Entity Name Entity type Gene Symbol Sources(; separated) Level4 Level3 Level2 Model_Of_Inheritance Phenotypes Omim Orphanet HPO Publications Description Flagged GEL_Status UserRatings_Green_amber_red version ready Mode of pathogenicity EnsemblId(GRch37) EnsemblId(GRch38) HGNC Position Chromosome Position GRCh37 Start Position GRCh37 End Position GRCh38 Start Position GRCh38 End STR Repeated Sequence STR Normal Repeats STR Pathogenic Repeats Region Haploinsufficiency Score Region Triplosensitivity Score Region Required Overlap Percentage Region Variant Type Region Verbose Name AGXT gene AGXT Eligibility statement prior genetic testing;Emory Genetics Laboratory;Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Primary Hyperoxaluria Type 1;Primary Hyperoxaluria;Hyperoxaluria, primary, type 1, 259900;Hyperoxaluria;primary hyperoxaluria False 3 100;0;0 5.5 True ENSG00000172482 ENSG00000172482 HGNC:341 APRT gene APRT Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal "Adenine phosphoribosyltransferase deficiency 614723" False 3 0;0;0 5.5 False ENSG00000198931 ENSG00000198931 HGNC:626 ATP6V0A4 gene ATP6V0A4 Eligibility statement prior genetic testing;Expert;Expert Review Green;NHS GMS Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Distal renal tubular acidosis 3, with or without sensorineural hearing loss, OMIM:602722 27274828;32123165;23729491;25572248;26208211;26571219;27247958;28233610;29202719;29725771;30230413;30256676;31348261;31929293;32613277;33881640;34159584 False 3 100;0;0 5.5 True ENSG00000105929 ENSG00000105929 HGNC:866 ATP6V1B1 gene ATP6V1B1 Eligibility statement prior genetic testing;Expert;Expert Review Green;NHS GMS Nephrocalcinosis or nephrolithiasis Renal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Distal renal tubular acidosis 2 with progressive sensorineural hearing loss, OMIM:267300;renal tubular acidosis, distal, 2, with progressive sensorineural hearing loss, MONDO:0009968 39837581;9916796;12566520;18798332 False 3 100;0;0 5.5 True ENSG00000116039 ENSG00000116039 HGNC:853 BSND gene BSND Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Bartter Syndrome;Bartter syndrome, type 4a, 602522;Sensorineural deafness with mild renal dysfunction, 602522 False 3 100;0;0 5.5 True ENSG00000162399 ENSG00000162399 HGNC:16512 CA2 gene CA2 Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Osteopetrosis, autosomal recessive 3, with renal tubular acidosis False 3 100;0;0 5.5 True ENSG00000104267 ENSG00000104267 HGNC:1373 CASR gene CASR Eligibility statement prior genetic testing;Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Nephrocalcinosis or nephrolithiasis Renal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Familial Hypocalciuric Hypercalcemia;Hypocalciuric hypercalcemia, type I, 145980Hyperparathyroidism, neonatal, 239200Hypocalcemia, autosomal dominant, 601198Hypocalcemia, autosomal dominant, with Bartter syndrome, 601198{Epilepsy idiopathic generalized, susceptibility to,;Hypocalcemia (dominant); Familial Hypocalciuric Hypercalcemia (dominant);hypocalciuric hypercalcaemia False 3 100;0;0 5.5 False Other ENSG00000036828 ENSG00000036828 HGNC:1514 CLCN5 gene CLCN5 Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Nephrocalcinosis or nephrolithiasis Renal X-LINKED: hemizygous mutation in males, biallelic mutations in females Dent Disease;Dent disease, 300009;Nephrolithiasis, type I, 310468Hypophosphatemic rickets, 300554;Proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis, 308990;Nephrocalcinosis with low molecular weight proteinuria and pregressive CKD False 3 100;0;0 5.5 True ENSG00000171365 ENSG00000171365 HGNC:2023 CLCNKB gene CLCNKB Expert;Expert Review Green;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Bartter syndrome, type 3, OMIM:607364;Bartter disease type 3, MONDO:0011822;Bartter syndrome, type 4b, digenic, OMIM:613090;Bartter disease type 