H3-3A Related Neurodevelopmental Delay via the H3-3A Gene

H3-3A (H3F3A) syndrome is an autosomal dominant neurodevelopmental disorder characterized by developmental delay and intellectual disability, manifesting early during postnatal development. It affects both males and females. Affected individuals are typically identified in infancy due to global motor and language delays along with other variable congenital abnormalities. To date, all known pathogenic changes have arisen de novo. Regarding the severity of delays, cognitive deficits are frequently more severe than physical. For example, over half of these patients achieve independent walking; however, a majority of patients remain completely nonverbal throughout life. While neurodevelopmental delays are the only feature seen in all patients, other frequently observed phenotypes include brain malformations identified on magnetic resonance imaging (70%), hypotonia (60%), oculomotor abnormalities (60%, primarily strabismus), seizures (50%), skeletal abnormalities (30%), short stature (30%), gastroesophageal reflux and feeding problems (25%), microcephaly (21%), chronic constipation (30%) and congenital heart defects (20%). Joint laxity, hearing loss, eczema, laryngomalacia, and digit abnormalities are also seen in less than 20% of patients. In addition to the hypotonia that is frequent in early life, a smaller portion of patients are born with or develop contractures or spasticity. Genital abnormalities (particularly cryptorchidism) are common in males (40%), but not observed in affected females. Other than this difference, males and females appear to be equally affected by the disorder in terms of severity, yet a slightly higher proportion of identified patients are male. While undergrowth and microcephaly are observed in over 20% of patients, a small subset of affected individuals present with the opposite phenotype— overgrowth, obesity, and macrocephaly. There is no recognizable facial gestalt; however, common craniofacial abnormalities include a prominent forehead, hypertelorism, and abnormal skull shape (Bryant et al. 2020. PubMed ID: 33268356). 

H3-3A syndrome is a rare disorder. While there is no treatment for this disorder, advantages of testing may include prognostic information, early identification and treatment of symptoms such as seizures and feeding problems, and the ability to join relevant family support groups. Because all known pathogenic variants in this gene are sporadic, a confirmed de novo finding (implicating lower recurrence risk) may ease anxiety for reproductive planning.

H3-3A syndrome is an autosomal dominant disorder caused by de novo alterations in the H3-3A gene. All identified pathogenic changes in H3-3A are missense alterations, and the significance of loss of function changes in humans is currently unknown. Indeed, on the whole, the gene is intolerant to missense variation but the intolerance to loss of function changes is less clear (Genome Aggregation Database).

Pathogenic variants are spread widely throughout the H3-3A protein and do not appear to cluster in any specific domains. Several of the pathogenic alterations identified are recurrent. The most commonly observed changes are p.Thr46Ile observed in four unrelated patients, and p.Gln125Arg, observed in three unrelated patients (NM_002107.5). Full penetrance is expected based on the current literature and gnomAD data for this gene. No inherited pathogenic changes have been observed, and none of the known pathogenic alterations are present in the gnomAD database of individuals without severe pediatric diseases.

H3-3A (previously called H3F3A) codes for an H3.3-type histone protein, which consists of three exons, and creates a 136 amino acid protein. Histone proteins help to package DNA neatly into chromatin, which creates chromosomes. The multiple different classes of histones are differentially regulated both by tissue type and developmental time. Other histone proteins that cause similar diseases to H3-3A syndrome in humans include H3-3B (H3-3B syndrome), H1-4 (Rahman Syndrome), and H4C3 (H4C3 syndrome). Of note, the H3-3B gene also codes for a H3.3 class histone. Its mature protein product is identical to H3-3A but has a different expression profile. Still, the neurodevelopmental syndrome caused by these two genes is nearly identical (Bryant et al. 2020. PubMed ID: 33268356). Of these four histone diseases, H3-3A syndrome is the most common.

Double knockout of both H3f3a and H3f3b in mice causes early embryonic lethality, and more minor reductions of expression of individual H3.3’s cause phenotypes of growth retardation, sterility, and increased early mortality. Similarly in Drosophila, complete disruption of both genes causes sterility and increased lethality, but individual knockouts are tolerated. Studies in yeast test the effects of various missense alterations, thus more closely mimicking the relevant human variant type. Finally, studies in zebrafish have also tested the effects of individual missense changes, and phenotypes may more closely mimic those observed in humans (Jang et al. 2015. PubMed ID: 26159997; Bush et al. 2013. PubMed ID: 23570311; Sakai et al. 2009. PubMed ID: 19781938; Lim et al. 2015. PubMed ID: 26369364; Bryant et al. 2020. PubMed ID: 33268356).

Pathogenic variants in H3-3A are expected to account for <0.1% of cases of early neurodevelopmental delays. In this context, it is important to note the extraordinarily broad genetic heterogeneity for neurodevelopmental delay phenotypes (McRae et al. 2017. PubMed ID: 28135719; Bowling et al. 2017. PubMed ID: 28554332). Testing a large panel of genes as well as using a trio approach (testing parents) is known to have higher diagnostic yield due to the extreme clinical and genetic heterogeneity of these phenotypes (Vissers et al. 2016. PubMed ID: 26503795).

Single nucleotide variants (SNVs) are the only variant type known to cause H3-3A syndrome (Bryant et al. 2020. PubMed ID: 33268356; Human Gene Mutation Database), therefore this test’s analytical sensitivity for H3-3A pathogenic changes is expected to be very high. In summary, this test is expected to detect all currently identified variant types in H3-3A.

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

This test provides full coverage of all coding exons of the H3-3A 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. 

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).