Variant List
This API endpoint handles listing (/variants) and retrieval (/variants/<ID>/) of genetic variants from the database
GET /api/genes/PRKN/variants/?format=api
{ "data": [ { "type": "SmallVariant", "id": "266", "attributes": { "frequencies": { "KGP_genomes_maf": null, "KGP_genomes_AFR_maf": null, "KGP_genomes_AMR_maf": null, "KGP_genomes_EAS_maf": null, "KGP_genomes_EUR_maf": null, "KGP_genomes_SAS_maf": null, "gnomad_maf": null, "gnomad_AFR_maf": null, "gnomad_AMR_maf": null, "gnomad_ASJ_maf": null, "gnomad_EAS_maf": null, "gnomad_FIN_maf": null, "gnomad_NFE_maf": null, "gnomad_OTH_maf": null, "gnomad_SAS_maf": null, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": null, "pp2_hvar_prediction": null, "cadd_prediction": null, "mutationtaster_prediction": null }, "status": "CU", "genomic_position_hg19": null, "genomic_position_hg38": null, "chromosome": "6", "annotation_flag": "not_found_in_databases", "lastmodified": "2021-10-18T11:00:49.514805", "ref_allele": null, "alt_allele": null, "cdna_change": null, "protein_change": "p.Ala138GlyfsTer7", "transcript_id": null, "dbsnp_id": "NA", "variant_effect": "frameshift" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI128" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/266/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/266/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/266/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/266/gene/?format=api" }, "data": { "type": "Gene", "id": "PRKN" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/266/?format=api" } }, { "type": "CopyNumberVariant", "id": "445", "attributes": { "status": "CU", "genomic_position_hg19": null, "genomic_position_hg38": null, "chromosome": "6", "annotation_flag": "cnv", "lastmodified": "2021-10-18T11:00:52.650592", "location": "exon2_4", "sequence": "exon2_4", "number_of_repeats": null, "type_cnv": "deletion" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI230" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/445/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/445/combinations/?format=api" } }, "gene_name": { "data": { "type": "Gene", "id": "PRKN" }, "links": { "related": "https://olida.ibsquare.be/api/genes/PRKN/?format=api" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/445/?format=api" } }, { "type": "CopyNumberVariant", "id": "446", "attributes": { "status": "CU", "genomic_position_hg19": null, "genomic_position_hg38": null, "chromosome": "6", "annotation_flag": "cnv", "lastmodified": "2021-10-18T11:00:52.658902", "location": "exon3", "sequence": "exon3", "number_of_repeats": null, "type_cnv": "deletion" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI230" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/446/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/446/combinations/?format=api" } }, "gene_name": { "data": { "type": "Gene", "id": "PRKN" }, "links": { "related": "https://olida.ibsquare.be/api/genes/PRKN/?format=api" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/446/?format=api" } }, { "type": "SmallVariant", "id": "262", "attributes": { "frequencies": { "KGP_genomes_maf": null, "KGP_genomes_AFR_maf": null, "KGP_genomes_AMR_maf": null, "KGP_genomes_EAS_maf": null, "KGP_genomes_EUR_maf": null, "KGP_genomes_SAS_maf": null, "gnomad_maf": null, "gnomad_AFR_maf": null, "gnomad_AMR_maf": null, "gnomad_ASJ_maf": null, "gnomad_EAS_maf": null, "gnomad_FIN_maf": null, "gnomad_NFE_maf": null, "gnomad_OTH_maf": null, "gnomad_SAS_maf": null, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": null, "pp2_hvar_prediction": null, "cadd_prediction": 5.032623, "mutationtaster_prediction": null }, "status": "CU", "genomic_position_hg19": 162622173, "genomic_position_hg38": 