4B, MONDO:0000909 28018459;23550235 False 3 100;0;0 5.5 True ENSG00000184908 ENSG00000184908 HGNC:2027 CLDN16 gene CLDN16 Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Hypomagnesemia 3, renal, OMIM:248250 False 3 100;0;0 5.5 True ENSG00000113946 ENSG00000113946 HGNC:2037 CLDN19 gene CLDN19 Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal hypomagensemia with nephrocalcinosis;Hypomagnesemia 5, renal, with ocular involvement PMID: 17033971 False 3 100;0;0 5.5 True ENSG00000164007 ENSG00000164007 HGNC:2040 CYP24A1 gene CYP24A1 Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Infantile Hypercalcemia;Hypercalcemia, infantile, 143880;Infantile hypercalcaemia False 3 100;0;0 5.5 True ENSG00000019186 ENSG00000019186 HGNC:2602 FAM20A gene FAM20A Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Amelogenesis imperfecta, type IG (enamel-renal syndrome) 204690 23468644;30394349;28298625;22732358 False 3 100;0;0 5.5 False ENSG00000108950 ENSG00000108950 HGNC:23015 GRHPR gene GRHPR Eligibility statement prior genetic testing;Emory Genetics Laboratory;Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Primary Hyperoxaluria;Primary Hyperoxaluria Type 2;Hyperoxaluria, primary, type II, 260000;Hyperoxaluria False 3 100;0;0 5.5 True ENSG00000137106 ENSG00000137106 HGNC:4570 HNF4A gene HNF4A Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Fanconi renotubular syndrome 4, with maturity-onset diabetes of the young, OMIM:616026 24285859;25819479 False 3 50;50;0 5.5 False ENSG00000101076 ENSG00000101076 HGNC:5024 HOGA1 gene HOGA1 Eligibility statement prior genetic testing;Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen;UKGTN Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Primary Hyperoxaluria;Hyperoxaluria, primary, type III, 613616;Hyperoxaluria False 3 100;0;0 5.5 True ENSG00000241935 ENSG00000241935 HGNC:25155 HPRT1 gene HPRT1 Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal X-LINKED: hemizygous mutation in males, biallelic mutations in females Hyperuricemia, HRPT-related, OMIM:300323;Lesch-Nyhan syndrome, OMIM:300322 31129767;27079129 False 3 100;0;0 5.5 False ENSG00000165704 ENSG00000165704 HGNC:5157 KCNJ1 gene KCNJ1 Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Antenatal Bartter Syndrome;Bartter syndrome, type 2, 241200;Type 2 Bartter syndrome;often initial transient hyperkalemia False 3 100;0;0 5.5 True ENSG00000151704 ENSG00000151704 HGNC:6255 MOCOS gene MOCOS Expert Review Green;Literature Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Xanthinuria, type II, OMIM:603592 11302742;17368066;14624414;25967871;34356852;32073534;30758870;27919260 False 3 100;0;0 5.5 False ENSG00000075643 ENSG00000075643 HGNC:18234 OCRL gene OCRL Expert;Expert Review Green;Radboud University Medical Center, Nijmegen Nephrocalcinosis or nephrolithiasis Renal X-LINKED: hemizygous mutation in males, biallelic mutations in females Lowe syndrome, OMIM:309000;Dent disease 2, OMIM:300555;As for CLCN5 (Nephrocalcinosis with low molecular weight proteinuria and pregressive CKD) but may include intellectual disability and other features of Lowe syndrome 33517444 False 3 100;0;0 5.5 True ENSG00000122126 ENSG00000122126 HGNC:8108 PHEX gene PHEX Expert list;Expert Review Green;Literature Nephrocalcinosis or nephrolithiasis Renal X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Hypophosphatemic rickets, X-linked dominant 307800 31514490;29460029 False 3 100;0;0 5.5 False ENSG00000102174 ENSG00000102174 HGNC:8918 RRAGD gene RRAGD Expert Review Green;NHS GMS;Other Nephrocalcinosis or nephrolithiasis Renal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted hypomagnesaemia;nephrocalcinosis;salt wasting;cardiomyopathy;tubular renal disease-cardiomyopathy syndrome, MONDO:0019130 34607910 False 3 100;0;0 5.5 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000025039 ENSG00000025039 HGNC:19903 SLC12A1 