Variant List
This API endpoint handles listing (/variants) and retrieval (/variants/<ID>/) of genetic variants from the database
GET /api/genes/NPHP3/variants/?format=api
{ "data": [ { "type": "SmallVariant", "id": "414", "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": "3", "annotation_flag": "not_found_in_databases", "lastmodified": "2021-10-18T11:00:52.081686", "ref_allele": null, "alt_allele": null, "cdna_change": "IVS24-1G>C", "protein_change": null, "transcript_id": null, "dbsnp_id": "NA", "variant_effect": "intronic" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI213" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/414/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/414/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/414/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/414/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP3" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/414/?format=api" } }, { "type": "SmallVariant", "id": "409", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0042, "KGP_genomes_AFR_maf": 0.0, "KGP_genomes_AMR_maf": 0.0072, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.0089, "KGP_genomes_SAS_maf": 0.0072, "gnomad_maf": 0.01363, "gnomad_AFR_maf": 0.003279, "gnomad_AMR_maf": 0.001696, "gnomad_ASJ_maf": 0.02173, "gnomad_EAS_maf": 0.0001371, "gnomad_FIN_maf": 0.0153, "gnomad_NFE_maf": 0.0189, "gnomad_OTH_maf": 0.01475, "gnomad_SAS_maf": 0.01431, "ESP_AA_maf": 0.001841, "ESP_EA_maf": 0.01509 }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Benign", "cadd_prediction": 0.598732, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 132441046, "genomic_position_hg38": 132722202, "chromosome": "3", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:42.932706", "ref_allele": "C", "alt_allele": "T", "cdna_change": "c.154G>A", "protein_change": "p.Ala52Thr", "transcript_id": "NM_153240.4", "dbsnp_id": "rs145643112", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI211" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/409/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/409/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/409/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/409/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP3" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/409/?format=api" } }, { "type": "SmallVariant", "id": "410", "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": "Benign", "cadd_prediction": 1.744625, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 132440838, "genomic_position_hg38": 132721994, "chromosome": "3", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:42.938992", "ref_allele": "G", "alt_allele": "C", "cdna_change": "c.362C>G", "protein_change": "p.Thr121Arg", "transcript_id": "NM_153240.4", "dbsnp_id": "NA", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI212" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/410/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/410/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/410/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/410/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP3" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/410/?format=api" } }, { "type": "SmallVariant", "id": "413", "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": 4.563152, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 132438629, "genomic_position_hg38": 132719785, "chromosome": "3", "annotation_flag": "manually_attributed", "lastmodified": "2023-06-06T16:57:42.951756", "ref_allele": "CACTT", "alt_allele": "C", "cdna_change": "c.435_438del", "protein_change": "p.Ser146LeufsTer2", "transcript_id": "NM_153240.5", "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/413/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/413/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/413/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/413/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP3" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/413/?format=api" } }, { "type": "SmallVariant", "id": "417", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0006, "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": 0.0031, "gnomad_maf": 0.0002667, "gnomad_AFR_maf": 0.0, "gnomad_AMR_maf": 8.677e-05, "gnomad_ASJ_maf": 0.0002978, "gnomad_EAS_maf": 5.438e-05, "gnomad_FIN_maf": 0.0, "gnomad_NFE_maf": 0.0001232, "gnomad_OTH_maf": 0.0003265, "gnomad_SAS_maf": 0.001438, "ESP_AA_maf": 0.0, "ESP_EA_maf": 0.0002326 }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 3.806321, "mutationtaster_prediction": null }, "status": "CU", "genomic_position_hg19": 132402277, "genomic_position_hg38": 132683433, "chromosome": "3", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:42.970817", "ref_allele": "G", "alt_allele": "A", "cdna_change": "c.3662C>T", "protein_change": "p.Ala1221Val", "transcript_id": "NM_153240.4", "dbsnp_id": "rs202048210", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI214" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/417/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/417/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/417/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/417/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP3" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/417/?format=api" } }, { "type": "SmallVariant", "id": "419", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0008, "KGP_genomes_AFR_maf": 