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PubMed:19370764 JSONTXT

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PubTator4TogoVar

Id Subject Object Predicate Lexical cue proteinmutation
19370764_0 478-485 ProteinMutation denotes p.T286M rs193302860

LitCoin-sentences

Id Subject Object Predicate Lexical cue
T1 0-189 Sentence denotes Identification and molecular characterization of six novel mutations in the UDP-N-acetylglucosamine-1-phosphotransferase gamma subunit (GNPTG) gene in patients with mucolipidosis III gamma.
T2 190-298 Sentence denotes Mucolipidosis type III (MLIII) is an autosomal recessive disorder affecting lysosomal hydrolase trafficking.
T3 299-452 Sentence denotes In a study of 10 patients from seven families with a clinical phenotype and enzymatic diagnosis of MLIII, six novel GNPTG gene mutations were identified.
T4 453-619 Sentence denotes These included missense (p.T286M) and nonsense (p.W111X) mutations and a transition in the obligate AG-dinucleotide of the intron 8 acceptor splice site (c.610-2A>G).
T5 620-815 Sentence denotes Three microdeletions were also identified, two of which (c.611delG and c.640_667del28) were located within the coding region whereas one (c.609+28_610-16del) was located entirely within intron 8.
T6 816-1072 Sentence denotes RT-PCR analysis of the c.610-2A>G transition demonstrated that the change altered splicing, leading to the production of two distinct aberrantly spliced forms, viz. the skipping of exon 9 (p.G204_K247del) or the retention of introns 8 and 9 (p.G204VfsX28).
T7 1073-1215 Sentence denotes RT-PCR analysis, performed on a patient homozygous for the intronic deletion (c.609+28_610-16del), failed to detect any GNPTG RNA transcripts.
T8 1216-1418 Sentence denotes To determine whether c.609+28_610-16del allele-derived transcripts were subject to nonsense-mediated mRNA decay (NMD), patient fibroblasts were incubated with the protein synthesis inhibitor anisomycin.
T9 1419-1552 Sentence denotes An RT-PCR fragment retaining 43 bp of intron 8 was consistently detected suggesting that the 33-bp genomic deletion had elicited NMD.
T10 1553-1735 Sentence denotes Quantitative real-time PCR and GNPTG western blot analysis confirmed that the homozygous microdeletion p.G204VfsX17 had elicited NMD resulting in failure to synthesize GNPTG protein.
T11 1736-1926 Sentence denotes Analysis of the sequences surrounding the microdeletion breakpoints revealed either intrinsic repetitivity of the deleted region or short direct repeats adjacent to the breakpoint junctions.
T12 1927-2173 Sentence denotes This is consistent with these repeats having mediated the microdeletions via replication slippage and supports the view that the mutational spectrum of the GNPTG gene is strongly influenced by the properties of the local DNA sequence environment.