gene SLC12A1 Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Bartter syndrome, type 1, OMIM:601678;Bartter disease type 1, MONDO:0100344 21631963;21189980;20219833;19513753;19096086;18830715;17998760;16807401;8640224;9355073;28095294;32506365 False 3 100;0;0 5.5 True ENSG00000074803 ENSG00000074803 HGNC:10910 SLC22A12 gene SLC22A12 Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Hypouricemia, renal, 220150 29486147;29958533;18492088;15912381 False 3 100;0;0 5.5 False ENSG00000197891 ENSG00000197891 HGNC:17989 SLC2A9 gene SLC2A9 Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Hypouricemia, renal, 2, 612076 19926891;21256783;19026395;21810765;29486147;24940677 False 3 100;0;0 5.5 False ENSG00000109667 ENSG00000109667 HGNC:13446 SLC34A1 gene SLC34A1 Expert;Expert Review Green;Illumina TruGenome Clinical Sequencing Services;Radboud University Medical Center, Nijmegen Nephrocalcinosis or nephrolithiasis Renal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Nephrolithiasis/osteoporosis, hypophosphatemic, 1, 612286;Hypophosphatemic Nephrolithiasis/Osteoporosis;Hypophosphatemic Nephrolithiasis/Osteoporosis (recessive);Nephrolithiasis with osteoporosis and hypophosphatemia;Nephrolithiasis with osteoporosis and hypophosphatemia PMID: 26047794;25050900;12324554 False 3 100;0;0 5.5 True ENSG00000131183 ENSG00000131183 HGNC:11019 SLC34A3 gene SLC34A3 Expert;Expert Review Green;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN Nephrocalcinosis or nephrolithiasis Renal BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Hypophosphatemic rickets with hypercalciuria, OMIM:241530;HHRH;hereditary hypophosphatemic rickets with hypercalciuria, MONDO:0009431 25296721;26543054;24924704;24700880;16358214;27939817;24700880;17968493 False 3 100;0;0 5.5 False ENSG00000198569 ENSG00000198569 HGNC:20305 SLC3A1 gene SLC3A1 Eligibility statement prior genetic testing;Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Cystinuria 220100 False 3 100;0;0 5.5 True ENSG00000138079 ENSG00000138079 HGNC:11025 SLC4A1 gene SLC4A1 Eligibility statement prior genetic testing;Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal BOTH monoallelic and biallelic, autosomal or pseudoautosomal distal renal tubular acidosis;Renal tubular acidosis, distal, AD, 179800;Renal tubular acidosis, distal, AR 611590 False 3 0;0;0 5.5 True ENSG00000004939 ENSG00000004939 HGNC:11027 SLC7A9 gene SLC7A9 Eligibility statement prior genetic testing;Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Cystinuria 220100 False 3 100;0;0 5.5 True ENSG00000021488 ENSG00000021488 HGNC:11067 STRADA gene STRADA Expert Review Green;Other Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Polyhydramnios, megalencephaly, and symptomatic epilepsy, 611087 27170158;17522105;28688840 False 3 50;0;50 5.5 False ENSG00000266173 ENSG00000266173 HGNC:30172 VIPAS39 gene VIPAS39 Expert Review Green;Literature Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Arthrogryposis, renal dysfunction, and cholestasis 2, OMIM:613404 20190753 False 3 0;0;0 5.5 False ENSG00000151445 ENSG00000151445 HGNC:20347 VPS33B gene VPS33B Expert Review Green;Literature Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Arthrogryposis, renal dysfunction, and cholestasis 1, OMIM:208085 15052268;22753090 False 3 0;0;0 5.5 False ENSG00000184056 ENSG00000184056 HGNC:12712 WDR72 gene WDR72 Expert list;Expert Review Green;NHS GMS Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal distal renal tubular acidosis, MONDO:0015827;Amelogenesis imperfecta, type IIA3, OMIM:613211;amelogenesis imperfecta hypomaturation type 2A3, MONDO:0013181 30028003;30779877;31959358;33033857 False 3 100;0;0 5.5 False ENSG00000166415 ENSG00000166415 HGNC:26790 XDH gene XDH Expert;Expert Review Green Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Xanthinuria, type I, 278300 27604308;9153281 False 3 0;0;0 