ABSTRACT

The growth hormone (GH)-insulin-like growth factor 1 (IGF1) axis is essential for the regulation of growth. IGF1 exerts its effects through the IGF1 receptor type 1 (IGF1R) that plays a pivotal role in fetal and postnatal growth. Pathogenic monoallelic IGF1R variants are known to cause pre- and postnatal growth restriction, often accompanied by normal or elevated serum IGF1 levels. Herein, the clinical and genetic characteristics of two cases with IGF1R novel variants, describing their growth patterns, endocrinological findings, and response to recombinant human GH (rhGH) therapy are presented. Case 1 was a 6.3-year-old boy, with birth weight of 2,500 g [-2.5 standard deviation score (SDS)] and a height of 101.5 cm (-3.2 SDS). Laboratory investigations revealed IGF1 and IGFBP3 levels of 117.8 ng/mL (0.9 SDS) and 4.55 µg/mL (1.3 SDS), respectively. Clinical exome sequencing (CES) identified a novel heterozygous c.3722+1G>A/p.(?) variant in the IGF1R (NM_000875.5) inherited from the mother. At 6.9 years of age, rhGH treatment was initiated at a dose of 0.035 mg/kg/day. The patient has been receiving rhGH for two years, achieving a height gain of +0.3 SDS per year, with an uneventful follow-up. Case 2 was a 3-year-old male with short stature and a history of being born small for gestational age (SGA) (-2.6 SDS). His height and weight were 70.0 cm (-2.1 SDS) and 8.8 kg (-1.1 SDS), respectively. He had a history of frequent respiratory infections. Pituitary hormone levels were normal, and he had no evidence of GH deficiency. CES revealed a novel heterozygous variant c.2275_2278 dup/p.(Ala760Glyfs*21) in the IGF1R. Identifying genetic causes of idiopathic short stature in SGA babies is important, as it facilitates more precise diagnoses, reduces unnecessary testing, and potentially enables targeted therapies. Our experience with rhGH therapy in one patient suggests a modest growth response, consistent with previous studies. However, elevated IGF1 levels during treatment highlight the importance of balancing therapeutic doses to optimize height gains without causing side effects.

Introduction

The growth hormone (GH)-insulin-like growth factor 1 (IGF1) axis plays a central role in human growth and metabolism (1). Among its components, the IGF1 receptor (IGF1R) mediates the effects of IGF1 and IGF2. These growth factors bind to IGF1R to promote growth both in fetal and postnatal life. Thus, dysfunctions in either the IGF1 or IGF1R genes, may lead to pre- and postnatal growth restrictions (2). Structurally, IGF1R is akin to the insulin receptor and operates as a heterotetrameric transmembrane glycoprotein (3). Its alpha subunit ensures ligand binding, while the beta subunit facilitates intrinsic tyrosine kinase activity for signal transduction (4).

IGF1R (MIM*147370), located on chromosome 15q26.3, encompasses 21 exons. Pathogenic variants in this gene may occur in both monoallelic and biallelic forms, with the latter generally being associated with more severe clinical manifestations. Over 170 IGF1R variants have been documented, including missense/nonsense variants and gross deletions (5). Clinically, these variants are frequently associated with intrauterine growth restriction (IUGR), short stature, microcephaly, delayed bone age, developmental delay, and dysmorphic features, including a receding hairline, triangular face, long/smooth philtrum, thin upper lip, and full lower lip. However, the expression and severity of these traits can vary, and not all individuals present with all these features, reflecting the multifactorial nature of these characteristics. In adults with IGF1R defects, a thorough evaluation is essential, particularly concerning components of metabolic syndrome and hypogonadism (6).

Identifying IGF1R defects in short stature remains challenging because of the variability in patient selection and genetic methodologies. A comprehensive approach, integrating both single nucleotide variants (SNVs) and copy number variant (CNVs) analyses, is essential for accurate diagnosis (7). Rapid advances in high-throughput next-generation sequencing (NGS) techniques have facilitated the diagnosis of patients with short stature due to IGF1R defects. This has reclassified numerous cases previously defined as idiopathic short stature into distinct genetic disorders.