162201141, "chromosome": "6", "annotation_flag": "manually_attributed", "lastmodified": "2023-06-06T16:57:42.070963", "ref_allele": "GT", "alt_allele": "G", "cdna_change": "c.523del", "protein_change": "p.Thr175ProfsTer2", "transcript_id": "None", "dbsnp_id": "NA", "variant_effect": "frameshift" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI127" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/262/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/262/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/262/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/262/gene/?format=api" }, "data": { "type": "Gene", "id": "PRKN" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/262/?format=api" } }, { "type": "SmallVariant", "id": "265", "attributes": { "frequencies": { "KGP_genomes_maf": null, "KGP_genomes_AFR_maf": null, "KGP_genomes_AMR_maf": null, "KGP_genomes_EAS_maf": null, "KGP_genomes_EUR_maf": null, "KGP_genomes_SAS_maf": null, "gnomad_maf": 5.198e-05, "gnomad_AFR_maf": 0.0, "gnomad_AMR_maf": 0.0, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.000708, "gnomad_FIN_maf": 0.0, "gnomad_NFE_maf": 0.0, "gnomad_OTH_maf": 0.0, "gnomad_SAS_maf": 0.0, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 3.999057, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 161771208, "genomic_position_hg38": 161350176, "chromosome": "6", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:42.088465", "ref_allele": "A", "alt_allele": "G", "cdna_change": null, "protein_change": "p.Cys441Arg", "transcript_id": null, "dbsnp_id": "rs778305273", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI128" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/265/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/265/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/265/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/265/gene/?format=api" }, "data": { "type": "Gene", "id": "PRKN" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/265/?format=api" } }, { "type": "SmallVariant", "id": "268", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0004, "KGP_genomes_AFR_maf": 0.0, "KGP_genomes_AMR_maf": 0.0, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.002, "KGP_genomes_SAS_maf": 0.0, "gnomad_maf": 0.001586, "gnomad_AFR_maf": 0.0004994, "gnomad_AMR_maf": 0.001943, "gnomad_ASJ_maf": 0.0008977, "gnomad_EAS_maf": 5.457e-05, "gnomad_FIN_maf": 0.0002323, "gnomad_NFE_maf": 0.002547, "gnomad_OTH_maf": 0.003128, "gnomad_SAS_maf": 0.0, "ESP_AA_maf": 0.0009079, "ESP_EA_maf": 0.00314 }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 4.009061, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 161771219, "genomic_position_hg38": 161350187, "chromosome": "6", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:42.100108", "ref_allele": "G", "alt_allele": "A", "cdna_change": null, "protein_change": "p.Pro437Leu", "transcript_id": null, "dbsnp_id": "rs149953814", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI129" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/268/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/268/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/268/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/268/gene/?format=api" }, "data": { "type": "Gene", "id": "PRKN" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/268/?format=api" } }, { "type": "SmallVariant", "id": "440", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0012, "KGP_genomes_AFR_maf": 0.0, "KGP_genomes_AMR_maf": 0.0, "KGP_genomes_EAS_maf": 0.006, "KGP_genomes_EUR_maf": 0.0, "KGP_genomes_SAS_maf": 0.0, "gnomad_maf": 0.0002824, "gnomad_AFR_maf": 0.0001845, "gnomad_AMR_maf": 0.0, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.003208, "gnomad_FIN_maf": 0.0, "gnomad_NFE_maf": 5.275e-05, "gnomad_OTH_maf": 0.0001629, "gnomad_SAS_maf": 6.533e-05, "ESP_AA_maf": 0.0006809, "ESP_EA_maf": 0.0001163 }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Possibly Damaging", "cadd_prediction": 4.245035, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 161807897, "genomic_position_hg38": 