Invitae Nephrolithiasis Panel
Test description
The Invitae Nephrolithiasis Panel analyzes genes that are associated with nephrolithiasis.
Genes tested
ADCY10 AGXT ALPL APRT ATP6V0A4 ATP6V1B1 ATP7B CA2 CASR CLCN5 CLCNKB CLDN16 CLDN19 CYP24A1 FAM20A FOXI1 GPHN GRHPR HOGA1 HPRT1 KCNJ1 MOCOS MOCS1 MOCS2 OCRL PEX6 PREPL SLC12A1 SLC22A12 SLC26A1 SLC2A9 SLC34A1 SLC34A3 SLC3A1 SLC4A1 SLC7A9 SLC9A3R1 UMOD VDR XDH
Order test
Primary panel (40 genes)
Customized gene selection (0 included, 0 excluded)
ADCY10 AGXT ALPL APRT ATP6V0A4 ATP6V1B1 ATP7B CA2 CASR CLCN5 CLCNKB CLDN16 CLDN19 CYP24A1 FAM20A FOXI1 GPHN GRHPR HOGA1 HPRT1 KCNJ1 MOCOS MOCS1 MOCS2 OCRL PEX6 PREPL SLC12A1 SLC22A12 SLC26A1 SLC2A9 SLC34A1 SLC34A3 SLC3A1 SLC4A1 SLC7A9 SLC9A3R1 UMOD VDR XDH
Clinical information
Disorders tested
- Familial idiopathic hypercalciuria
- Primary hyperoxaluria, type 1 (PH1)
- Hypophosphatasia
- Adenine phosphoribosyltransferase (APRT)
- Distal renal tubular acidosis (dRTA) with progressive nerve deafness
- Wilson disease
- Carbonic anhydrase 2 (CA2) deficiency
- CASR-related conditions:
- Familial hypocalciuric hypercalcemia (FHH)
- Autosomal dominant hypocalcemia (ADH)
- ADH with Bartter syndrome
- Neonatal severe hyperparathyroidism (NSHPT)
- Dent disease
- Bartter syndrome type 3 (BSIII)
- Familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC)
- Infantile hypercalcemia
- Enamel-renal syndrome
- Distal renal tubular acidosis (dRTA)
- Primary hyperoxaluria, type 2 (PH2)
- Primary hyperoxaluria type 3 (PH3)
- HPRT1 deficiency, Lesch-Nyhan syndrome
- Bartter syndrome type 2 (BSII)
- Xanthinuria type II
- Molybdenum cofactor deficiency
- Lowe syndrome
- Zellweger spectrum disorder (ZSD)
- Congenital myasthenic syndrome 22 (CMS22), Hypotonia-cystinuria syndrome
- Bartter syndrome type 1
- Renal hypouricemia
- Calcium oxalate urolithiasis, nephrolithiasis
- Familial hypouricemia
- Infantile hypercalcemia, Hypophosphatemic nephrolithiasis/osteoporosis, Fanconi renotubular syndrome
- Hereditary hypophosphatemic rickets with hypercalciuria (HHRH)
- Cystinuria, Hypotonia-cystinuria deletion syndrome
- Distal renal tubular acidosis (dRTA), dRTA with haemolytic anemia
- Cystinuria type B
- Hypophosphatemic nephrolithiasis and osteoporosis
- Tubulointerstitial kidney disease (ADTKD), Medullary cystic kidney disease type 2 (MCKD2)
- Vitamin D-dependent rickets type 2A (VDDR2A)
- Xanthinuria type I
Clinical description
To view the complete clinical description of this panel, click here.
Inheritance
Genes on the Nephrolithiasis panel can be inherited in an autosomal dominant, autosomal recessive, or X-linked pattern. Several genes on the Nephrolithiasis panel can be inherited in both autosomal dominant and autosomal recessive patterns. Recessive genes are more likely to be the cause for affected infants and children and autosomal dominant inheritance for adult-onset forms (PMID: 25296721, 26787776).
Assay
Assay and technical information
Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).
Our sequence analysis covers clinically important regions of each gene, including coding exons and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below, depending on the specific gene or test. In addition, the analysis covers select non-coding variants. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions.
Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.
| Gene | Transcript reference | Sequencing analysis | Deletion/Duplication analysis |
|---|---|---|---|
| ADCY10 | NM_018417.5 | ||
| AGXT | NM_000030.2 | ||
| ALPL | NM_000478.5 | ||
| APRT | NM_000485.2 | ||
| ATP6V0A4 | NM_020632.2 | ||
| ATP6V1B1 | NM_001692.3 | ||
| ATP7B | NM_000053.3 | ||
| CA2 | NM_000067.2 | ||
| CASR | NM_000388.3 | ||
| CLCN5 | NM_000084.4 | ||
| CLCNKB* | NM_000085.4 | ||
| CLDN16 | NM_006580.3 | ||
| CLDN19 | NM_148960.2 | ||
| CYP24A1 | NM_000782.4 | ||
| FAM20A | NM_017565.3 | ||
| FOXI1 | NM_012188.4 | ||
| GPHN | NM_020806.4 | ||
| GRHPR | NM_012203.1 | ||
| HOGA1 | NM_138413.3 | ||
| HPRT1 | NM_000194.2 | ||
| KCNJ1 | NM_000220.4 | ||
| MOCOS | NM_017947.2 | ||
| MOCS1 | NM_001075098.3 | ||
| MOCS2 | NM_176806.3; NM_004531.4 | ||
| OCRL | NM_000276.3 | ||
| PEX6 | NM_000287.3 | ||
| PREPL | NM_006036.4 | ||
| SLC12A1 | NM_000338.2 | ||
| SLC22A12 | NM_144585.3 | ||
| SLC26A1 | NM_213613.3 | ||
| SLC2A9 | NM_020041.2 | ||
| SLC34A1 | NM_003052.4 | ||
| SLC34A3 | NM_080877.2 | ||
| SLC3A1 | NM_000341.3 | ||
| SLC4A1 | NM_000342.3 | ||
| SLC7A9 | NM_014270.4 | ||
| SLC9A3R1 | NM_004252.4 | ||
| UMOD | NM_003361.3 | ||
| VDR | NM_001017535.1 | ||
| XDH | NM_000379.3 |
CLCNKB: Deletion/duplication analysis is not offered for this gene.