Herein, we present two patients with novel heterozygous IGF1R variants, detailing their clinical presentations and discussing the outcomes of recombinant human GH (rhGH) therapy in one patient.

Subjects and Methods

Clinical Evaluation

Height measurements were obtained using calibrated Harpenden stadiometers (Holtain, Crymych, UK), and weight was measured with standard equipment. Standard deviation scores (SDS) for all measurements were computed using growth charts specific to Turkish children (8). Small for gestational age (SGA) was defined as a birth weight (BW) or length more than two standard deviations below the mean for gestational age (9).

Hormonal Assays

Plasma GH levels were assessed using electrochemiluminescence immunoassay on a Roche Cobas platform (Roche Diagnostics  İstanbul, Türkiye). IGF1 and IGF binding protein 3 (IGFBP3) were analyzed by immunoassays using the IMMULITE 2000 system (Siemens Healthcare İstanbul, Türkiye). IGF1 and IGFBP3 SDS were calculated using the online tool Child Metrics (10, 11, 12).

Molecular Analyses

After obtaining informed consent from the parents, DNA isolation was performed from peripheral blood samples under the standard protocols of the QIAAmp DNA Mini kit (Qiagen, Hilden, Germany). Sequencing was performed using the Illumina NextSeq platform, and each patient was read at least 20X depth in the clinical exome sequencing (CES) panel. Bioinformatic analyses and variant calling were performed using the Sophia-DDM-V5.08 bioinformatics analysis program (SOPHIA Genetics, Rolle, Switzerland). This test evaluates the coding regions and exon-intron boundaries in the relevant genes.  During the analysis, only pathogenic (P), likely pathogenic (LP), or variants of unknown significance were reported according to current scientific knowledge based on the ClinVar database (13). This database is constantly updated, and the data in the report is as of the date the report was written (2024); changes are possible in the future. The interpretation of the variants was based on the American College of Medical Genetics and Genomics (ACMG) 2015 guideline (14). To assess the population frequency of the variants, data from gnomAD, the 1000 Genomes Project, dbSNP, and ExAC were utilized (15). CNVs were also examined with this analysis. Segregation analyses were performed for the parents.

Case Presentations

Clinical and molecular genetic characteristics of two patients from two unrelated families are described.

Patient 1 (P1)

A 6.3-year-old boy was referred for evaluation of short stature. He was born at term with a BW of 2,500 g (-2.5 SDS), which confirmed a diagnosis of being SGA. Parents were unrelated. His neurodevelopmental milestones were normal for age, except for delayed walking, which he achieved at three years.

At the time of assessment, his height was 101.5 cm (-3.4 SDS), and his weight was 15.1 kg (-2.8 SDS). Body proportions were normal for his age, and head circumference (HC) was -1.8 SDS. Midparental height (MPH) was -1.7 SDS, and his mother was notably short (148.0 cm, -2.6 SDS). Pubertal examination was Tanner stage I. He had distinctive facial features, including a long philtrum and retro-micrognathia. The bone age assessment was aligned with his chronological age, and the skeletal survey was normal. The ophthalmological evaluation identified strabismus, for which a follow-up was recommended.

Laboratory results showed normal liver, renal, and thyroid function tests. His IGF1 and IGFBP3 levels were 117.8 ng/mL (0.95 SDS) and 4.55 µg/mL (1.3 SDS), respectively. GH stimulation test revealed a peak GH concentration of 14.4 ng/mL, ruling out GH deficiency. Chromosome analysis was 46,XY. 

At 6.9 years of age, rhGH treatment was initiated at a dose of 0.035 mg/kg/day. The patient has been receiving rhGH for two years, achieving a height gain of +0.3 SDS per year, with an uneventful follow-up. Patient 1’s mother was also evaluated for her short stature. The IGF1 and IGFBP3 levels were 251 ng/mL (-0.51 SDS) and 4.24 µg/mL, respectively. She had no evidence of insulin resistance, and her metabolic profile was normal. Clinical and laboratory findings of P1 at diagnosis and during rhGH treatment are summarized in Table 1 and Figure 1.