LitCoin-entities

Id Subject Object Predicate Lexical cue db_id
5988 76-134 GeneOrGeneProduct denotes UDP-N-acetylglucosamine-1-phosphotransferase gamma subunit NCBIGene:84572
5989 136-141 GeneOrGeneProduct denotes GNPTG NCBIGene:84572
5990 151-159 OrganismTaxon denotes patients NCBITaxon:9606
5991 165-188 DiseaseOrPhenotypicFeature denotes mucolipidosis III gamma MESH:C565367
5992 190-212 DiseaseOrPhenotypicFeature denotes Mucolipidosis type III MESH:D009081
5993 214-219 DiseaseOrPhenotypicFeature denotes MLIII MESH:D009081
5994 227-255 DiseaseOrPhenotypicFeature denotes autosomal recessive disorder MESH:D030342
5995 316-324 OrganismTaxon denotes patients NCBITaxon:9606
5996 398-403 DiseaseOrPhenotypicFeature denotes MLIII MESH:D009081
5997 415-420 GeneOrGeneProduct denotes GNPTG NCBIGene:84572
5998 478-485 SequenceVariant denotes p.T286M DBSNP:rs193302860
5999 501-508 SequenceVariant denotes p.W111X DBSNP:rs137852884
6000 553-568 SequenceVariant denotes AG-dinucleotide DBSNP:rs193302855
6001 607-617 SequenceVariant denotes c.610-2A>G DBSNP:rs193302855
6002 677-686 SequenceVariant denotes c.611delG DBSNP:rs193302856
6003 691-705 SequenceVariant denotes c.640_667del28 DBSNP:rs193302859
6004 758-776 SequenceVariant denotes c.609+28_610-16del c|DEL|609+28_610-16|
6005 839-849 SequenceVariant denotes c.610-2A>G DBSNP:rs193302855
6006 1005-1019 SequenceVariant denotes p.G204_K247del p|DEL|204_247|
6007 1058-1070 SequenceVariant denotes p.G204VfsX28 p|FS|G|204|V|28
6008 1105-1112 OrganismTaxon denotes patient NCBITaxon:9606
6009 1151-1169 SequenceVariant denotes c.609+28_610-16del c|DEL|609+28_610-16|
6010 1193-1198 GeneOrGeneProduct denotes GNPTG NCBIGene:84572
6011 1237-1255 SequenceVariant denotes c.609+28_610-16del c|DEL|609+28_610-16|
6012 1335-1342 OrganismTaxon denotes patient NCBITaxon:9606
6013 1407-1417 ChemicalEntity denotes anisomycin MESH:D000841
6014 1512-1534 SequenceVariant denotes 33-bp genomic deletion g|DEL||33
6015 1584-1589 GeneOrGeneProduct denotes GNPTG NCBIGene:84572
6016 1656-1668 SequenceVariant denotes p.G204VfsX17 p|FS|G|204|V|17
6017 1721-1726 GeneOrGeneProduct denotes GNPTG NCBIGene:84572
6018 2083-2088 GeneOrGeneProduct denotes GNPTG NCBIGene:84572

LitCoin_Mondo

Id Subject Object Predicate Lexical cue mondo_id
T1 165-178 DiseaseOrPhenotypicFeature denotes mucolipidosis 0019248
T2 190-212 DiseaseOrPhenotypicFeature denotes Mucolipidosis type III 0018931

LitCoin-SeqVar

Id Subject Object Predicate Lexical cue
T1 478-485 SequenceVariant denotes p.T286M
T2 501-508 SequenceVariant denotes p.W111X
T3 607-617 SequenceVariant denotes c.610-2A>G
T4 677-686 SequenceVariant denotes c.611delG
T5 691-705 SequenceVariant denotes c.640_667del28
T6 839-849 SequenceVariant denotes c.610-2A>G
T7 1005-1019 SequenceVariant denotes p.G204_K247del
T8 1058-1070 SequenceVariant denotes p.G204VfsX28
T9 1656-1668 SequenceVariant denotes p.G204VfsX17

