{ "glytoucan_ac": "G06583FZ", "species": [ { "taxid": 9606, "name": "Homo sapiens", "annotation_category": "direct", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "GlyGen", "id": "GLY_000888", "url": "https://data.glygen.org/GLY_000888" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" }, { "taxid": 10090, "name": "Mus musculus", "annotation_category": "direct", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" }, { "taxid": 4932, "name": "Saccharomyces cerevisiae", "annotation_category": "subsumption", "evidence": [ { "database": "Subsumption", "id": "G55782QX", "url": "https://www.glygen.org/glycan/G55782QX" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae [4932]" } ], "mass": 2854.96, "classification": [ { "type": { "name": "N-linked", "url": "" }, "subtype": { "name": "High mannose", "url": "" } } ], "composition": [ { "name": "6-Deoxy-Hexose", "residue": "dhex", "count": 0, "cid": "840", "url": "https://pubchem.ncbi.nlm.nih.gov/compound/840" }, { "name": "Hexose", "residue": "hex", "count": 15, "cid": "206", "url": "https://pubchem.ncbi.nlm.nih.gov/compound/206" }, { "name": "N-Acetylhexosamine", "residue": "hexnac", "count": 2, "cid": "899", "url": "https://pubchem.ncbi.nlm.nih.gov/compound/899" }, { "name": "Hexuronic Acid", "residue": "hexa", "count": 0, "cid": "610", "url": "https://pubchem.ncbi.nlm.nih.gov/compound/610" }, { "name": "2-Amino-2-Deoxy-Hexose", "residue": "hexn", "count": 0, "cid": "739", "url": "https://pubchem.ncbi.nlm.nih.gov/compound/739" }, { "name": "N-Acetyl-Neuraminic Acid", "residue": "neuac", "count": 0, "cid": "439197", "url": "https://pubchem.ncbi.nlm.nih.gov/compound/439197" }, { "name": "N-Glycolyl-Neuraminic Acid", "residue": "neugc", "count": 0, "cid": "440001", "url": "https://pubchem.ncbi.nlm.nih.gov/compound/440001" }, { "name": "Phosphate", "residue": "p", "count": 0, "cid": "1061", "url": "https://pubchem.ncbi.nlm.nih.gov/compound/1061" }, { "name": "Pentose", "residue": "pent", "count": 0, "cid": "229", "url": "https://pubchem.ncbi.nlm.nih.gov/compound/229" }, { "name": "Sulfate", "residue": "s", "count": 0, "cid": "1117", "url": "https://pubchem.ncbi.nlm.nih.gov/compound/1117" }, { "name": "Other", "residue": "other", "count": 0 } ], "motifs": [], "enzyme": [], "biomarkers": [], "binding_proteins": [], "sites": [ { "start_pos": "371", "site_seq": "NTSGSNQQAFLLENVPCNNASCEEARRMFK", "site_lbl": "Asn371", "residue": "Asn", "glycoprotein": [ { "uniprot_canonical_ac": "Q8TB96-1", "start_pos": 371, "end_pos": 371, "residue": "Asn", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "protein_name": "T-cell immunomodulatory protein", "gene_name": "ITFG1", "tax_id": 9606, "tax_name": "Homo sapiens", "tax_common_name": "Human", "length": 612, "chemical_mass": 68108.0 } ] }, { "start_pos": "371", "site_seq": "N", "site_lbl": "Asn371", "residue": "Asn", "glycoprotein": [ { "uniprot_canonical_ac": "Q8TB96-1", "start_pos": 371, "end_pos": 371, "residue": "Asn", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "protein_name": "T-cell immunomodulatory protein", "gene_name": "ITFG1", "tax_id": 9606, "tax_name": "Homo sapiens", "tax_common_name": "Human", "length": 612, "chemical_mass": 68108.0 } ] }, { "start_pos": "371", "site_seq": "", "site_lbl": "N371", "residue": "", "snv": [ { "weight": 100, "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-loss (NAS->SAS).", "chr_id": "16", "chr_pos": "47260654", "evidence": [ { "id": "rs1966198844", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1966198844" }, { "id": "rs1966198844", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1966198844#frequency_tab" } ] } ], "glycoprotein": [ { "uniprot_canonical_ac": "Q8TB96-1", "start_pos": 371, "end_pos": 371, "residue": "Asn", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "protein_name": "T-cell immunomodulatory protein", "gene_name": "ITFG1", "tax_id": 9606, "tax_name": "Homo sapiens", "tax_common_name": "Human", "length": 612, "chemical_mass": 68108.0 } ] }, { "start_pos": "304", "site_seq": "YKVPAEILANTSDNAGFCIPEGNCLGSGVLNVSICK", "site_lbl": "Asn304", "residue": "Asn", "glycoprotein": [ { "uniprot_canonical_ac": "Q14108-1", "start_pos": 304, "end_pos": 304, "residue": "Asn", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "protein_name": "Lysosome membrane protein 2", "gene_name": "SCARB2", "tax_id": 9606, "tax_name": "Homo sapiens", "tax_common_name": "Human", "length": 478, "chemical_mass": 54290.0 } ] }, { "start_pos": "304", "site_seq": "N", "site_lbl": "Asn304", "residue": "Asn", "glycoprotein": [ { "uniprot_canonical_ac": "Q14108-1", "start_pos": 304, "end_pos": 