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Inherited SHANK1 pathogenic variant in 3-year-old male with neurodevelopmental delay, behavioral challenges, laryngomalacia and overgrowth: a case report

Clinical Genetics and Therapeutics
  • Primary Categories:
    • Clinical- Pediatric
  • Secondary Categories:
    • Clinical- Pediatric
Introduction
The SHANK gene family encodes scaffolding proteins involved in modulating synaptic responses in the brain. Though SHANK3 (OMIM #606230) is associated with the well-known Phelan-McDermid syndrome (OMIM #606232), less is known about SHANK1 (OMIM #604999) disease associations. Sixteen reported cases of de novo SHANK1 variants have indicated an association to several neurodevelopmental disorders, including autism spectrum, attention deficit hyperactivity disorder (ADHD), learning disability, motor delays, and speech delays. No cases of parental inheritance have been reported to our knowledge.

Case Presentation
We report a 3-year-old male with developmental delays, aggression, learning problems, laryngomalacia, and overgrowth. This patient was born at 38 weeks to a 32-year-old primigravid mother and 26-year-old father via assisted vaginal delivery. Prenatal ultrasounds revealed no abnormalities. There was no exposure to teratogens. Family history had been notable for learning disability and ADHD (father) as well as autoimmune disease with syncope, GI dysfunction, and joint problems (mother). His birth weight was 2.79 kg (15th percentile), length was 52.1 cm (70th percentile), and head circumference was 32.5 cm (15th percentile). The neonatal course was complicated by respiratory distress, feeding difficulty, and hypothermia. He was referred for a genetics evaluation at 3 years due to dysmorphism and behavioral concerns. Physical exam revealed generalized overgrowth with a height of 105.2 cm (97th percentile), weight of 19.7 kg (99th percentile), and head circumference of 52.0 cm (94th percentile). Notable anomalies included early fontanelle closure, laryngomalacia, irregular speech development, and angry outbursts, including self-injury. Dysmorphic features included high hair line, sparse hair, double hair whorl, frontal bossing, widows peak, anterior cowlicks, arched eyebrows, bulbous nasal tip, high arched palate, dermatographia, and a 3mm left thigh hemangioma. Hypotonia was also noted.

Diagnostic Workup
Following a chromosome microarray that revealed no abnormalities, whole exome sequencing revealed an intragenic pathogenic variant c.3004del (p.H1002Tfs*341) in the SHANK1 gene, inherited from his father (whose status as adopted disallowed further paternal family history). Thus, the condition demonstrates an autosomal dominant mode of inheritance.

Treatment and Management
This finding did not result in any treatment changes.

Outcome and Follow-Up
The patient was provided with genetic counseling to discuss the neurodevelopmental implications of this condition. He was also referred to developmental pediatrics to further explore multidisciplinary therapies.

Discussion
In the 16 reported cases of SHANK1-associated neurodevelopmental disorders, the most frequently reported features were speech and language delay (11 out of 15), autism spectrum (10 out of 15), learning disability (8 out of 15), behavior issues (9 out of 15), dysmorphic features (5 out of 8), and hypotonia (5 out of 7). Motor delays (6 out of 16), macrocephaly (2 out of 7), and seizures (3 out of 8) have also been reported. All the cases involved de novo variants, and none had an identical c3004 deletion. This patient presents with many of the neurodevelopmental disorders described in de novo SHANK1 variants, including language delay and behavior issues, as well as associated anatomic abnormalities, such as dysmorphism, macrocephaly, and hypotonia. He expands the current understanding of SHANK1-associated neurodevelopmental disorders by introducing autosomal dominant inheritance and the atypical findings of laryngomalacia and overgrowth.

Conclusion
This patient presents the first reported case of an inherited SHANK1-associated neurodevelopmental disorder to our knowledge and introduces abnormalities not previously associated with de novo SHANK1 disorders. Continuing to monitor the progression of this patient will further elucidate the implications of this rare condition.

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