Variant List
This API endpoint handles listing (/variants) and retrieval (/variants/<ID>/) of genetic variants from the database
GET /api/genes/NPHP4/variants/?format=api
{ "data": [ { "type": "SmallVariant", "id": "411", "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": "1", "annotation_flag": "not_found_in_databases", "lastmodified": "2021-10-18T11:00:52.036716", "ref_allele": null, "alt_allele": null, "cdna_change": "IVS16-1G>C", "protein_change": null, "transcript_id": null, "dbsnp_id": "NA", "variant_effect": "intronic" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI212" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/411/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/411/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/411/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/411/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP4" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/411/?format=api" } }, { "type": "SmallVariant", "id": "412", "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": 1.235e-05, "gnomad_AFR_maf": 6.821e-05, "gnomad_AMR_maf": 0.0, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.0, "gnomad_NFE_maf": 1.823e-05, "gnomad_OTH_maf": 0.0, "gnomad_SAS_maf": 0.0, "ESP_AA_maf": 0.0, "ESP_EA_maf": 0.0001191 }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 3.224497, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 5950972, "genomic_position_hg38": 5890912, "chromosome": "1", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:42.945479", "ref_allele": "C", "alt_allele": "T", "cdna_change": "c.2260G>A", "protein_change": "p.Gly754Arg", "transcript_id": "NM_015102.4", "dbsnp_id": "rs373962831", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI212" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/412/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/412/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/412/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/412/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP4" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/412/?format=api" } }, { "type": "SmallVariant", "id": "415", "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": 5.155698, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 5927904, "genomic_position_hg38": 5867844, "chromosome": "1", "annotation_flag": "manually_attributed", "lastmodified": "2023-06-06T16:57:42.958152", "ref_allele": "ACAGT", "alt_allele": "A", "cdna_change": "c.3364delACTG", "protein_change": "p.Thr1122TrpfsTer22", "transcript_id": "NM_015102.5", "dbsnp_id": "NA", "variant_effect": "frameshift" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI213" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/415/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/415/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/415/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/415/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP4" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/415/?format=api" } }, { "type": "SmallVariant", "id": "788", "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": 0.0003822, "gnomad_AFR_maf": 6.48e-05, "gnomad_AMR_maf": 8.719e-05, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.0004179, "gnomad_NFE_maf": 0.0007012, "gnomad_OTH_maf": 0.0001659, "gnomad_SAS_maf": 6.554e-05, "ESP_AA_maf": 0.0, "ESP_EA_maf": 0.0004804 }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 2.867867, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 6046343, "genomic_position_hg38": 5986283, "chromosome": "1", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:45.220451", "ref_allele": "C", "alt_allele": "A", "cdna_change": "c.7G>T", "protein_change": "p.Asp3Tyr", "transcript_id": "NM_015102.4", "dbsnp_id": "rs145078518", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI359" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/788/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/788/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/788/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/788/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP4" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/788/?format=api" } }, { "type": "SmallVariant", "id": "3035", "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": 6.035e-05, "gnomad_AFR_maf": 0.0, "gnomad_AMR_maf": 0.0002028, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 5.564e-05, "gnomad_FIN_maf": 0.0, "gnomad_NFE_maf": 2.658e-05, "gnomad_OTH_maf": 0.0001654, "gnomad_SAS_maf": 9.805e-05, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 3.364488, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 5935016, "genomic_position_hg38": 5874956, "chromosome": "1", "annotation_flag": null, "lastmodified": "2023-06-06T16:57:58.729048", "ref_allele": "C", "alt_allele": "T", "cdna_change": "c.2962G>A", "protein_change": "p.Ala988Thr", "transcript_id": "NM_015102.5", "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI1445" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/3035/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/3035/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/3035/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/3035/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP4" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/3035/?format=api" } }, { "type": "SmallVariant", "id": "3485", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0018, "KGP_genomes_AFR_maf": 0.0, "KGP_genomes_AMR_maf": 0.0, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.0, "KGP_genomes_SAS_maf": 