CHARGE and Kallmann Syndromes Panel

CHARGE syndrome is a severe developmental disorder characterized by multiple congenital defects involving sensory and mediastinal organs. It is a clinically heterogeneous disorder in regards to symptoms and severity. Hallmark features include ocular coloboma; choanal atresia; cranial nerve abnormalities leading to facial palsy, loss of sense of smell, feeding, swallowing and breathing difficulties; and external and inner ear malformations resulting in hearing loss and reduced sense of balance. Additional features include hypogonadotropic hypogonadism, which manifests as incomplete or absent puberty and infertility; genital hypoplasia; distinctive facial features growth and developmental delay; a wide variety of heart defects; cleft lip and/or palate; and olfactory dysfunction in the form of aplasia or hypoplasia (Blake et al. 1998; Pinto et al. 2005). CHARGE syndrome is usually diagnosed during childhood. Diagnosis is made based on the presence of a combination of major and minor clinical features (Blake et al. 1998; Verloes et al. 2005). Magnetic resonance imaging (MRI) of the temporal bones reveals abnormalities in the semicircular canal (Amiel et al 2001). In rare cases, CHARGE syndrome has been detected in adults only after the birth of a child with the major characteristic features of the disease (Hughes et al. 2014). It has also been diagnosed antenatally (Legendre et al. 2012). CHARGE syndrome affects individuals worldwide with an incidence of approximately 1 case in 12,500 live births (Källén et al. 1999). Higher incidences have been reported in the Atlantic provinces of Newfoundland and Labrador, and the Maritime Provinces (Issekutz et al. 2005). See also (Lalani et al. 2012) and the CHARGE Syndrome Foundation (http://www.chargesyndrome.org/foundation.asp).

Kallmann syndrome (KS) is characterized by hypogonadotropic hypogonadism and impaired sense of smell as the result of deficient hypothalamic gonadotropin-releasing hormone and agenesis of the olfactory lobes. Additional features include unilateral failure of kidney development; abnormalities in tooth development; cleft lip and/or palate; and bimanual synkinesis, which is manifested by involuntary movements of one hand that mimic the other hand (Kaplan et al. 2010).

CHARGE syndrome has phenotypic overlap with Kallmann syndrome and hypogonadotropic hypogonadism (Kim et al. 2008; Jongmans et al. 2009). It has been argued that some patients presenting with a clinical diagnosis of Kallmann syndrome may represent unrecognized mild cases of CHARGE syndrome (Ogata et al. 2006).

CHARGE syndrome is an autosomal dominant condition. About 95% of patients with a clinical diagnosis of CHARGE syndrome based on the Blake or Verloes criteria have heterozygous pathogenic variants in the CHD7 gene (Vissers et al. 2004; Verloes et al. 2005; Blake et al. 2011). Over 680 different causative variants, located throughout the length of the gene, are listed in public databases (Human Gene Mutation Database; CHD7 Mutation Database). The great majority result in premature termination of protein synthesis, and include nonsense, splicing, small deletions and insertions. Large pathogenic deletions have been reported in less than 5% of patients with a clinical diagnosis of CHARGE syndrome (Bergman et al. 2008; Wincent et al. 2009; Blake et al. 2011). Chromosomal abnormalities as the result of balanced translocations, rearrangements, or interstitial deletions have also been reported in rare cases (Hurst et al. 1991; Johnson 2006; Arrington et al. 2005). Although most disease-causing variants are de novo, familial cases have been reported (Jongmans et al. 2008; Hughes et al. 2014). In these families, clinical features are usually variable among affected individuals and may be very mild. Parental mosaicism, both somatic and germline, has been detected (Jongmans et al 2006; Pauli et al. 2009).

CHD7 encodes the chromodomain helicase DNA-binding protein 7 that is required for normal mammalian development.

Kallmann syndrome is genetically heterogeneous with various inheritance patterns. Several genes have been associated with the disorder, including ANOS1, CHD7, and SEMA3E.

About 30 CHD7 pathogenic variants have been reported in patients with Kallmann syndrome; they account for ~ 11% of patients with a clinical diagnosis (Marcos et al. 2014). Unlike CHARGE-causative variants, the majority of Kallmann syndrome causative variants are missense. To date, no large deletions, duplications, or complex rearrangements were reported. Most cases are sporadic.

Pathogenic variants in the SEMA3E gene appear to be a rare cause of CHARGE or Kallmann syndromes. To date, only one patient with CHARGE syndrome was reported to have a pathogenic missense variant in SEMA3E (Lalani et al. 2004). A different missense variant was reported in one patient with Kallmann syndrome (Cariboni et al. 2015).

The semaphorin 3E protein is involved in the control of vascular patterning, which is critical for normal organogenesis (Gu et al. 2005).

Over 150 pathogenic variants in the ANOS1 gene have been reported in patients with Kallmann syndrome. The majority of these variants are truncating (HGMD). They account for ~ 8% of all KS cases (Dode et al. 2009). Large deletions have been reported in up to 25% of X-linked KS patients analyzed (Ahmadzadeh et al. 2015). Female carriers of ANOS1 pathogenic variants are usually not affected (Oliveira et al. 2011).

The ANOS1 gene is located on the X chromosome. It encodes anosmin-1, which is involved in the growth and migration of olfactory neurons.

The sensitivity of this test varies based on the criteria used for diagnosis. Pathogenic variants in CHD7 are detected in over 95% of patients with a clinical diagnosis based on Blake or Verloes criteria (Blake et al. 1998; Verloes et al. 2005). CHD7 pathogenic variants are found in 60-70% of patients who are suspected to have CHARGE syndrome (Blake et al. 2011). About 11% of patients with a clinical diagnosis of Kallmann syndrome have pathogenic variants in CHD7 (Marcos et al. 2014).

Pathogenic variants in the ANOS1 gene account for ~ 8% of all KS cases (Dode et al. 2009). Pathogenic variants in the SEMA3E gene appear to be a rare cause of CHARGE or Kallmann syndromes.

Large pathogenic deletions in CHD7 have been reported in less than 5% of patients with a clinical diagnosis of CHARGE syndrome (Bergman et al. 2008; Wincent et al. 2009; Blake et al. 2011).

Large deletions in the ANOS1 gene have been reported in up to 25% of X-linked Kallmann syndrome patients analyzed (Ahmadzadeh et al. 2015).

Large pathogenic deletions in the SEMA3E gene have not been reported.

This panel provides 100% coverage of all coding exons of the genes listed, plus ~10 bases of flanking noncoding DNA. We define coverage as ≥20X NGS reads or Sanger sequencing.