304, "residue": "Asn", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "protein_name": "Lysosome membrane protein 2", "gene_name": "SCARB2", "tax_id": 9606, "tax_name": "Homo sapiens", "tax_common_name": "Human", "length": 478, "chemical_mass": 54290.0 } ] }, { "start_pos": "304", "site_seq": "", "site_lbl": "N304", "residue": "", "snv": [ { "weight": 100, "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-loss (NTS->DTS).", "chr_id": "4", "chr_pos": "76174228", "evidence": [ { "id": "rs1732197179", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1732197179" }, { "id": "rs1732197179", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1732197179#frequency_tab" } ] }, { "weight": 100, "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-loss (NTS->STS).", "chr_id": "4", "chr_pos": "76174227", "evidence": [ { "id": "rs150870503", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150870503" }, { "id": "rs150870503", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150870503" }, { "id": "rs150870503", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150870503#frequency_tab" }, { "id": "rs150870503", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150870503" } ], "disease": [ { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] }, { "disease_id": "DOID:0111444", "name": "progressive myoclonus epilepsy 4", "description": "A progressive myoclonus epilepsy characterized by progressive myoclonic epilepsy often associated with renal failure that has_material_basis_in homozygous or compound heterozygous of mutation in the SCARB2 gene on chromosome 4q21.1.", "url": "http://disease-ontology.org/term/DOID:0111444", "evidence": [ { "id": "254900", "database": "MIM", "url": "https://www.omim.org/entry/254900" }, { "id": "0111444", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111444" } ] } ] } ], "glycoprotein": [ { "uniprot_canonical_ac": "Q14108-1", "start_pos": 304, "end_pos": 304, "residue": "Asn", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "protein_name": "Lysosome membrane protein 2", "gene_name": "SCARB2", "tax_id": 9606, "tax_name": "Homo sapiens", "tax_common_name": "Human", "length": 478, "chemical_mass": 54290.0 } ] }, { "start_pos": "213", "site_seq": "IVKNVDRYCEAAQSEIQVLEHLNTTDPHSTFR", "site_lbl": "Asn213", "residue": "Asn", "glycoprotein": [ { "uniprot_canonical_ac": "P22518-1", "start_pos": 213, "end_pos": 213, "residue": "Asn", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "protein_name": "Dual specificity protein kinase CLK1", "gene_name": "Clk1", "tax_id": 10090, "tax_name": "Mus musculus", "tax_common_name": "Mouse", "length": 483, "chemical_mass": 57093.0 } ] }, { "start_pos": "1025", "site_seq": "TLNISSPVSVAEFTYTTSVFADGIKPLSK", "site_lbl": "Asn1025", "residue": "Asn", "glycoprotein": [ { "uniprot_canonical_ac": "B9EKR1-1", "start_pos": 1025, "end_pos": 1025, "residue": "Asn", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "protein_name": "Receptor-type tyrosine-protein phosphatase zeta", "gene_name": "Ptprz1", "tax_id": 10090, "tax_name": "Mus musculus", "tax_common_name": "Mouse", "length": 2312, "chemical_mass": 254405.0 } ] }, { "start_pos": "1025", "site_seq": "N", "site_lbl": "Asn1025", "residue": "Asn", "glycoprotein": [ { "uniprot_canonical_ac": "B9EKR1-1", "start_pos": 1025, "end_pos": 1025, "residue": "Asn", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "protein_name": "Receptor-type tyrosine-protein phosphatase zeta", "gene_name": "Ptprz1", "tax_id": 10090, "tax_name": "Mus musculus", "tax_common_name": "Mouse", "length": 2312, "chemical_mass": 254405.0 } ] }, { "start_pos": "242", "site_seq": "ISPNQLCSVPNSSLLGHPFPPNVPPVLSPLQRAQLLGGAQLQPGR", "site_lbl": "Asn242", "residue": "Asn", "glycoprotein": [ { "uniprot_canonical_ac": "Q3TC46-1", "start_pos": 242, "end_pos": 242, "residue": "Asn", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "protein_name": "Protein PAT1 homolog 1", "gene_name": "Patl1", "tax_id": 10090, "tax_name": "Mus musculus", "tax_common_name": "Mouse", "length": 770, "chemical_mass": 86770.0 } ] }, { "start_pos": "178", "site_seq": "GRFHGGKSSGNSSSSLGEMVSGTFR", "site_lbl": "Asn178", "residue": "Asn", "glycoprotein": [ { "uniprot_canonical_ac": "Q8R0S4-3", "start_pos": 178, "end_pos": 178, "residue": "Asn", "evidence": [ { "database": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "protein_name": "Voltage-dependent L-type calcium channel subunit beta-4", "gene_name": "Cacnb4", "tax_id": 10090, "tax_name": "Mus musculus", "tax_common_name": "Mouse", "length": 519, "chemical_mass": 57950.0 } ] } ], "record_id": "G06583FZ" }