0.0092, "gnomad_maf": 0.0008762, "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": 0.0, "gnomad_OTH_maf": 0.0003317, "gnomad_SAS_maf": 0.006994, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Possibly Damaging", "cadd_prediction": 3.753381, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 5927818, "genomic_position_hg38": 5867758, "chromosome": "1", "annotation_flag": null, "lastmodified": "2024-02-29T15:02:27.003330", "ref_allele": "G", "alt_allele": "A", "cdna_change": "c.3454C>T", "protein_change": "p.Pro1152Ser", "transcript_id": "NM_015102.3", "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI1658" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/3485/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/3485/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/3485/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/3485/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP4" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/3485/?format=api" } }, { "type": "SmallVariant", "id": "3490", "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": "Possibly Damaging", "cadd_prediction": 3.228836, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 5950942, "genomic_position_hg38": 5890882, "chromosome": "1", "annotation_flag": null, "lastmodified": "2024-02-29T15:02:27.162917", "ref_allele": "C", "alt_allele": "T", "cdna_change": "c.2290G>A", "protein_change": "p.Ala764Thr", "transcript_id": "NM_015102.3", "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI1661" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/3490/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/3490/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/3490/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/3490/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP4" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/3490/?format=api" } }, { "type": "SmallVariant", "id": "3494", "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": "Tolerated", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 2.825437, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 5964694, "genomic_position_hg38": 5904634, "chromosome": "1", "annotation_flag": null, "lastmodified": "2024-02-29T15:02:27.270603", "ref_allele": "T", "alt_allele": "C", "cdna_change": "c.2126A>G", "protein_change": "p.Asp709Gly", "transcript_id": "NM_015102.3", "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI1663" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/3494/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/3494/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/3494/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/3494/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP4" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/3494/?format=api" } }, { "type": "SmallVariant", "id": "3496", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0006, "KGP_genomes_AFR_maf": 0.0, "KGP_genomes_AMR_maf": 0.0014, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.0, "KGP_genomes_SAS_maf": 0.002, "gnomad_maf": 0.0002126, "gnomad_AFR_maf": 0.0, "gnomad_AMR_maf": 0.0001159, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.0, "gnomad_NFE_maf": 0.000115, "gnomad_OTH_maf": 0.0003303, "gnomad_SAS_maf": 0.001111, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": "Tolerated", "pp2_hvar_prediction": "Benign", "cadd_prediction": 0.020103, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 5965427, "genomic_position_hg38": 5905367, "chromosome": "1", "annotation_flag": null, "lastmodified": "2024-02-29T15:02:27.325904", "ref_allele": "G", "alt_allele": "A", "cdna_change": "c.1880C>T", "protein_change": "p.Thr627Met", "transcript_id": "NM_015102.3", "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI1664" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/3496/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/3496/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/3496/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/3496/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP4" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/3496/?format=api" } }, { "type": "SmallVariant", "id": "3500", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0094, "KGP_genomes_AFR_maf": 0.0008, "KGP_genomes_AMR_maf": 0.0101, "KGP_genomes_EAS_maf": 0.001, "KGP_genomes_EUR_maf": 0.0199, "KGP_genomes_SAS_maf": 0.0184, "gnomad_maf": 0.02469, "gnomad_AFR_maf": 0.004996, "gnomad_AMR_maf": 0.009935, "gnomad_ASJ_maf": 0.03528, "gnomad_EAS_maf": 0.0003441, "gnomad_FIN_maf": 0.0354, "gnomad_NFE_maf": 0.03259, "gnomad_OTH_maf": 0.02579, "gnomad_SAS_maf": 0.02525, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": "Tolerated", "pp2_hvar_prediction": "Benign", "cadd_prediction": -0.343399, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 5951013, "genomic_position_hg38": 5890953, "chromosome": "1", "annotation_flag": null, "lastmodified": "2024-02-29T15:02:27.437122", "ref_allele": "C", "alt_allele": "T", "cdna_change": "c.2219G>A", "protein_change": "p.Arg740His", "transcript_id": "NM_015102.3", "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI1666" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/3500/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/3500/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/3500/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/3500/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP4" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/3500/?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": 10 } }