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Intellectual Disability via the MYT1L 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
MYT1L 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
15257MYT1L81479 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.


Genetic Counselors


  • Renee Bend, PhD

Clinical Features and Genetics

Clinical Features

Intellectual Disability (ID) is a heterogeneous group of neurodevelopmental disorders, characterized by congenital limitation in intellectual functioning (intelligence quotient, IQ ≤70) and adaptive behavior. It is diagnosed in ~1–3% of the population before 18 years of age (American Association of Intellectual and Developmental Disabilities, AAIDD).

Deficiency of MYT1L hypothetically impairs neural development, thereby leading to mental retardation 39 (MRD39). The clinical features of MRD39 may include (but may not be limited to) severe intellectual disability, developmental delay, speech and language delay, motor delay, obesity, brachycephaly, microcephaly, neonatal hypotonia, hyperlaxity, seizures, feeding difficulties, sleep disturbances, strabismus, behavioral abnormalities such as autism, stereotypic movements, hyperactivity, attention-deficit, aggressiveness, and variable facial dysmorphism including short, square-shaped face, broad forehead, upslanted palpebral fissures, narrow eyes, broad base and bridge of the nose, upturned nose, large ears and large mouth (de Ligt et al. 2012. PubMed ID: 23033978; De Rocker et al. 2015. PubMed ID: 25232846; Mayo et al. 2015. PubMed ID: 26240977). Of note, MYT1L has also been associated with schizophrenia (Stevens et al. 2011. PubMed ID: 21990140).


MRD39 is an autosomal dominant disorder, caused by pathogenic variants (primarily de novo) in human Myelin transcription factor 1-like gene (MYT1L). MYT1L maps to chromosome 2p25.3 and consists of 20 coding exons that translate an 1186 amino acid polypeptide. MYT1L contains one MYT domain and six to seven zinc-finger binding motifs and hypothetically acts as a neural-lineage specific transcription factor (Vierbuchen et al. 2010. PubMed ID: 20107439; Pang et al. 2011. PubMed ID: 21617644). Although small frameshift deletions, missense, nonsense and splice variants have been reported in MYT1L, the majority of the pathogenic variants are gross deletions/duplications and complex rearrangements involving MYT1L (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PG-Select

This test is predicted to detect pathogenic variants in <0.1% of individuals with intellectual disability (ID). In this context, it is important to note that although pathological variants over 800 genes have been identified in individuals with ID, a genetic diagnosis is still lacking in most cases due to extreme clinical and genetic heterogeneity of the condition (Vissers et al. 2016. PubMed ID: 26503795). Analytical sensitivity should be high because all single nucleotide pathogenic variants reported within this gene to date are detectable by sequencing. However, the majority of reported pathogenic variants (37/55) involving MYT1L are gross deletions/duplications (Human Gene Mutation Database).

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This test provides full coverage of all coding exons of the MYT1L 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.

Indications for Test

This test is primarily implicated for the patients with intellectual disabilities who are negative for any kind of cytogenetic abnormalities, and Fragile-X syndrome and also for the family members of the patients who have MYT1L pathogenic variants. Prenatal diagnosis is possible, if the genetic diagnosis has been firmly established in an affected family member.


Official Gene Symbol OMIM ID
MYT1L 613084
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Mental Retardation, Autosomal Dominant 39 AD 616521


  • de Ligt et al. 2012. PubMed ID: 23033978
  • De Rocker et al. 2015. PubMed ID: 25232846
  • Human Gene Mutation Database (Bio-base).
  • Mayo et al. 2015. PubMed ID: 26240977
  • Pang et al. 2011. PubMed ID: 21617644
  • Stevens et al. 2011. PubMed ID: 21990140
  • Vierbuchen et al. 2010. PubMed ID: 20107439
  • Vissers et al. 2016. PubMed ID: 26503795


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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View Ordering Instructions

1) Select Test Method (Platform)

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2) Select Additional Test Options

No Additional Test Options are available for this test.

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