A novel missense variant of FGFR1 in a Japanese girl with Kallmann syndrome and holoprosencephaly.

Clinical Pediatric Endocrinology Vol.32 / No.1 January 2023 pp 79–81 Mutation-in-Brief A novel missense variant of FGFR1 in a Japanese girl with Kallmann syndrome and holoprosencephaly Noboru Uchida1, 2, Yusuke Mizuno1, 2, Shohei Seno3, Yutaro Koyama3, Tsutomu Takahashi1, Hironori Shibata2, Satoshi Narumi2, 4, Tomonobu Hasegawa2, and Tomohiro Ishii2 1Department of Pediatrics, Saiseikai Utsunomiya Hospital, Utsunomiya, Japan 2Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan 3Department of Cardiology, Tokyo Metropolitan Children’s Medical Center, Tokyo, Japan 4Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan Highlight ● A novel missense variant of FGFR1, p.Glu531Lys, is associated with Kallmann syndrome and holoprosencephaly. Key words: fibroblast growth factor receptor 1 (FGFR1), Kallmann syndrome, holoprosencephaly, novel variant Introduction Fibroblast growth factor receptor 1 (FGFR1), a receptor tyrosine kinase, acts as a cell surface receptor for fibroblast growth factors and plays an essential role in the regulation of embryonic neurogenesis. Pathogenic variants of FGFR1, the gene encoding FGFR1, have been reported in cases of Kallmann syndrome (KS) (1) or holoprosencephaly (HPE) (2). Herein, we report the case of a Japanese girl with KS and HPE, carrying a novel pathogenic variant of FGFR1. Case Report The proband was a Japanese girl who was born at term after an uneventful pregnancy. She was the first child of phenotypically normal parents with no significant family history. Her birth weight and length were 3060 g (+ 0.59 SD) and 49.7 cm (+ 0.49 SD), respectively. She had no cleft lip, hypotelorism, nor absence of the nasal septum. Her development was almost normal except for walking. She needed orthotics for bilateral clubfoot from the age of 1 yr and 6 mo and was able to walk by herself at the age of 2 yr. She had neither polydipsia nor polyurea. At 3 yr of age, medical attention was sought for diarrhea and vomiting of three days durations. Her height and weight were 91.0 cm (–1.43 SD) and 12.8 kg (–0.90 SD), respectively. She did not show any facial dysmorphic features except for a flat nasal tip. Her serum sodium and urea nitrogen levels were 162 mEq/L, 49.2 mg/dL, respectively. The urine specific gravity was 1.029. Intravenous fluid therapy was initiated. On the third day of admission, her serum sodium, osmolality, and arginine vasopressin Received: August 18, 2022 Accepted: September 14, 2022 Advanced Epub: October 7, 2022 Corresponding author: Tomohiro Ishii, M.D., Ph.D., Department of Pediatrics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan E-mail: This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial No Derivatives (by-nc-nd) License <http://creativecommons.org/licenses/by-nc-nd/4.0/>. Copyright© 2023 by The Japanese Society for Pediatric Endocrinology Clin Pediatr Endocrinol levels were 154 mEq/L, 306 mOsm/L, and 1.2 pg/mL, respectively. Her urine osmolality was 376 mOsm/L. Brain MRI revealed a continuous frontal cortex across the midline and the absence of the septum pellucidum, corpus callosum, and olfactory bulbs (Fig. 1). Loading tests with insulin, gonadotropin-releasing hormone, and thyrotropin-releasing hormone, after improvement in dehydration, revealed gonadotropin insufficiency (Table 1). After discharge, her serum sodium level remained within normal limits except for a few episodes of hypernatremia in the case of gastroenteritis. We diagnosed her with KS and lobar-type HPE, presenting with partial diabetes insipidus and bilateral clubfoot. With age, dyscalculia and dysgraphia became apparent, and she scored 55 on a preschool intelligence test. She could not distinguish the scents in her daily life. She also experienced hyperacusis. She was enrolled in a support class for children with special needs in an elementary 80 school. After genetic counseling, written informed consent was obtained from her mother. The study was approved by the Ethics Committee of Keio University School of Medicine (IRB number: 20140289; date of approval: May 25, 2015). Genomic DNA was extracted from peripheral blood samples of the proband. Next-generation sequencing-based screening of the major causative genes of KS and HPE (CCDC141, CHD7, DUSP6, FEZF1, FGF17, FGF8, FGFR1, FLRT3, GLI2, HS6ST1, IL17RD, KAL1, NELF, POLR3B, PROK2, PROKR2, SEMA3A, SEMA3E, SIX3, SOX10, SPRY4, and WDR11) identified a novel heterozygous variant, c.1591G>A, p.Glu531Lys, in FGFR1. We verified the presence of this variant using PCR-based direct sequencing (Fig. 1). No genetic testing of the parents was performed. p.Glu531Lys variant is not found in the Human Genetic Variation Database (HGVD; http://www. Fig. 1. (A) Axial flare (left), sagittal T1-weighted (center), and coronal T2-weighted MRI images (right) of the patient’s brain at 3 yr of age. Frontal cortex is not fully separated and continuous on both sides (white arrow). Septum pellucidum and corpus callosum are completely absent. High-intensity signal is preserved in the posterior lobe. Olfactory bulb is not clearly identified. (B) Partial sequence chromatogram of exon 12 of the proband’s FGFR1 gene. A black arrow shows a variant of c.1591G>A, p.Glu531Lys. (C) Three-dimensional structure of the intracellular kinase domain of FGFR1 (left), and enlarged views of wild (upper right) and variant-type (lower right) salt-bridges. Residues corresponding to Glu531 and Lys514 are shown as spheres and sticks. Red and blue atoms show oxygen and nitrogen, respectively. The p.Glu531Lys was predicted to lose ionic bond formation (dotted line) in the salt-bridge. Uchida et al. doi: 10.1297/cpe.32.2022-0060 Clin Pediatr Endocrinol 81 Table 1. Hormone levels after stimulation with insulin, gonadotropin-releasing hormone, and thyrotropin-releasing hormone min GH (ng/mL) ACTH (pg/mL) Cortisol (µg/dL) LH (mIU/mL) FSH (mIU/mL) TSH (µIU/mL) PRL (ng/mL) 0 15 30 60 90 120 2.24 10.1 5.8 < 0.20 < 0.20 1.27 11.4 1.42 7.7 7.0 6.24 196.8 14.9 < 0.20 1.92 10.43 113.7 16.3 74.0 24.4 0.22 2.37 9.39 78.0 28.7 21.6 < 0.20 2.25 7.47 36.0 23.1 17.1 < 0.20 2.30 5.72 25.4 hgvd.genome.med.kyoto-u.ac.jp), Genome aggregation database (gnomAD; https://gnomad.broadinstitute. org/) or Japanese multi omics reference panel (jMorp; https://jmorp.megabank.tohoku.ac.jp/202206/). In silico analyses of p.Glu531Lys by PolyPhen-2 (http://genetics. bwh.harvard.edu/pph2/) and PROVEAN (http://provean. jcvi.org/index.php) predicted “probably damaging” and “deleterious” with scores of 1.000 and –3.57, respectively. Glu531 forms a salt-bridge with Lys514 and interacts with the glycine-rich loop to facilitate binding of adenosine triphosphate and substrate in the tyrosine kinase domain (3, 4). In the three-dimensional model, the PyMOL Molecular Graphics System (http://www. pymol.o (...truncated)