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Table 1 Genetic description and clinical data of family with dominant calcium-sensing receptor (CaSR) variant

From: Sequencing the CaSR locus in Pakistani stone formers reveals a novel loss-of-function variant atypically associated with nephrolithiasis

Family ID/individuals Age of onset (years) NL Episodes Stone composition (age at stone retrieval in years) Variant genomic change Total allele frequency in ExAC, gnomAD v2.1.1, gnomAD v3.1.1 databases (H, het, total) Canonical transcript NM_000388 Predicted Effect Alternative transcript NM_001178065 predicted effect
KS72        
 II 3 18 2 CaOxMo 56%, CaOxDi 41%, Struvite 3% (18) GRCh37
Chr3:122000958A>G
Absent c.1609-2A>G c.1637A>G
     GRCh38
Chr3:12228211A>G
  Splice Site Effect (MaxEnt -100%, NNSPLICE -100%, SSF -100%) p.Gln546Arg (SIFT Tol 0.27; MT Del; PP2 Ben 0.032
 II 4 19 2 CaOxMo 55%, CaOxDi 40%, Struvite 5% (19)     
  1. CaOxMo Calcium oxalate monohydrate, CaOxDi Calcium oxalate dehydrate, ID identification code, H Homozygous subjects, het Heterozygous subjects, MaxEnt Maximum entropy splice site scoring software, MT “MutationTaster” prediction score, NL nephrolithiasis, NNSSPLICE Splice site prediction by neural network software, PP2 PolyPhen-2 prediction score, SIFT “Sorting Tolerant From Intolerant” prediction score, SSF splice site finder software, total total alleles
  2. This variant was submitted from an independent case to ClinVar (RCV001059152.1) during the current study