LitCoin-GeneOrGeneProduct-v0

Id Subject Object Predicate Lexical cue
T1 53-58 GeneOrGeneProduct denotes novel
T2 59-68 GeneOrGeneProduct denotes mutations
T3 76-99 GeneOrGeneProduct denotes UDP-N-acetylglucosamine
T4 102-120 GeneOrGeneProduct denotes phosphotransferase
T5 121-134 GeneOrGeneProduct denotes gamma subunit
T6 136-141 GeneOrGeneProduct denotes GNPTG
T7 179-182 GeneOrGeneProduct denotes III
T8 183-188 GeneOrGeneProduct denotes gamma
T9 209-212 GeneOrGeneProduct denotes III
T10 276-285 GeneOrGeneProduct denotes hydrolase
T11 409-414 GeneOrGeneProduct denotes novel
T12 415-420 GeneOrGeneProduct denotes GNPTG
T13 426-435 GeneOrGeneProduct denotes mutations
T14 468-476 GeneOrGeneProduct denotes missense
T15 510-519 GeneOrGeneProduct denotes mutations
T16 594-600 GeneOrGeneProduct denotes splice
T17 790-798 GeneOrGeneProduct denotes entirely
T18 898-906 GeneOrGeneProduct denotes splicing
T19 923-933 GeneOrGeneProduct denotes production
T20 961-968 GeneOrGeneProduct denotes spliced
T21 985-993 GeneOrGeneProduct denotes skipping
T22 1193-1198 GeneOrGeneProduct denotes GNPTG
T23 1203-1214 GeneOrGeneProduct denotes transcripts
T24 1219-1228 GeneOrGeneProduct denotes determine
T25 1271-1282 GeneOrGeneProduct denotes transcripts
T26 1308-1316 GeneOrGeneProduct denotes mediated
T27 1317-1321 GeneOrGeneProduct denotes mRNA
T28 1322-1327 GeneOrGeneProduct denotes decay
T29 1379-1386 GeneOrGeneProduct denotes protein
T30 1397-1406 GeneOrGeneProduct denotes inhibitor
T31 1419-1424 GeneOrGeneProduct denotes An RT
T32 1438-1447 GeneOrGeneProduct denotes retaining
T33 1448-1453 GeneOrGeneProduct denotes 43 bp
T34 1566-1575 GeneOrGeneProduct denotes real-time
T35 1584-1589 GeneOrGeneProduct denotes GNPTG
T36 1598-1602 GeneOrGeneProduct denotes blot
T37 1721-1726 GeneOrGeneProduct denotes GNPTG
T38 1727-1734 GeneOrGeneProduct denotes protein
T39 1972-1980 GeneOrGeneProduct denotes mediated
T40 2056-2066 GeneOrGeneProduct denotes mutational
T41 2083-2088 GeneOrGeneProduct denotes GNPTG

LitCoin-GeneOrGeneProduct-v2

Id Subject Object Predicate Lexical cue
T1 53-58 GeneOrGeneProduct denotes novel
T2 76-99 GeneOrGeneProduct denotes UDP-N-acetylglucosamine
T3 102-120 GeneOrGeneProduct denotes phosphotransferase
T4 121-134 GeneOrGeneProduct denotes gamma subunit
T5 136-141 GeneOrGeneProduct denotes GNPTG
T6 183-188 GeneOrGeneProduct denotes gamma
T7 276-285 GeneOrGeneProduct denotes hydrolase
T8 409-414 GeneOrGeneProduct denotes novel
T9 415-420 GeneOrGeneProduct denotes GNPTG
T10 961-968 GeneOrGeneProduct denotes spliced
T11 1193-1198 GeneOrGeneProduct denotes GNPTG
T12 1317-1321 GeneOrGeneProduct denotes mRNA
T13 1322-1327 GeneOrGeneProduct denotes decay
T14 1379-1386 GeneOrGeneProduct denotes protein
T15 1397-1406 GeneOrGeneProduct denotes inhibitor
T16 1566-1575 GeneOrGeneProduct denotes real-time
T17 1584-1589 GeneOrGeneProduct denotes GNPTG
T18 1598-1602 GeneOrGeneProduct denotes blot
T19 1721-1726 GeneOrGeneProduct denotes GNPTG
T20 1727-1734 GeneOrGeneProduct denotes protein
T21 2083-2088 GeneOrGeneProduct denotes GNPTG

LitCoin-Disease-MeSH

Id Subject Object Predicate Lexical cue originalLabel
T1 165-188 DiseaseOrPhenotypicFeature denotes mucolipidosis III gamma C565367
T2 190-212 DiseaseOrPhenotypicFeature denotes Mucolipidosis type III D009081
T3 214-219 DiseaseOrPhenotypicFeature denotes MLIII D009081
T4 227-255 DiseaseOrPhenotypicFeature denotes autosomal recessive disorder DISEASE
T5 398-403 DiseaseOrPhenotypicFeature denotes MLIII D009081

