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Order Code RSCGP Nephrocalcinosis, Nephrolithiasis, and Renal Electrolyte Imbalance Gene Panel, Varies


Ordering Guidance


A next-generation sequencing (NGS) panel of the 6 genes associated with Bartter syndrome, a rare renal salt-wasting disorder, is available. See RBART / Bartter Syndrome Gene Panel, Varies. It is inappropriate to order both RBART and this test on the same patient because the genes on the RBART panel are included on this panel.

 

Testing for CASR is available individually. See CASRG / CASR Full Gene Sequencing with Deletion/Duplication, Varies.

 

With a few exceptions, this panel is focused on conditions where the primary phenotype is impaired osmoregulation that may result in secondary extrarenal symptoms. If interested in testing for syndromic disorders that are associated with kidney disease but feature broader clinical phenotypes and multisystem involvement, see NEPHP / Comprehensive Nephrology Gene Panel, Varies.

 

Targeted testing for familial variants (also called site-specific or known mutations/variants testing) is available for the genes on this panel. See FMTT / Familial Variant, Targeted Testing, Varies. To obtain more information about this testing option, call 800-533-1710.

 

Customization of this panel and single gene analysis for any gene present on this panel are available. For more information, see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies.



Shipping Instructions


Specimen preferred to arrive within 96 hours of collection.



Specimen Required


Patient Preparation: A previous bone marrow transplant from an allogenic donor will interfere with testing. Call 800-533-1710 for instructions for testing patients who have received a bone marrow transplant.

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Any anticoagulant

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send whole specimen in original tube. Do not aliquot.

Specimen Stability Information: Ambient (preferred)/Refrigerated


Forms

1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing-Spanish (T826)

2. Hereditary Renal Genetic Testing Patient Information (T918)

3. If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:

-Renal Diagnostics Test Request (T830)

-Biochemical Genetics Test Request (T798)

Useful For

Providing a genetic evaluation for patients with a personal or family history suggestive of a hereditary form of nephrocalcinosis, nephrolithiasis, or renal electrolyte imbalance

 

Establishing a diagnosis for a variety of hereditary conditions associated with renal salt wasting or abnormal salt retention; impaired acid-base, water, and calcium homeostasis; or kidney crystallization

Genetics Test Information

This test utilizes next-generation sequencing to detect single nucleotide, deletion-insertion, and copy number variants in 72 genes associated with nephrocalcinosis, nephrolithiasis, and renal electrolyte imbalance: ABCC6, ADCY10, AGXT, ALPL, AP2S1, APRT, AQP2, ATP6V0A4, ATP6V1B1, ATP7B, AVP, AVPR2, BSND, CA2, CASR, CLCN5, CLCNKA, CLCNKB, CLDN16, CLDN19, CNNM2, CUL3, CYP11B1, CYP11B2, CYP24A1, CYP27B1, CYP2R1, DMP1, EGF, ENPP1, FAM20A, FGF23, FOXI1, FXYD2, GALNT3, GATA3, GNA11, GRHPR, HNF4A, HOGA1, HPRT1, KCNJ1, KCNJ5, KL, KLHL3, MAGED2, MOCOS, NR3C2, OCRL, PHEX, PRPS1, SCNN1A, SCNN1B, SCNN1G, SLC12A1, SLC12A3, SLC22A12, SLC26A1, SLC2A9, SLC3A1, SLC34A1, SLC34A3, SLC4A1, SLC4A4, SLC7A9, SLC9A3R1, TRPM6, UMOD, VDR, WNK1, WNK4, and XDH. See Targeted Genes and Methodology Details for Nephrocalcinosis, Nephrolithiasis, and Renal Electrolyte Imbalance Gene Panel and Method Description for additional details.

 

Identification of a disease-causing variant may assist with diagnosis, prognosis, clinical management, familial screening, and genetic counseling for hereditary forms of nephrocalcinosis, nephrolithiasis, and renal electrolyte imbalance.

 

Method Name

Sequence Capture and Amplicon-Based Next-Generation Sequencing (NGS)

Reporting Name

Renal Stone/Electrolyte Gene Panel

Specimen Type

Varies

Specimen Minimum Volume

1 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Varies

Reject Due To

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

Reference Values

An interpretive report will be provided.

Method Description

Capture-based and amplicon-based next-generation sequencing (NGS) is performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 30X. Sensitivity is estimated at above 99% for single nucleotide variants, above 94% for deletions-insertion (delins) less than 40 base pairs (bp), above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS and/or a polymerase chain reaction-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed.

 

There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences.(Unpublished Mayo method)

 

See Targeted Genes and Methodology Details for Nephrocalcinosis, Nephrolithiasis, and Renal Electrolyte Imbalance Gene Panel for details regarding the targeted genes analyzed for each test and specific gene regions not routinely covered.

 

Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.

 

Genes analyzed: ABCC6, ADCY10, AGXT, ALPL, AP2S1, APRT, AQP2, ATP6V0A4, ATP6V1B1, ATP7B, AVP, AVPR2, BSND, CA2, CASR, CLCN5, CLCNKA, CLCNKB, CLDN16, CLDN19, CNNM2, CUL3, CYP11B1, CYP11B2, CYP24A1, CYP27B1, CYP2R1, DMP1, EGF, ENPP1, FAM20A, FGF23, FOXI1, FXYD2, GALNT3, GATA3, GNA11, GRHPR, HNF4A, HOGA1, HPRT1, KCNJ1, KCNJ5, KL, KLHL3, MAGED2, MOCOS, NR3C2, OCRL, PHEX, PRPS1, SCNN1A, SCNN1B, SCNN1G, SLC12A1, SLC12A3, SLC22A12, SLC26A1, SLC2A9, SLC3A1, SLC34A1, SLC34A3, SLC4A1, SLC4A4, SLC7A9, SLC9A3R1, TRPM6, UMOD, VDR, WNK1, WNK4, XDH

Day(s) Performed

Varies

Performing Laboratory

Mayo Clinic Laboratories in Rochester

CPT Code Information

81404 x 4

81405 x 2

81406 x 8

81407 x 2

81479

81479 (if appropriate for government payers)