5.5 False ENSG00000158125 ENSG00000158125 HGNC:12805 SLC9A3R1 gene SLC9A3R1 Expert;Expert Review Amber;Radboud University Medical Center, Nijmegen Nephrocalcinosis or nephrolithiasis Renal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Nephrolithiasis/osteoporosis, hypophosphatemic, 2, 612287 False 2 100;0;0 5.5 True ENSG00000109062 ENSG00000109062 HGNC:11075 ADCY10 gene ADCY10 Expert;Expert Review Red Nephrocalcinosis or nephrolithiasis Renal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown PMID: 24907563 (review) False 1 50;0;50 5.5 True ENSG00000143199 ENSG00000143199 HGNC:21285 AGK gene AGK Expert Review Red;Radboud University Medical Center, Nijmegen Nephrocalcinosis or nephrolithiasis Renal Hyperoxaluria, primary, type 1, 259900 False 1 0;0;100 5.5 True ENSG00000006530 ENSG00000006530 HGNC:21869 AP2S1 gene AP2S1 Expert Review Red;Radboud University Medical Center, Nijmegen Nephrocalcinosis or nephrolithiasis Renal MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Hypocalciuric hypercalcemia, familial, type III, 600740;Familial hypocalciuric hypercalcemia type III False 1 0;0;100 5.5 True ENSG00000042753 ENSG00000042753 HGNC:565 CLCNKA gene CLCNKA Expert Review Red;Radboud University Medical Center, Nijmegen Nephrocalcinosis or nephrolithiasis Renal Other Bartter syndrome, type 4b, digenic, OMIM:613090;Bartter disease type 4B, MONDO:0000909 15044642;18310267;32488762 False 1 0;0;100 5.5 True ENSG00000186510 ENSG00000186510 HGNC:2026 FGF23 gene FGF23 Expert list Nephrocalcinosis or nephrolithiasis Renal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown False 1 100;0;0 5.5 False ENSG00000118972 ENSG00000118972 HGNC:3680 GNA11 gene GNA11 Radboud University Medical Center, Nijmegen Nephrocalcinosis or nephrolithiasis Renal Hypocalciuric hypercalcemia, type II, 145981 False 1 0;0;100 5.5 False ENSG00000088256 ENSG00000088256 HGNC:4379 SLC26A1 gene SLC26A1 Expert list;Expert Review Red Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Nephrolithiasis, calcium oxalate, MIM#167030 27210743;20160351;30383413;27125215;24250268;36719378 False 1 33;0;67 5.5 False ENSG00000145217 ENSG00000145217 HGNC:10993 SLC26A6 gene SLC26A6 Literature Nephrocalcinosis or nephrolithiasis Renal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Enteric hyperoxaluria and nephrolithiasis 35115415 False 1 0;0;0 5.5 False ENSG00000225697 ENSG00000225697 HGNC:14472 SLC36A2 gene SLC36A2 Expert Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal False 1 0;0;100 5.5 False ENSG00000186335 ENSG00000186335 HGNC:18762 SLC6A19 gene SLC6A19 Expert Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal 19033659 False 1 0;0;100 5.5 False ENSG00000174358 ENSG00000174358 HGNC:27960 SLC6A20 gene SLC6A20 Expert Nephrocalcinosis or nephrolithiasis Renal BOTH monoallelic and biallelic, autosomal or pseudoautosomal False 1 0;0;100 5.5 False ENSG00000163817 ENSG00000163817 HGNC:30927 SLC9A3 gene SLC9A3 Expert Nephrocalcinosis or nephrolithiasis Renal BOTH monoallelic and biallelic, autosomal or pseudoautosomal False 1 0;0;100 5.5 False ENSG00000066230 ENSG00000066230 HGNC:11073 TRPM6 gene TRPM6 Expert Review Red;Illumina TruGenome Clinical Sequencing Services Nephrocalcinosis or nephrolithiasis Renal BIALLELIC, autosomal or pseudoautosomal Hypomagnesemia with Secondary Hypocalcemia False 1 0;0;100 5.5 False ENSG00000119121 ENSG00000119121 HGNC:17995 VDR gene VDR Expert Nephrocalcinosis or nephrolithiasis Renal MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown False 1 0;0;100 5.5 False ENSG00000111424 ENSG00000111424 HGNC:12679 ZNF365 gene ZNF365 Expert;Expert Review Red Nephrocalcinosis or nephrolithiasis Renal BOTH monoallelic and biallelic, autosomal or pseudoautosomal Possible cause of uric acid stones;{Nephrolithiasis, uric acid, susceptibility to} False 1 50;0;50 5.5 True ENSG00000138311 ENSG00000138311 HGNC:18194