LitCoin-GeneOrGeneProduct-v3

Id Subject Object Predicate Lexical cue
T1 76-99 GeneOrGeneProduct denotes UDP-N-acetylglucosamine
T2 102-120 GeneOrGeneProduct denotes phosphotransferase
T3 121-134 GeneOrGeneProduct denotes gamma subunit
T4 136-141 GeneOrGeneProduct denotes GNPTG
T5 276-285 GeneOrGeneProduct denotes hydrolase
T6 415-420 GeneOrGeneProduct denotes GNPTG
T7 1193-1198 GeneOrGeneProduct denotes GNPTG
T8 1584-1589 GeneOrGeneProduct denotes GNPTG
T9 1721-1726 GeneOrGeneProduct denotes GNPTG
T10 2083-2088 GeneOrGeneProduct denotes GNPTG

LitCoin_Mondo_095

Id Subject Object Predicate Lexical cue mondo_id
T1 165-188 DiseaseOrPhenotypicFeature denotes mucolipidosis III gamma 0009652
T2 190-212 DiseaseOrPhenotypicFeature denotes Mucolipidosis type III 0018931
T3 214-219 DiseaseOrPhenotypicFeature denotes MLIII 0018931
T4 398-403 DiseaseOrPhenotypicFeature denotes MLIII 0018931

LitCoin-MeSH-Disease-2

Id Subject Object Predicate Lexical cue ID:
T1 165-188 DiseaseOrPhenotypicFeature denotes mucolipidosis III gamma C565367
T2 190-212 DiseaseOrPhenotypicFeature denotes Mucolipidosis type III D009081
T3 214-219 DiseaseOrPhenotypicFeature denotes MLIII D009081
T4 227-255 DiseaseOrPhenotypicFeature denotes autosomal recessive disorder DISEASE
T5 398-403 DiseaseOrPhenotypicFeature denotes MLIII D009081

LitCoin-MONDO_bioort2019

Id Subject Object Predicate Lexical cue #label
T1 165-188 DiseaseOrPhenotypicFeature denotes mucolipidosis III gamma C565367
T2 190-212 DiseaseOrPhenotypicFeature denotes Mucolipidosis type III D009081
T3 214-219 DiseaseOrPhenotypicFeature denotes MLIII D009081
T4 227-255 DiseaseOrPhenotypicFeature denotes autosomal recessive disorder DISEASE
T5 398-403 DiseaseOrPhenotypicFeature denotes MLIII D009081

LitCoin-Chemical-MeSH-CHEBI

Id Subject Object Predicate Lexical cue ID:
T1 76-99 ChemicalEntity denotes UDP-N-acetylglucosamine http://purl.obolibrary.org/obo/CHEBI_16264
T2 102-120 ChemicalEntity denotes phosphotransferase D010770
T3 276-285 ChemicalEntity denotes hydrolase D006867
T4 1407-1417 ChemicalEntity denotes anisomycin D000841

LitCoin-NCBITaxon-2

Id Subject Object Predicate Lexical cue
T1 151-159 OrganismTaxon denotes patients
T2 316-324 OrganismTaxon denotes patients
T3 1105-1112 OrganismTaxon denotes patient
T4 1335-1342 OrganismTaxon denotes patient