Patient 2 (P2)

A 3-year-old boy was referred for evaluation of growth failure. He was born at term with a BW of 2,300 g (-2.6 SDS). His perinatal history reported concerns about short femur length, though no definitive diagnosis was made at birth. His parents were unrelated.

At 1 year of age, his height was 70.0 cm (-2.1 SDS), weight was 8.8 kg (-1.1 SDS), and HC was 45.0 cm (-1.4 SDS). His mother was 158.0 cm (-0.87 SDS), his father was 166.0 cm (-1.65 SDS), and the MPH SDS was -1.25. The bone age corresponded to a chronological age of 3 to 6 months. Developmental milestones for gross motor and speech skills showed mild delays. Initial evaluations revealed normal IGF1 (88.53 ng/mL, -0.9 SDS) and IGFBP3 (4.2 ng/mL, -1.1 SDS). GH deficiency was ruled out with a glucagon stimulation test (peak GH: 8.0 ng/mL). The skeletal survey was normal.

At 2 years of age, his height velocity increased (+10.9 cm/year), however, height SDS remained below the expected range. At this time, his IGF1 level was elevated (164 ng/mL, 2.1 SDS), prompting further investigation for potential IGF1R variants.

His metabolic profile, including glucose (78 mg/dL), insulin (2.4 µIU/mL), triglyceride (35.5 mg/dL), and low density lipoprotein cholesterol (85 mg/dL), were normal.

The patient had recurrent respiratory infections, and selective immunoglobulin A deficiency was diagnosed, leading to a referral to clinical immunology for further evaluation.

At his most recent evaluation at 3.5 years old, his height and weight were 90.3 cm (-2.5 SDS) and 13.0 kg (-1.6 SDS), respectively. The arm span was 89.0 cm. The family was counseled about the possibility of initiating rhGH therapy.

The images of the patients and left-hand radiography are illustrated in Figure 2.

Molecular Genetic Results

Pedigree and Integrative Genomic Viewer of the NGS data are shown in Figure 3.

Analysis by CES in P1 revealed a heterozygous c.3722+1G>A/p.(?) variant in the IGF1R gene (NM_000875.5). This splice-site variant was classified as LP according to ACMG criteria (PVS1, PM2). This variant was classified as “deleterious” (MT, DANN, BayesDel) according to in silico prediction tools (16). For the splice-altering characteristics variant, SpliceAI is described as “Strong-Splice-altering” (17). This variant was not observed in the gnomAD (exomes and genomes) database (15). This IGF1R variant was also not reported in the HGMD professional database (November 2024) (5). Segregation analyses by Sanger sequencing revealed that his mother was also heterozygous for this variant.

In P2, the CES analysis identified a heterozygous c.2275_2278 dup/p.(Ala760Glyfs*21) variant in IGF1R (NM_000875.5), which is predicted to result in frameshift and premature termination. This variant was classified as LP according to ACMG criteria (PVS1, PM2) and was not observed in the gnomAD database (15). Once again, this IGF1R variant was also not reported in the HGMD professional database (November 2024) (5). Segregation analyses revealed that this variant was de novo.

Discussion

This report describes two rare cases of short stature due to novel heterozygous IGF1R variants, one involving a splice-site alteration and the other a frameshift variant. While the clinical features of these cases align with those previously reported, our findings contribute by documenting novel mutations and providing additional insights into growth response to rhGH therapy.

