Kleefstra Syndrome via the EHMT1 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
1518 EHMT1$1340.00 81479 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
In one study, EHMT1 mutations were found in 25% of patients who displayed core features of Kleefstra syndrome (Kleefstra et al. Am J Hu Genet 91(1):73-82, 2012).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 EHMT1$990.00 81479 Add to Order
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Turnaround Time

The great majority of tests are completed within 20 days.

Clinical Sensitivity
Approximately 50% of EHMT1 variants reported in KS cases are large deletions that would be detectable via microarray (Human Gene Mutation Database).

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Clinical Features
Kleefstra syndrome (KS; OMIM:610253), formerly 9q subetelomeric deletion syndrome (9qSTD), is a cognitive disorder characterized by moderate to severe intellectual disability, childhood hypotonia and distinct facial features. Craniofacial features commonly seen in KS patients include: a flat face with hypertelorism, upslanting palpebral fissures, brachycephaly, tented upper lip with an everted lower lip and prognathism (Kleefstra et al. Am J Hu Genet 79(2):370-377, 2006). Aggression and behavioral problems in KS patients often have adolescent or adult onset. Variable features of KS that are seen in a subset of patients include seizures, hearing loss, cardiac anomaly, male genital defects, obesity and synophrys (Willemsen et al. Mol Syndromol 2(3-5):202-212, 2011).
Kleefstra syndrome is caused by dominant loss-of-function mutations in or deletions of the EHMT1 gene. Nearly all cases of KS are sporadic, resulting from de novo mutations. KS phenotypes are similar in patients with point mutations in the EHMT1 gene and those with subtelomeric deletions of chromosome 9 (Kleefstra et al., 2006). The severity of the disease generally prevents inheritance of KS. A rare case of autosomal dominant inheritance of KS was reported where the parent was found to be mosaic for an EHMT1 mutation (Rump et al. Eu J Hu Genet 21(8):887-890, 2013). Mutations in EHMT1 are found in ~25% of KS cases (Kleefstra et al. Am J Hu Genet 91(1):73-82, 2012). Patients with gross duplications of 9q34.3 that include the EHMT1 gene have been reported to have learning disabilities and speech problems, suggesting that EHMT1 overexpression is also detrimental to cognitive development (Yatsenko et al. Hum Genet 131(12):1895-1910, 2012).

EHMT1 encodes the histone methyltransferase EHMT1. Histones contain amino acid ‘tails’ which can be modified in a variety of ways. Histone tail modifications regulate chromatin structure and influence which regions of the genome are transcribed. EHMT1 is a putative histone 3 lysine 9 (H3K9) methyltransferase. Methylation of histone 3 lysine 9 leads to transcriptional repression. It is hypothesized that misexpression of EHMT1 target genes, due to loss of histone methylation, underlies the KS phenotype in patients with EHMT1 mutations (Kleefstra et al., 2012).
Testing Strategy
Testing involves PCR amplification from genomic DNA and bidirectional Sanger sequencing of the coding exons and ~10bp of adjacent noncoding sequences. This testing strategy will reveal coding sequence changes, splice site mutations and small insertions or deletions in the EHMT1 gene, but will not detect large deletions, insertions or rearrangements in the EHMT1 locus. We will also sequence any single exon (Test #100) in family members of patients with a known mutation or to confirm research results.
Indications for Test
Candidates for EHMT1 testing are patients who display the core features of KS: moderate to severe intellectual disability, childhood hypotonia and characteristic facial features. Due to overlapping clinical features, patients diagnosed with Down syndrome, but with no evidence of Trisomy 21 and patients diagnosed with Smith-Magenis syndrome (SMS)  who lack the 17p11.2 deletion might be good candidates for EHMT1 testing (Kleefstra et al., 2006). Carrier testing is recommended in parents of a child with KS to rule out the possibility of germline mosaicism (Rump et al., 2013).


Official Gene Symbol OMIM ID
EHMT1 607001
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Chromosome 9Q Deletion Syndrome 610253

Related Test

Smith-Magenis and Potocki-Lupski syndromes via RAI1 Gene Sequencing with CNV Detection


Genetic Counselors
  • Human Gene Mutation Database (Bio-base).
  • Kleefstra, T. et al. (2006). "Loss-of-Function Mutations in Euchromatin Histone Methyl Transferase 1 (EHMT1) Cause the 9q34 Subtelomeric Deletion Syndrome." Am J Hu Genet 79(2):370-377. PubMed ID: 16826528
  • Kleefstra, T. et al. (2012). "Disruption of an EHMT1-Associated Chromatin-Modification Moduce Causes Intellectual Disability." Am J Hu Genet 91(1):73-82. PubMed ID: 22726846
  • Rump, A. et al. (2013). "A mosaic maternal splice donor mutaiton in the EHMT1 gene leads to aberrant transcripts and to Kleefstra syndrome in the offspring." Eu J Hu Genet 21(8):887-890. PubMed ID: 23232695
  • Willemsen, M. H. et al. (2011). "Update on Kleefstra Syndrome." Mol Syndromol 2(3-5):202-212. PubMed ID: 22670141
  • Yatsenko, S.A. et al. (2012). “Human subtelomeric copy number gains suggest a DNA replication mechanism for formation: beyond breakage-fusion-bridge for telomere stabilization.” Hum Genet 131(12):1895-1910. PubMed ID: 22890305
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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 10 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of February 2018, we compared 26.8 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 14 years of our lab operation we have Sanger sequenced roughly 14,300 PCR amplicons. Only one error has been identified, and this was an error in analysis of sequence data.

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 10 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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