LitCoin-training-merged

Id Subject Object Predicate Lexical cue #label ID:
T4 1407-1417 ChemicalEntity denotes anisomycin D000841
T3 276-285 ChemicalEntity denotes hydrolase D006867
T2 102-120 ChemicalEntity denotes phosphotransferase D010770
T1 76-99 ChemicalEntity denotes UDP-N-acetylglucosamine http://purl.obolibrary.org/obo/CHEBI_16264
T10 2083-2088 GeneOrGeneProduct denotes GNPTG
T9 1721-1726 GeneOrGeneProduct denotes GNPTG
T8 1584-1589 GeneOrGeneProduct denotes GNPTG
T7 1193-1198 GeneOrGeneProduct denotes GNPTG
T6 415-420 GeneOrGeneProduct denotes GNPTG
T5 276-285 GeneOrGeneProduct denotes hydrolase
T83713 136-141 GeneOrGeneProduct denotes GNPTG
T32761 121-134 GeneOrGeneProduct denotes gamma subunit
T77693 102-120 GeneOrGeneProduct denotes phosphotransferase
T96512 76-99 GeneOrGeneProduct denotes UDP-N-acetylglucosamine
T40480 398-403 DiseaseOrPhenotypicFeature denotes MLIII D009081
T97845 227-255 DiseaseOrPhenotypicFeature denotes autosomal recessive disorder DISEASE
T31204 214-219 DiseaseOrPhenotypicFeature denotes MLIII D009081
T66929 190-212 DiseaseOrPhenotypicFeature denotes Mucolipidosis type III D009081
T80233 165-188 DiseaseOrPhenotypicFeature denotes mucolipidosis III gamma C565367
T52953 1335-1342 OrganismTaxon denotes patient
T98852 1105-1112 OrganismTaxon denotes patient
T81223 316-324 OrganismTaxon denotes patients
T18937 151-159 OrganismTaxon denotes patients
T30193 1656-1668 SequenceVariant denotes p.G204VfsX17
T92199 1058-1070 SequenceVariant denotes p.G204VfsX28
T27499 1005-1019 SequenceVariant denotes p.G204_K247del
T66685 839-849 SequenceVariant denotes c.610-2A>G
T51441 691-705 SequenceVariant denotes c.640_667del28
T94882 677-686 SequenceVariant denotes c.611delG
T32283 607-617 SequenceVariant denotes c.610-2A>G
T52346 501-508 SequenceVariant denotes p.W111X
T47349 478-485 SequenceVariant denotes p.T286M

DisGeNET

Id Subject Object Predicate Lexical cue
T0 80-134 gene:84572 denotes N-acetylglucosamine-1-phosphotransferase gamma subunit
T1 165-188 disease:C1854896 denotes mucolipidosis III gamma
T2 136-141 gene:84572 denotes GNPTG
T3 165-188 disease:C1854896 denotes mucolipidosis III gamma
R1 T0 T1 associated_with N-acetylglucosamine-1-phosphotransferase gamma subunit,mucolipidosis III gamma
R2 T2 T3 associated_with GNPTG,mucolipidosis III gamma

DisGeNET5_gene_disease

Id Subject Object Predicate Lexical cue
19370764-0#80#134#gene84572 80-134 gene84572 denotes N-acetylglucosamine-1-phosphotransferase gamma subunit
19370764-0#136#141#gene84572 136-141 gene84572 denotes GNPTG
19370764-0#165#188#diseaseC1854896 165-188 diseaseC1854896 denotes mucolipidosis III gamma
80#134#gene84572165#188#diseaseC1854896 19370764-0#80#134#gene84572 19370764-0#165#188#diseaseC1854896 associated_with N-acetylglucosamine-1-phosphotransferase gamma subunit,mucolipidosis III gamma
136#141#gene84572165#188#diseaseC1854896 19370764-0#136#141#gene84572 19370764-0#165#188#diseaseC1854896 associated_with GNPTG,mucolipidosis III gamma

tmVarCorpus

Id Subject Object Predicate Lexical cue
T1 478-485 ProteinMutation:p|SUB|T|286|M denotes p.T286M
T2 501-508 ProteinMutation:p|SUB|W|111|X denotes p.W111X
T3 607-617 DNAMutation:c|SUB|A|610-2|G denotes c.610-2A>G
T4 677-686 DNAMutation:c|DEL|611|G denotes c.611delG
T5 691-705 DNAMutation:c|DEL|640_667|28 denotes c.640_667del28
T6 758-776 DNAMutation:c|DEL|609+28_610-16| denotes c.609+28_610-16del
T7 839-849 DNAMutation:c|SUB|A|610-2|G denotes c.610-2A>G
T8 1005-1019 ProteinMutation:p|DEL|204_247| denotes p.G204_K247del
T9 1058-1070 ProteinMutation:p|FS|G|204|V|28 denotes p.G204VfsX28
T10 1151-1169 DNAMutation:c|DEL|609+28_610-16| denotes c.609+28_610-16del
T11 1237-1255 DNAMutation:c|DEL|609+28_610-16| denotes c.609+28_610-16del
T12 1656-1668 ProteinMutation:p|FS|G|204|V|17 denotes p.G204VfsX17