A Chinese family with Noonan syndrome caused by a heterozygous variant in LZTR1: a case report and literature review

Patient 1 The proband (Fig. 1, III-3), a 6.6-year-old girl, was admitted to our hospital because of short stature. As the first child of nonconsanguineous parents, she was born at 41 weeks of gestation via vaginal delivery, whose birth weight and length were 1800 g (<P3^rd) and 47 cm (<P3^rd), respectively. She showed significant growth retardation since the newborn stage, and now her height, weight and body mass index (BMI) were 90.5 m (− 6.3 SD), 11 kg (− 4.9 SD) and 13.4 kg/m² (P10-25th), respectively. Her ratios of arm span/height and sitting height/height were 0.92 (− 2 SD) and 0.58 (+ 3 SD) according to the standard reference values [12]. Her psychomotor development was mildly delayed.

Physical examination: She showed the following typical features of Noonan syndrome (Fig. 2): hypertelorism; downslanting palpebral fissures; epicanthal folds; low-set, oval-shaped, posteriorly rotated ears with a thick helix; a short broad nose with a depressed root and full tip; a deeply grooved and long philtrum; high and wide peaks of the vermilion; a highly arched palate; micrognathia; a short neck; cubitus valgus; scoliosis; café au lait spots; and mild hypertrichosis. She also presented with squinting, refractive errors and nystagmus.

Auxiliary examination: The IGF-1 level was 61 μg/L (− 1.9 SD) and growth hormone (GH) stimulation test (insulin and levodopa stimulation test) showed that GH peak was 5.54 ng/mL (cut-off value: < 7 ng/mL). The electrocardiogram test showed frequent premature ventricular beats (the second and third rhythms), X-rays and MRI of the spine showed hemivertebral deformity of the third thoracic vertebra and scoliosis (Cobb’s angle = 28°), and her bone age was 5.5 years old. In addition, hormone levels of the adrenal gland, thyroid gland and gonad were normal; the tumor markers (includes AFP, HCG and CEA) were also negative. No abnormalities were found during the ultrasound examination of the heart, liver, kidneys, uterus or ovaries, so did the MRI of the craniocerebrum. Besides, her karyotype was 46, XX.

According to the clinical manifestation and laboratory tests, she was diagnosed as Noonan syndrome with GH deficiency clinically [13]. Due to her serious scoliosis and hemivertebral deformity, recombined human GH treatment was not recommended.

Patient 2 (Fig. 1, III-4) was the younger sister of the proband. Her birth weight and height were 3000 g (P50th) and 49 cm (P25th), respectively, with a gestational age of 38 weeks. Her height and weight were 82.5 cm (− 2.7 SD) and 10.7 kg (− 1.8 SD) at the age of 2.5 years. She had similar facial appearance to patient 1. She had no skeletal abnormities except for pectus carinatum. She didn’t show mental retardation, nor did she have any diseases of the heart and genitourinary system. The patient was also diagnosed as Noonan syndrome clinically (Fig. 3).

Suspected patient 3 (Fig. 1, II-6) was the mother of patients 1 and 2. She was 27 years old, and her height was 153 cm (− 1.7 SD). She showed the mild phenotype of Noonan syndrome: hypertelorism; downslanting palpebral fissures; low-set, oval-shaped, posteriorly rotated ears with a thick helix; a highly arched palate; and prominent nasolabial folds. She didn’t show mental retardation, nor did she have any diseases of the heart, genitourinary system and skeletal system (Fig. 3).

Suspected patient 4 (Fig. 1, I-3) and suspected patient 5 (Fig. 1, II-7) were the mother and younger sister of patient 3, respectively. They had appearance features similar to those of patient 3. Their heights were 151 cm (− 1.9 SD) and 153 cm (− 1.7 SD), respectively.

Suspected patient 6 (Fig. 1, III-5) was the daughter of patient 5. At the age of 3 years, she showed a short stature (84.3 cm, − 3.2 SD) and similar facial appearance to patients 1. She didn’t show mental retardation, nor did she have any diseases of the heart, genitourinary system and skeletal system.

After obtaining the informed consent from her family, whole exome sequencing (WES) analysis was performed on the proband and her family. Genomic library was built using a standard library construction kit, and exons were captured using the target sequence capture probe. All of the exons (including the 50 bp flanking piece on either side) were captured in a single reaction, and genes related to the RASopathies were thus considered. The average sequencing depth, average coverage and 10X coverage (coverage of sites with depth greater than 10) in the target region were 153.02X, 99.43 and 96.28%, respectively. A standard bioinformatics pipeline was utilized for variant identification with the help of Genome Analysis Toolkit (GATK) [14] software following the best practice guidelines recommended by the GATK [15, 16]. Candidate variants were retained as follows: (1) rare variants with a minor allele frequency of < 1% in the ExAC, dbSNP, 1000 Genomes, gnomAD and local databases, and (2) functional variants including frameshift, splice, nonsense, missense and synonymous variants that can affect splicing. Then, we utilized a hypothesis-free approach to analyze all of the phenotype-related genes. Nonetheless, exome sequencing is limited in detecting large deletions/duplications and deep intronic variants.

Eventually, we identified a heterozygous variant, c.1149 + 1G > T, under accession number NM_006767.3 in the LZTR1 gene. No other variants were detected in the LZTR1 gene or in the other RASopathy genes in the proband. The proband did not harbor other mutations that have been associated with Noonan syndrome, GH deficiency, skeletal dysplasia and other genetic diseases. The splicing variant was ranked as “likely pathogenic” according to the 2015-ACMG Standards and Guidelines [17]. Sanger sequencing showed that the variant of the proband and her sister was inherited from the proband’s mother, but her father without Noonan syndrome didn’t carry the variant (Fig. 3). Unfortunately, patients 4–6 rejected the genetic analysis, and patients 2–6 didn’t agree to share their photos.