Osteopetrosis via the TCIRG1 Gene
Summary and Pricing 
Test Method
Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 7841 | TCIRG1 | 81479 | 81479,81479 | $990 | Order Options and Pricing |
Pricing Comments
Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.
Turnaround Time
3 weeks on average for standard orders or 2 weeks on average for STAT orders.
Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.
Targeted Testing
For ordering sequencing of targeted known variants, go to our Targeted Variants page.
Clinical Features and Genetics
Clinical Features
Osteopetrosis (also called Marble bone disease) is a disorder of increased bone density and bone mass caused by malfunction of bone resorption. Affected patients are at high risk of frequent bone fractures, delayed healing, hip osteoarthritis and osteomyelitis. Some patients may have vision loss, hearing loss, paralysis of facial muscles, and bone marrow abnormalities caused by abnormal dense bone structure. Other features include short stature, development delay, dental abnormalities, hepatosplenomegaly, intellectual disability, and epilepsy (Tolar et al. 2004; Del Fattore et al. 2008; Sobacchi et al. 2013). Osteopetrosis is currently known to be caused by mutations in the following genes: CLCN7, LRP5, TCIRG1, TNFSF11, CA2, OSTM1, PLEKHM1, SNX10 and TNFRSF11A.
Genetics
Mutations in the TCIRG1 gene cause autosomal recessive osteopetrosis type I (also called malignant infantile psteopetrosis, or Albers-Schoenberg). The TCIRG1 protein coded by the TCIRG1 gene is an A3 subunit of vacuolar H(+)-ATPase, which regulates the pH value of intracellular compartments to maintain proper function of osteoclasts during bone resorption. To date, more than 100 unique pathogenic variants have been reported. They are: 20% missense, 16% nonsense, 30% splicing, 26% small deletion and insertion. Only 4 gross deletions have been reported (Pangrazio et al; 2009; Human Gene Mutation Database). A few population specific pathogenic variants have been reported. For example, the c.1213G>A, p.Gly405Arg variant was found in in 8 of 9 Costa Rican families, and the c.1331G>T, p. Arg444Leu variant was found in 5 of 9 Costa Rican families (Sobacchi et al. 2001). A founder splicing pathogenic variant c.117+4 was found in the Ashkenazi Jewish population (Anderson et al. 2014).
Clinical Sensitivity - Sequencing with CNV PG-Select
In one study, TCIRG1 pathogenic variants were identified in 50% of the 42 unrelated patients with malignant infantile osteopetrosis (Sobacchi et al. 2001).
Testing Strategy
This test provides full coverage of all coding exons of the TCIRG1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.
Indications for Test
Candidates for this test are patients with symptoms consistent with osteopetrosis and the family members of patients who have known TCIRG1 mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TCIRG1.
Candidates for this test are patients with symptoms consistent with osteopetrosis and the family members of patients who have known TCIRG1 mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in TCIRG1.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| TCIRG1 | 604592 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Osteopetrosis Autosomal Recessive 1 | AR | 259700 |
Related Tests
Citations
- Anderson SL, Jalas C, Fedick A, Reid KF, Carpenter TO, Chirnomas D, Treff NR, Ekstein J, Rubin BY. 2014. A founder mutation in the TCIRG1 gene causes osteopetrosis in the Ashkenazi Jewish population: A founder mutation in the TCIRG1 gene causes osteopetrosis. Clinical Genetics n/a-n/a. PubMed ID: 24989235
- Del Fattore A. et al. 2008. Bone. 42: 19-29. PubMed ID: 17936098
- Human Gene Mutation Database (Bio-base).
- Pangrazio A, Caldana ME, Sobacchi C, Panaroni C, Susani L, Mihci E, Cavaliere ML, Giliani S, Villa A, Frattini A. 2009. Characterization of a Novel Alu-Alu Recombination-Mediated Genomic Deletion in the TCIRG1 Gene in Five Osteopetrotic Patients. J Bone Miner Res 24: 162–167. PubMed ID: 18715141
- Sobacchi C, Frattini A, Orchard P, Porras O, Tezcan I, Andolina M, Babul-Hirji R, Baric I, Canham N, Chitayat D, Dupuis-Girod S, Ellis I, Etzioni A, Fasth A, Fisher A, Gerritsen B, Gulino V, Horwitz E, Klamroth V, Lanino E, Mirolo M, Musio A, Matthijs G, Nonomaya S, Notarangelo LD, Ochs HD, Superti Furga A, Valiaho J, van Hove JL, Vihinen M, Vujic D, Vezzoni P, Villa A. 2001. The mutational spectrum of human malignant autosomal recessive osteopetrosis. Hum. Mol. Genet. 10: 1767-1773. PubMed ID: 11532986
- Sobacchi C, Schulz A, Coxon FP, Villa A, Helfrich MH. 2013. Osteopetrosis: genetics, treatment and new insights into osteoclast function. Nature Reviews Endocrinology 9: 522-536. PubMed ID: 23877423
- Tolar J. et al. 2004. New England Journal of Medicine. 351: 2839-49. PubMed ID: 15625335
Ordering/Specimens
Ordering Options
We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.
myPrevent - Online Ordering
- The test can be added to your online orders in the Summary and Pricing section.
- Once the test has been added log in to myPrevent to fill out an online requisition form.
- PGnome sequencing panels can be ordered via the myPrevent portal only at this time.
Requisition Form
- A completed requisition form must accompany all specimens.
- Billing information along with specimen and shipping instructions are within the requisition form.
- All testing must be ordered by a qualified healthcare provider.
For Requisition Forms, visit our Forms page
If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.
Specimen Types
Specimen Requirements and Shipping Details
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ORDER OPTIONS
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