ClinVar Miner

Variants from Rare Kidney Stone Consortium and the Mayo Clinic Hyperoxaluria Center, Mayo Clinic

Location: United States  Primary collection method: research
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If a variant has more than one submission, it may be counted in more than one significance column. If this is the case, the total number of variants will be less than the sum of the other cells.

pathogenic likely pathogenic uncertain significance likely benign benign total
148 93 116 0 1 358

Gene and significance breakdown #

Total genes and gene combinations: 59
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Gene or gene combination pathogenic likely pathogenic uncertain significance benign total
AGXT 25 14 8 0 47
SLC34A3 18 8 10 0 36
HOGA1 12 10 8 0 30
GRHPR 15 3 2 0 20
SLC34A1 4 7 8 0 19
CYP24A1 8 1 7 0 16
SLC3A1 11 2 2 0 15
SLC4A1 4 2 8 0 14
SLC7A9 7 4 1 0 12
APRT 3 7 0 0 10
CLDN16 5 4 1 0 10
CLCN5 6 1 1 0 8
KCNJ1 4 4 0 0 8
ATP6V1B1 2 1 4 0 7
BSND 0 3 4 0 7
PKHD1 2 2 2 0 6
PREPL, SLC3A1 2 3 0 0 5
SLC12A1 1 2 2 0 5
ALPL 1 2 1 0 4
ATP6V0A4 1 1 2 0 4
CASR 0 1 3 0 4
HNF4A 1 1 2 0 4
NHERF1 0 0 3 1 4
OCRL 3 0 1 0 4
SCN10A 0 0 4 0 4
ADCY10, DCAF6 1 0 2 0 3
CLCNKA, LOC106501712 0 1 2 0 3
CLCNKB, LOC106501713 1 0 2 0 3
IDUA, SLC26A1 0 1 2 0 3
ABCC6 1 0 1 0 2
CLCN5, LOC126863258 1 1 0 0 2
CLDN14 0 1 1 0 2
CLDN19 1 1 0 0 2
CYP27B1 1 1 0 0 2
CYP2R1, PDE3B 0 0 2 0 2
FGF23 0 0 2 0 2
KL 0 0 2 0 2
SLC12A3 1 1 0 0 2
SLC2A9 0 0 2 0 2
SLC4A4 0 0 2 0 2
UMOD 0 0 2 0 2
WNK4 0 0 2 0 2
APRT, LOC130059760 1 0 0 0 1
CA2 1 0 0 0 1
CAMKMT, SLC3A1 1 0 0 0 1
CFTR 1 0 0 0 1
CFTR, LOC111674475 1 0 0 0 1
CYP3A4 0 0 1 0 1
GATA3 0 0 1 0 1
HPRT1 0 1 0 0 1
LOC126807073, SLC4A4 0 1 0 0 1
LOC130003098, SLC34A3 1 0 0 0 1
OGDH 0 0 1 0 1
OXGR1 0 0 1 0 1
SACK1H 0 0 1 0 1
SLC22A12 0 0 1 0 1
TRPM6 0 0 1 0 1
VDR 0 0 1 0 1
XDH 0 1 0 0 1

Condition and significance breakdown #

Total conditions: 52
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Condition pathogenic likely pathogenic uncertain significance benign total
Primary hyperoxaluria, type I 25 14 8 0 47
Autosomal recessive hypophosphatemic bone disease 19 8 10 0 37
Cystinuria 21 9 3 0 33
Primary hyperoxaluria type 3 12 10 8 0 30
Primary hyperoxaluria, type II 15 3 2 0 20
Hypophosphatemic nephrolithiasis/osteoporosis 1; Fanconi renotubular syndrome 2; Hypercalcemia, infantile, 2 4 7 8 0 19
Hypercalcemia, infantile, 1 8 1 7 0 16
Autosomal dominant distal renal tubular acidosis; Renal tubular acidosis, distal, 4, with hemolytic anemia 4 2 8 0 14
Adenine phosphoribosyltransferase deficiency 4 7 0 0 11
Dent disease type 1; Hypophosphatemic rickets, X-linked recessive; X-linked recessive nephrolithiasis with renal failure; Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis 7 2 1 0 10
Primary hypomagnesemia 5 4 1 0 10
Bartter disease type 2 4 4 0 0 8
Bartter disease type 4A 0 3 4 0 7
Renal tubular acidosis with progressive nerve deafness 2 1 4 0 7
Polycystic kidney disease 4 2 2 2 0 6
Bartter disease type 1 1 2 2 0 5
Adult hypophosphatasia; Childhood hypophosphatasia; Infantile hypophosphatasia 1 2 1 0 4
Dent disease type 2; Lowe syndrome 3 0 1 0 4
Episodic pain syndrome, familial, 2 0 0 4 0 4
Familial hypocalciuric hypercalcemia 1; Autosomal dominant hypocalcemia 1 0 1 3 0 4
Hypophosphatemic nephrolithiasis/osteoporosis 2 0 0 3 1 4
Renal tubular acidosis, distal, 3, with or without sensorineural hearing loss 1 1 2 0 4
Autosomal recessive proximal renal tubular acidosis 0 1 2 0 3
Bartter disease type 3 1 0 2 0 3
Bartter disease type 4B 0 1 2 0 3
Familial idiopathic hypercalciuria 1 0 2 0 3
Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young 1 0 2 0 3
Nephrolithiasis susceptibility caused by SLC26A1 0 1 2 0 3
Autosomal dominant hypophosphatemic rickets; Tumoral calcinosis, hyperphosphatemic, familial, 2 0 0 2 0 2
Autosomal recessive inherited pseudoxanthoma elasticum; Pseudoxanthoma elasticum, forme fruste; Arterial calcification, generalized, of infancy, 2 1 0 1 0 2
Autosomal recessive nonsyndromic hearing loss 29 0 1 1 0 2
Bronchiectasis with or without elevated sweat chloride 1; Cystic fibrosis; Hereditary pancreatitis; Congenital bilateral aplasia of vas deferens from CFTR mutation 2 0 0 0 2
Familial hypokalemia-hypomagnesemia 1 1 0 0 2
Familial juvenile hyperuricemic nephropathy type 1 0 0 2 0 2
Hypouricemia, renal, 2 0 0 2 0 2
Pseudohypoaldosteronism type 2B 0 0 2 0 2
Renal hypomagnesemia 5 with ocular involvement 1 1 0 0 2
Tumoral calcinosis, hyperphosphatemic, familial, 3 0 0 2 0 2
Vitamin D hydroxylation-deficient rickets, type 1B 0 0 2 0 2
Vitamin D-dependent rickets, type 1A 1 1 0 0 2
Amelogenesis imperfecta, type 3A 0 0 1 0 1
Dalmatian hypouricemia 0 0 1 0 1
Hereditary xanthinuria type 1 0 1 0 0 1
Hypoparathyroidism, deafness, renal disease syndrome 0 0 1 0 1
Intestinal hypomagnesemia 1 0 0 1 0 1
Maturity-onset diabetes of the young type 1; Type 2 diabetes mellitus; Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young 0 1 0 0 1
Nephrolithiasis, calcium oxalate, 2, with or without nephrocalcinosis 0 0 1 0 1
Osteopetrosis with renal tubular acidosis 1 0 0 0 1
Oxoglutaricaciduria 0 0 1 0 1
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency; Lesch-Nyhan syndrome 0 1 0 0 1
Vitamin D-dependent rickets type II with alopecia 0 0 1 0 1
Vitamin D-dependent rickets, type 3 0 0 1 0 1

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