374-382 OrganismTaxon denotes patients
T2 457-465 OrganismTaxon denotes patients
T3 635-643 OrganismTaxon denotes patients
T4 781-789 OrganismTaxon denotes patients

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 102-123 ChemicalEntity denotes Deoxyguanosine kinase C019165
T2 125-128 ChemicalEntity denotes dGK C019165
T3 1116-1119 ChemicalEntity denotes dGK C019165
T4 1172-1199 ChemicalEntity denotes purine deoxyribonucleosides http://purl.obolibrary.org/obo/CHEBI_60173
T5 1530-1533 ChemicalEntity denotes dGK C019165

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T5 1530-1533 ChemicalEntity denotes dGK C019165
T4 1172-1199 ChemicalEntity denotes purine deoxyribonucleosides http://purl.obolibrary.org/obo/CHEBI_60173
T3 1116-1119 ChemicalEntity denotes dGK C019165
T2 125-128 ChemicalEntity denotes dGK C019165
T1 102-123 ChemicalEntity denotes Deoxyguanosine kinase C019165
T15 1530-1533 GeneOrGeneProduct denotes dGK
T14 1450-1455 GeneOrGeneProduct denotes DGUOK
T13 1406-1411 GeneOrGeneProduct denotes DGUOK
T12 1374-1378 GeneOrGeneProduct denotes span
T11 1179-1199 GeneOrGeneProduct denotes deoxyribonucleosides
T10 1116-1119 GeneOrGeneProduct denotes dGK
T9 1096-1102 GeneOrGeneProduct denotes alpha5
T8 988-1003 GeneOrGeneProduct denotes putative impact
T7 629-634 GeneOrGeneProduct denotes DGUOK
T6 393-398 GeneOrGeneProduct denotes DGUOK
T88655 368-373 GeneOrGeneProduct denotes DGUOK
T42015 297-302 GeneOrGeneProduct denotes DGUOK
T12124 125-128 GeneOrGeneProduct denotes dGK
T24709 102-123 GeneOrGeneProduct denotes Deoxyguanosine kinase
T93033 18-23 GeneOrGeneProduct denotes DGUOK
T23871 725-748 DiseaseOrPhenotypicFeature denotes moderate hyperintensity DISEASE
T90268 687-720 DiseaseOrPhenotypicFeature denotes subtentorial abnormal myelination DISEASE
T99729 562-589 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion DISEASE
T1799 527-557 DiseaseOrPhenotypicFeature denotes respiratory chain deficiencies D028361
T71838 164-191 DiseaseOrPhenotypicFeature denotes mitochondrial DNA depletion DISEASE
T51318 102-140 DiseaseOrPhenotypicFeature denotes Deoxyguanosine kinase (dGK) deficiency DISEASE
T91302 49-100 DiseaseOrPhenotypicFeature denotes hepatocerebral mitochondrial DNA depletion syndrome C580039
T75256 781-789 OrganismTaxon denotes patients
T30636 635-643 OrganismTaxon denotes patients
T73141 457-465 OrganismTaxon denotes patients
T23475 374-382 OrganismTaxon denotes patients
T3536 420-431 SequenceVariant denotes c.444-62C>A

DisGeNET

Id Subject Object Predicate Lexical cue
T0 18-23 gene:1716 denotes DGUOK
T1 49-100 disease:C3711385 denotes hepatocerebral mitochondrial DNA depletion syndrome
T2 393-398 gene:1716 denotes DGUOK
T3 562-589 disease:C0342782 denotes mitochondrial DNA depletion
T4 393-398 gene:1716 denotes DGUOK
T5 527-557 disease:C0949857 denotes respiratory chain deficiencies
R1 T0 T1 associated_with DGUOK,hepatocerebral mitochondrial DNA depletion syndrome
R2 T2 T3 associated_with DGUOK,mitochondrial DNA depletion
R3 T4 T5 associated_with DGUOK,respiratory chain deficiencies

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
19394258-0#18#23#gene1716 18-23 gene1716 denotes DGUOK
19394258-0#49#100#diseaseC3711385 49-100 diseaseC3711385 denotes hepatocerebral mitochondrial DNA depletion syndrome
19394258-3#9#14#gene1716 393-398 gene1716 denotes DGUOK
19394258-3#143#173#diseaseC0949857 527-557 diseaseC0949857 denotes respiratory chain deficiencies
19394258-3#178#205#diseaseC0342782 562-589 diseaseC0342782 denotes mitochondrial DNA depletion
18#23#gene171649#100#diseaseC3711385 19394258-0#18#23#gene1716 19394258-0#49#100#diseaseC3711385 associated_with DGUOK,hepatocerebral mitochondrial DNA depletion syndrome
9#14#gene1716143#173#diseaseC0949857 19394258-3#9#14#gene1716 19394258-3#143#173#diseaseC0949857 associated_with DGUOK,respiratory chain deficiencies
9#14#gene1716178#205#diseaseC0342782 19394258-3#9#14#gene1716 19394258-3#178#205#diseaseC0342782 associated_with DGUOK,mitochondrial DNA depletion

PubCasesHPO

Id Subject Object Predicate Lexical cue
AB1 700-720 HP:0012447 denotes abnormal myelination

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 420-431 DNAMutation:c|SUB|C|444-62|A denotes c.444-62C>A