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Christianson Type X-Linked Mental Retardation via the SLC9A6 Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
SLC9A6 81406 81406,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
6973SLC9A681406 81406,81479 $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.


Genetic Counselors


  • Li Fan, MD, PhD, FCCMG, FACMG

Clinical Features and Genetics

Clinical Features

Variants in the SLC9A6 gene (OMIM 300231) cause syndromic X-linked mental retardation of the Christianson type (OMIM 300243), a syndrome with remarkable clinical overlap with Angelman syndrome (AS; OMIM 105830). Christianson type XLMR is characterized by affected males with profound mental retardation, seizures, absent speech, and microcephaly (Christianson et al. Med Genet 36:759-766, 1999). Other features include frequent smiling and episodes of unprovoked laughter (Gilfillan et al. Am J Hum Genet 82:1003-1010, 2008). Cerebellar atrophy has been demonstrated in affected males (Christianson et al. 1999; Gilfillan et al. 2008), and a reduced life expectancy has also been observed. Impaired ocular movements, including esotropia, are a frequent finding (Schroer et al. Am J Med Genet Part A 152A:2775-2783, 2010). Carrier females have been reported with mild mental retardation or learning problems (Christianson et al., 1999) and severe dyslexia (Gilfillan et al. 2008). As a consequence of the significant overlap of features between Christianson type XLMR and Angelman syndrome, it has been suggested that males with symptoms consistent with Angelman syndrome, but who test normal for UBE3A defects, are candidates for SLC9A6 testing (Gilfillan et al. 2008). Neuropathological and radiological findings include generalized cerebral atrophy with atrophy of the white matter and neuronal loss (Garbern et al. Brain 133:1391-1402, 2010; Schroer et al. 2010). The former authors also reported finding Tau-positive intracellular inclusions in the glial cells throughout the white matter of patients.


Christianson type X-linked mental retardation is inherited in an X-linked recessive manner. The SLC9A6 gene encodes isoform A6 of the solute carrier family 9 proteins which localizes to mitochondria and functions as a sodium/hydrogen exchanger (Numata et al. J Biol Chem 273:6951-6959, 1998). A small number of SLC9A6 variants have been described. Types of variant thus far reported include nonsense variants and frame-shifting small deletions (Gilfillan et al. 2008; Garbern et al. 2010) and an intragenic deletion (Whibley et al. Am J Hum Genet 87:173-188, 2010). At PreventionGenetics, patients with splicing and small duplication variants have been found.

Clinical Sensitivity - Sequencing with CNV PG-Select

The etiology of this disorder has only recently been described (Gilfillan et al. 2008). Thus, it is not possible to reliably predict clinical sensitivity of SLC9A6 testing. This gene is likely one of multiple causes of the 10%-15% of Angelman syndrome cases that are unrelated to UBE3A. Sequence analysis of all exons of the X chromosome in 208 XLMR families resulted in the identification of two cases with SLC9A6 variants (Tarpey et al. Nat Genet 41:535-543, 2009).

Testing Strategy

This test provides full coverage of all coding exons of the SLC9A6 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Males with microcephaly, mental retardation, absent speech, seizures, and unprovoked laughter. Males with an Angelman syndrome phenotype who have normal UBE3A methylation and sequencing studies.


Official Gene Symbol OMIM ID
SLC9A6 300231
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Angelman Syndrome via the UBE3A Gene


  • Christianson, A. L., et.al. (1999). "X linked severe mental retardation, craniofacial dysmorphology, epilepsy, ophthalmoplegia, and cerebellar atrophy in a large South African kindred is localised to Xq24-q27." J Med Genet 36(10): 759-66. PubMed ID: 10528855
  • Garbern, J. Y., et.al. (2010). "A mutation affecting the sodium/proton exchanger, SLC9A6, causes mental retardation with tau deposition." Brain 133(Pt 5): 1391-402. PubMed ID: 20395263
  • Gilfillan, G. D., et.al. (2008). "SLC9A6 mutations cause X-linked mental retardation, microcephaly, epilepsy, and ataxia, a phenotype mimicking Angelman syndrome." Am J Hum Genet 82(4): 1003-10. PubMed ID: 18342287
  • Numata, M., et.al. (1998). "Identification of a mitochondrial Na+/H+ exchanger." J Biol Chem 273(12): 6951-9. PubMed ID: 9507001
  • Schroer, R. J., et.al. (2010). "Natural history of Christianson syndrome." Am J Med Genet A 152A(11): 2775-83. PubMed ID: 20949524
  • Tarpey, P. S., et.al. (2009). "A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation." Nat Genet 41(5): 535-43. PubMed ID: 19377476
  • Whibley, A. C., et.al. (2010). "Fine-scale survey of X chromosome copy number variants and indels underlying intellectual disability." Am J Hum Genet 87(2): 173-88. PubMed ID: 20655035


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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