MYT1L

Gene Facts

• HGNC Symbol: MYT1L (HGNC:7623)
• HGNC Name: myelin transcription factor 1 like
• Gene type: protein-coding gene
• Locus type: gene with protein product
• Previous symbols: No previous names found
• Alias symbols: KIAA1106, NZF1, ZC2HC4B, ZC2H2C2
• %HI: 21.8
• pLI: 1
• LOEUF: 0.09
• Cytoband: 2p25.3
• Genomic Coordinates:

  GRCh37/hg19:	chr2:1792885-2335047
  GRCh38/hg38:	chr2:1789113-2331275

• MANE Select Transcript: NM_001303052.2 ENST00000647738.2
• Function: Transcription factor that plays a key role in neuronal differentiation by specifically repressing expression of non-neuronal genes during neuron differentiation. In contrast to other transcription repressors that inhibit specific lineages, mediates repression of multiple differentiation programs. Also represses expression of negative regulators of neurogenesis, such as members of the Notch signaling pathway, including HES1. The combination of three transcription factors, ASCL1, POU3F2/BRN2 and M... (Source: Uniprot)

Dosage Sensitivity Summary (Gene)

• Dosage ID: ISCA-1416
• ClinGen Curation ID: CCID:007513
• Curation Status: Complete
• Issue Type: Dosage Curation - Gene
• Haploinsufficiency: Sufficient Evidence for Haploinsufficiency (3)
• Triplosensitivity: No Evidence for Triplosensitivity (0)
• Last Evaluated: 03/09/2017

Haploinsufficiency (HI) Score Details

• HI Score: 3
• HI Evidence Strength: Sufficient Evidence for Haploinsufficiency

HI Disease

• intellectual disability, autosomal dominant 39

HI Evidence

• PUBMED: 27824329
  Wang et al. (2016) report a de novo nonsense variant (p.Gln848*) in MYT1L identified in a male with autism, developmental delay, sleep problems, attention problems, anxiety, febrile seizures, a "pigeon-toed" gait, and motor tics. No comment was made on whether or not this individual was obese. The individual was studied as part of a larger cohort of 1543 Chinese individuals with autism spectrum disorders (ASD) sequenced for 189 ASD risk genes determined by the authors. The authors note that MYT1L showed no evidence of rare, likely-gene-disruptive variants in ExAC. The authors also note that an additional instance of a de novo, likely-gene-disruptive variant was observed in the Autism Sequencing Cohort (ASC), and additional missense variants (2 total) were also observed in the ASC and in the Simons Simplex Collection (SSC).
• PUBMED: 23033978
  de Ligt et al. (2012) performed trio-based exome sequencing on 100 individuals with severe intellectual disability, defined as having an IQ below 50. In Trio 92 (discussed in the supplementary material) they identified a de novo splice site variant in MYT1L (NM_015025.2 c.2636+1G>A). This variant was identified in a female patient described as follows: "This female was born after a normal pregnancy and delivery with a high birth weight (4750 grams, >+2 SD). She had neonatal hypotonia and feeding difficulties. Parents had noticed a developmental delay since the age of 6 months. She could walk without support at the age of 28 months and started to speak her first single words at the age of 3.5 years. She made stereotypic movements. At the age of 12 years she had an IQ of about 45 and showed autistic features. Upon physical examination at the age of 12 years and 8 months she had normal growth parameters and mild facial dysmorphism, including a broad base and bridge of the nose and a large mouth. SNP array analysis, Angelman methylation studies, UBE3A, and a metabolic screen were normal."
• PUBMED: 25232846
  de Rocker et al. (2015) report two de novo LOF variants (c.2636+1G>A (NM_015025.2) and NM_015025.2: c.1917T>G ; p.(Tyr639*)) in individuals with intellectual disability (patients 14 and 15, respectively). Patient 14 is described in the supplementary material as having: a history of neonatal hypotonia and feeding difficulties; developmental delay since the age of 6 months; stereotypic movements; an IQ of about 45 (at the age of 12 years); autistic features; normal growth parameters (at age 12 years); and mild facial dysmorphism. Patient 15 is described as having: history of developmental delay; IQ of 50 at 9 years of age; autism spectrum disorder; weight at the 90th percentile; and mild dysmorphic features.

• HI Evidence Comments: Additionally, Mayo et al. (2015) (PMID:26240977) report a de novo intragenic deletion [(arr(hg19) 2p25.3(1,843,177x2,1,844,493-1,983,593x1,2,000,941x2)dn)] of MYT1L in a 4.5 year old non-obese female with developmental delay and autistic features. Lee et al. 2012 (PMID:22547139) evaluated several case-control studies of individuals with schizophrenia (5325 patients and 9279 controls total) and report 10 instances of microduplications involving MYT1L. These microduplications were observed in 9 patients and 1 control; all but one appear to disrupt MYT1L and also involve neighboring gene PXDN. The authors purport that the rate of duplications in the childhood-onset schizophrenia population is significantly higher than that of the control population (p=0.0002), as well as significantly higher than the rate of the adult-onset schizophrenia cases (p=0.01). However, the authors do not perform any functional studies on the observed variants to assess whether they disrupt or otherwise affect gene function.

Triplosensitivity (TS) Score Details

• TS Score: 0
• TS Evidence Strength: No Evidence for Triplosensitivity
• TS Evidence Comments: Lee et al. 2012 (PMID:22547139) evaluated several case-control studies of individuals with schizophrenia (5325 patients and 9279 controls total) and report 10 instances of microduplications involving MYT1L. These microduplications were observed in 9 patients and 1 control; all but one appear to disrupt MYT1L and also involve neighboring gene PXDN. The one duplication that appears to only involve MYT1L was originally reported in the supplemental BED file associated with PMID 19181681, and appears to affect most (but not quite all) of the gene. Lee et al. purport that the rate of duplications in the childhood-onset schizophrenia population is significantly higher than that of the control population (p=0.0002), as well as significantly higher than the rate of the adult-onset schizophrenia cases (p=0.01). However, the authors do not perform any functional studies on the observed variants to assess whether they disrupt or otherwise affect gene function.