0.0008, "KGP_genomes_AMR_maf": 0.0, "KGP_genomes_EAS_maf": 0.0, "KGP_genomes_EUR_maf": 0.003, "KGP_genomes_SAS_maf": 0.0, "gnomad_maf": 0.00189, "gnomad_AFR_maf": 0.0006173, "gnomad_AMR_maf": 0.001735, "gnomad_ASJ_maf": 9.921e-05, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 0.001294, "gnomad_NFE_maf": 0.003159, "gnomad_OTH_maf": 0.002778, "gnomad_SAS_maf": 0.0, "ESP_AA_maf": 0.0009083, "ESP_EA_maf": 0.003953 }, "predictions": { "sift_prediction": "Tolerated", "pp2_hvar_prediction": "Benign", "cadd_prediction": 2.144782, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 132427063, "genomic_position_hg38": 132708219, "chromosome": "3", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:42.983684", "ref_allele": "T", "alt_allele": "C", "cdna_change": null, "protein_change": "p.Asn386Ser", "transcript_id": null, "dbsnp_id": "rs142021049", "variant_effect": "missense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI215" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/419/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/419/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/419/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/419/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP3" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/419/?format=api" } }, { "type": "SmallVariant", "id": "786", "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": 7.963e-06, "gnomad_AFR_maf": 0.0, "gnomad_AMR_maf": 0.0, "gnomad_ASJ_maf": 0.0, "gnomad_EAS_maf": 0.0, "gnomad_FIN_maf": 4.624e-05, "gnomad_NFE_maf": 8.8e-06, "gnomad_OTH_maf": 0.0, "gnomad_SAS_maf": 0.0, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": null, "pp2_hvar_prediction": null, "cadd_prediction": 7.996462, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 132419192, "genomic_position_hg38": 132700348, "chromosome": "3", "annotation_flag": "automatically_attributed", "lastmodified": "2023-06-06T16:57:45.207608", "ref_allele": "G", "alt_allele": "A", "cdna_change": "c.1729C>T", "protein_change": "p.Arg577Ter", "transcript_id": "NM_153240.4", "dbsnp_id": "rs119456962", "variant_effect": "nonsense" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI359" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/786/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/786/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/786/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/786/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP3" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/786/?format=api" } }, { "type": "SmallVariant", "id": "787", "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": 5.949538, "mutationtaster_prediction": "Disease causing" }, "status": "CU", "genomic_position_hg19": 132402330, "genomic_position_hg38": 132683486, "chromosome": "3", "annotation_flag": "manually_attributed", "lastmodified": "2023-06-06T16:57:45.213950", "ref_allele": "AG", "alt_allele": "A", "cdna_change": "c.3608delC", "protein_change": "p.Ala1203ValfsTer16", "transcript_id": "NM_153240.5", "dbsnp_id": "rs1060499938", "variant_effect": "frameshift" }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI359" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/787/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/787/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/787/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/787/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP3" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/787/?format=api" } }, { "type": "SmallVariant", "id": "3480", "attributes": { "frequencies": { "KGP_genomes_maf": 0.0034, "KGP_genomes_AFR_maf": 0.0, "KGP_genomes_AMR_maf": 0.0043, "KGP_genomes_EAS_maf": 0.001, "KGP_genomes_EUR_maf": 0.007, "KGP_genomes_SAS_maf": 0.0061, "gnomad_maf": 0.008231, "gnomad_AFR_maf": 0.0009231, "gnomad_AMR_maf": 0.001446, "gnomad_ASJ_maf": 0.02114, "gnomad_EAS_maf": 0.0001087, "gnomad_FIN_maf": 0.0122, "gnomad_NFE_maf": 0.01027, "gnomad_OTH_maf": 0.009314, "gnomad_SAS_maf": 0.009833, "ESP_AA_maf": null, "ESP_EA_maf": null }, "predictions": { "sift_prediction": "Deleterious", "pp2_hvar_prediction": "Damaging", "cadd_prediction": 3.408684, "mutationtaster_prediction": "Polymorphism" }, "status": "CU", "genomic_position_hg19": 132403418, "genomic_position_hg38": 132684574, "chromosome": "3", "annotation_flag": null, "lastmodified": "2024-02-29T15:02:26.870507", "ref_allele": "C", "alt_allele": "T", "cdna_change": "c.3550G>A", "protein_change": "p.Ala1184Thr", "transcript_id": null, "dbsnp_id": "NA", "variant_effect": null }, "relationships": { "in_combination": { "meta": { "count": 1 }, "data": [ { "type": "Combination", "id": "OLI1656" } ], "links": { "self": "https://olida.ibsquare.be/api/variants/3480/relationships/in_combination?format=api", "related": "https://olida.ibsquare.be/api/variants/3480/combinations/?format=api" } }, "gene_name": { "links": { "self": "https://olida.ibsquare.be/api/variants/3480/relationships/gene_name?format=api", "related": "https://olida.ibsquare.be/api/variants/3480/gene/?format=api" }, "data": { "type": "Gene", "id": "NPHP3" } } }, "links": { "self": "https://olida.ibsquare.be/api/variants/3480/?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 } }