161386865, "chromosome": "6", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:43.103460", "ref_allele": "G", "alt_allele": "A", "cdna_change": "c.1096C>T", "protein_change": "p.Arg366Trp", "transcript_id": "NM_004562.2", "dbsnp_id": "rs56092260", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI228" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/440/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/440/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/440/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/440/gene/?format=api" }, "data": { "type": "Gene", "id": "PRKN" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/440/?format=api" } }, { "type": "SmallVariant", "id": "442", "attributes": { "frequencies": { "KGP_genomes_maf": null, "KGP_genomes_AFR_maf": null, "KGP_genomes_AMR_maf": null, "KGP_genomes_EAS_maf": null, "KGP_genomes_EUR_maf": null, "KGP_genomes_SAS_maf": null, "gnomad_maf": null, "gnomad_AFR_maf": null, "gnomad_AMR_maf": null, "gnomad_ASJ_maf": null, "gnomad_EAS_maf": null, "gnomad_FIN_maf": null, "gnomad_NFE_maf": null, "gnomad_OTH_maf": null, "gnomad_SAS_maf": null, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 4.040731, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 161771228, "genomic_position_hg38": 161350196, "chromosome": "6", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:43.115665", "ref_allele": "A", "alt_allele": "T", "cdna_change": null, "protein_change": "p.Met434Lys", "transcript_id": null, "dbsnp_id": "rs1582953433", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI229" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/442/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/442/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/442/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/442/gene/?format=api" }, "data": { "type": "Gene", "id": "PRKN" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/442/?format=api" } }, { "type": "SmallVariant", "id": "2752", "attributes": { "frequencies": { "KGP_genomes_maf": null, "KGP_genomes_AFR_maf": null, "KGP_genomes_AMR_maf": null, "KGP_genomes_EAS_maf": null, "KGP_genomes_EUR_maf": null, "KGP_genomes_SAS_maf": null, "gnomad_maf": 3.978e-06, "gnomad_AFR_maf": 0.0, "gnomad_AMR_maf": 0.0, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.0, "gnomad_NFE_maf": 8.798e-06, "gnomad_OTH_maf": 0.0, "gnomad_SAS_maf": 0.0, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": "Tolerated", "pp2_hvar_prediction": "Possibly Damaging", "cadd_prediction": 2.567124, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 162864418, "genomic_position_hg38": 162443386, "chromosome": "6", "annotation_flag": null, "lastmodified": "2023-06-06T16:57:57.028936", "ref_allele": "T", "alt_allele": "G", "cdna_change": null, "protein_change": "p.Lys32Thr", "transcript_id": null, "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 3 }, "data": [ { "type": "Combination", "id": "OLI1310" }, { "type": "Combination", "id": "OLI1311" }, { "type": "Combination", "id": "OLI1312" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/2752/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/2752/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/2752/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/2752/gene/?format=api" }, "data": { "type": "Gene", "id": "PRKN" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/2752/?format=api" } } ], "meta": { "database_name": "OLIgogenic diseases DAtabase (OLIDA)", "resource_url": "olida.ibsquare.be", "api_release_year": "2021", "api_developer": [ [ "Arnau Dillen", "arnau.dillen@ulb.ac.be" ], [ "Charlotte Nachtegael", "charlotte.nachtegael@ulb.be" ] ], "api_version": "0.3", "api_maintainers": [ [ "Charlotte Nachtegael", "charlotte.nachtegael@ulb.be" ] ], "api_documentation": [ "olida.ibsquare.be/api/swagger", "olida.ibsquare.be/api/redoc" ], "copyright": "Copyright (c) 2025 · OLIDA All Rights Reserved.", "license": "CC Attribution-NonCommercial 4.0 International License", "ontologies": { "ORDO": "http://bioportal.bioontology.org/ontologies/ORDO", "GENO": "http://purl.obolibrary.org/obo/geno.owl", "MI": "http://purl.obolibrary.org/obo/mi.owl", "NCIT": "http://purl.obolibrary.org/obo/ncit.owl", "OGI": "http://purl.obolibrary.org/obo/ogi.owl", "OGG": "http://purl.obolibrary.org/obo/ogg.owl" }, "relevant_publications_doi": [ "10.1093/nar/gkv1068", "10.1093/database/baac023" ], "Variant serializers": [ "SmallVariantSerializer", "CopyNumberVariantSerializer" ], "size": 9 } }