Christianson Type X-Linked Mental Retardation via the SLC9A6 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
562 SLC9A6$870.00 81406 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity
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 mutations (Tarpey et al. Nat Genet 41:535-543, 2009).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 SLC9A6$690.00 81479 Add to Order
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Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Features
Mutations 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 mutations have been described. Types of mutation thus far reported include nonsense mutations 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 mutations have been found.
Testing Strategy
The solute carrier family 9, subunit A6 protein is encoded by exons 1-16 of the SLC9A6 gene located on chromosome Xq26.3. Testing is accomplished by amplifying each coding exon and ~20 bp of adjacent noncoding sequence, then determining the nucleotide sequence using standard dideoxy sequencing methods and a capillary electrophoresis instrument. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results.
Indications for Test
Males with microcephaly, mental retardation, absent speech, seizures, 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 Tests

Angelman Syndrome by MS-MLPA
Angelman Syndrome via the UBE3A Gene


Genetic Counselors
  • Christianson, A. L., (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., (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., (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., (1998). "Identification of a mitochondrial Na+/H+ exchanger." J Biol Chem 273(12): 6951-9. PubMed ID: 9507001
  • Schroer, R. J., (2010). "Natural history of Christianson syndrome." Am J Med Genet A 152A(11): 2775-83. PubMed ID: 20949524
  • Tarpey, P. S., (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., (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
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Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

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Ordering Options

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.
  • 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.


(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.


(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.


(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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