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Autism Spectrum Disorders via the KMT5B (SUV420H1) Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
8141 KMT5B 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8141KMT5B81479 81479,81479 $890 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days 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.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Greg Fischer, PhD

Clinical Features and Genetics

Clinical Features

Autism Spectrum Disorders (ASD) include several neurodevelopmental disorders characterized by varying degrees of social impairment, communication ability, and propensity for restricted interests and repetitive behavior(s) (Levy et al. 2009). ASD usually presents by age 3. Diagnosis is based on the degree and severity of symptoms and behaviors (Diagnostic and Statistical Manual of Mental Disorders (DSM-5); McPartland et al. 2016). Comorbidities occur in more than 70% of cases and include intellectual disability (ID), epilepsy, language deficits, and gastrointestinal problems (Sztainberg and Zoghbi 2016). Recent studies using whole exome trio studies have identified novel gene candidates, with familial and de novo variants from several hundred genes now implicated in the development of ASD (Bourgeron 2016).

Genetics

Genetic aberrations are reported to be responsible for 50%-90% and 15%-50% of ASD and ID cases, respectively, and inheritance overall is multifactorial (Larsen et al. 2016; Karam et al. 2015). Incidence of ASD is approximately 1 in 68 individuals with a male-to-female ratio of 4:1 (Center for Disease Control 2014). De novo missense and likely gene disrupting variants are 15% and 75% more frequent in ASD patients than unaffected controls, respectively (Iossifov et al. 2014). Several studies have identified de novo missense, nonsense, and frameshift variants in KMT5B within individuals presenting with a neurodevelopmental disorder (Iossifov et al. 2012; Sanders et al. 2012; De Rubeis et al. 2014; Stessman et al. 2017). Based on the large number of reported heterozygous de novo variants in affected individuals, it appears KMT5B pathogenic variants lead to ASD/ID symptoms in an autosomal dominant manner. However, the precise molecular mechanism is unclear (Stessman et al. 2017).

KMT5B (lysine (K)-specific methyltransferase 5B) (also known as SUV420H1, suppressor of variegation 4-20 homolog 1) is a histone lysine N-methyltransferase involved in chromatin modifications and gene regulation. The role of KMT5B in brain development is unclear; however histone H4 K20 trimethylation via KMT5B has been shown to regulate the cell cycle of baboon neural stem progenitor cells (Rhodes et al. 2016). RNAi knockdown studies of the Drosophila KMT5B homolog also suggest an impact on habitual learning (Stessman et al. 2017). Individuals with likely gene disrupting variants in KMT5B present with intellectual disability/developmental delay (100% of cases to date), ASD (83%), language delay (75%), motor delay (60%), febrile seizures (60%), and in some cases attention deficits (Stessman et al. 2017).

In human cells, the KMT5B (SUV420H1) gene encodes two alternatively splice isoforms, the longest including 10 exons that encode an 885 amino acid protein. Both isoforms contain a SET domain (residues 191-303). This domain is present in all known human histone methyltransferases and hypothesized to mediate interactions with dual-specificity phosphatase-like proteins (Lachner and Jenuwein 2002; Wu et al. 2013). At least 4 de novo variants have been reported within the SET domain, however, likely gene disrupting variants upstream and downstream of the SET domain have been reported (Stessman et al. 2017).

Clinical Sensitivity - Sequencing with CNV PGxome

Currently, the contribution of de novo and inherited factors to Autism Spectrum Disorder (ASD) risk is estimated to be approximately 50%-60% (Krumm et al. 2015). KMT5B is categorized as a ‘high confidence’ gene candidate for ASD in the Simons Foundation Autism Research Initiative (SFARI) Database (https://gene.sfari.org/GeneDetail/KMT5B). However, more than 700 genes have been associated with ASD features (Bourgeron 2016). Based on multiple recent large sequencing studies, causative variants in KMT5B were collectively identified in approximately 0.07% of ASD probands (14/19,778) (Iossifov et al. 2014; DeRubies et al. 2014; Stessman et al. 2017).

Testing Strategy

This test provides full coverage of all coding exons of the KMT5B gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

To our knowledge, nearly all reported pathogenic variants in KMT5B have been de novo in nature. However, individuals with family members having known KMT5B variants and/or displaying ASD, intellectual disability, or developmental delay features (also language and motor delay, febrile seizures, and attention deficits) are good candidates for this test.

Gene

Official Gene Symbol OMIM ID
KMT5B 610881
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Mental Retardation, Autosomal Dominant 51 AD 617788

Citations

  • Bourgeron T. 2016. Comptes Rendus Biologies. 339: 300-7. PubMed ID: 27289453
  • Center for Disease Control and Prevention. 2014. Morbidity and Mortality Weekly Report. Surveillance Summaries (Washington, D.C. : 2002). 63: 1-21. PubMed ID: 24670961
  • De Rubeis S. et al. 2014. Nature. 515: 209-15. PubMed ID: 25363760
  • Iossifov I. et al. 2012. Neuron. 74: 285-99. PubMed ID: 22542183
  • Iossifov I. et al. 2014. Nature. 515: 216-21. PubMed ID: 25363768
  • Karam S.M. et al. 2015. American Journal of Medical Genetics. Part A. 167: 1204-14. PubMed ID: 25728503
  • Krumm N. et al. 2015. Nature Genetics. 47: 582-8. PubMed ID: 25961944
  • Lachner M., Jenuwein T. 2002. Current Opinion in Cell Biology. 14: 286-98. PubMed ID: 12067650
  • Larsen E. et al. 2016. Molecular Autism. 7: 44. PubMed ID: 27790361
  • Levy S.E. et al. 2009. Lancet. 374: 1627-38. PubMed ID: 19819542
  • McPartland J.C. et al. 2016. Encyclopedia of Mental Health. 2: 124-130.
  • Rhodes C.T. et al. 2016. Neuroepigenetics. 6: 10-25. PubMed ID: 27429906
  • Sanders S.J. et al. 2012. Nature. 485: 237-41. PubMed ID: 22495306
  • Stessman H.A. et al. 2017. Nature Genetics. 49: 515-526. PubMed ID: 28191889
  • Sztainberg Y., Zoghbi H.Y. 2016. Nature Neuroscience. 19: 1408-17. PubMed ID: 27786181
  • Wu H. et al. 2013. Febs Letters. 587: 3859-68. PubMed ID: 24396869

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


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
Total Price: $
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