Although virtually all patients with monoallelic IGF1R variants present with pre- and postnatal growth restrictions, the extent varies remarkably. Walenkamp et al. (18) reported the detection of pathogenic IGF1R variants in approximately 2% of patients with short stature who were SGA. SGA-born cases represent a diverse group with varying clinical features. The reduced size at birth can be attributed to fetal, maternal, placental, and/or genetic factors. While many SGA babies achieve normal growth by the age of 2 years, about 15% remain below -2.0 SDS in height and continue to be short. Genetic factors have been identified in a limited number of short SGA children, notably having point mutations and deletions in the IGF1 and IGF1R genes (19). Klammt et al. (20) reported eight SGA patients who were in the range of -1.5 to -3.5 SDS due to IGF1R variants. Both of our patients were born SGA and were unable to catch up with growth by two years of age. P2 had a history of short extremities in the prenatal evaluation, but later postnatal examination revealed proportionate short stature.

In the study of Gonc et al. (7), patients with short stature without GH deficiency having either a low BW or microcephaly were evaluated to detect IGF1R defects, and variants were detected in 14% of the cohort. Two IGF1R deletions and five heterozygous variants (one frameshift, four missense) were identified. All patients with IGF1R defects had a height, BW, and HC lower than -2.5 SDS, -1.4 SDS, and -1.36 SDS, respectively. IGF1 levels ranged from -2.44 to 2.13 SDS (7). Although the height SDS of P2 was similar, in our study, P1’s height SDS at presentation was below -3.0 SDS.

Features described in cases with IGF1 resistance include mild facial dysmorphism (triangular face, brachycephaly, hypotelorism, low-set and prominent ears and micro-retrognathia), neurodevelopmental delay, and mild glucose intolerance (17). In our cases, some dysmorphic features, such as clinodactyly and micro-retrognathia, were also observed. Although the patients experienced delayed attainment of certain milestones, neuromotor development remained within normal limits. There were no abnormalities in carbohydrate metabolism. Given their prepubertal age, some clinical features may emerge later, and continuous monitoring will be necessary.

Cases of heterozygous IGF1R variants are typically characterized by IUGR, persistent postnatal growth failure, elevated serum IGF1 levels, and microcephaly (21). Our patients presented with moderately elevated IGF1 SDS values and did not exhibit microcephaly.

Most of the 170 variants identified in the IGF1R gene are missense/nonsense (n=107) and gross deletions (n=27). Splice-altering (n=9), small deletions (n=7), small indels (n=1), gross insertions (n=6), complex rearrangements (n=3), and regulatory region (n=3) variants have also been described (5). To date, splice-site variants (n=9) described are localized in the introns 1,  2, 3, 7, 8, 9, 10, and 18.

The c.3722+1G>A is a splice-site variant occurring at the donor site of intron 20. This variant is predicted to disrupt the normal splicing process, potentially leading to the exclusion of exon 20 from the mature mRNA transcript. Exon 20 encodes a portion of the tyrosine kinase domain of the IGF1R protein (catalytic domain of insulin receptor-like protein Tyrosine kinases), which is crucial for its signaling function. Alterations in this domain may impair the receptor’s ability to transduce signals, affecting growth and development processes.

The IGF1R c.2275_2278dup/ p.(Ala760Glyfs*21) variant is a frameshift duplication located in exon 13 of the IGF1R gene (NM_000875.5). This exon encodes part of the extracellular fibronectin type III domain, which is critical for ligand binding and proper receptor function (22). Variants in specific domains (e.g., fibronectin type III or tyrosine kinase) often lead to growth failure and altered IGF1 signaling, as seen in patients with short stature due to IGF1R variants (23).

Previous studies have highlighted significant variability in height, IGF1 levels, and intrauterine growth in individuals with the same heterozygous IGF1R variants. This variability is likely due to the complex structure of IGF1R and its interaction with the insulin receptor, which modulates IGF1 signaling. Although growth is influenced by multiple factors beyond IGF1 signaling, genetic testing for IGF1R alterations is crucial for accurate diagnosis, particularly in cases exhibiting elevated IGF1 levels or an exaggerated IGF1 response to rhGH therapy (24, 25). 

The phenotype of short stature associated with IGF1R variants is not fully elucidated, and no approved therapy is currently available. However, effectiveness of rhGH treatment has been studied (18). In this report, P1 was treated with rhGH, and the height SDS gain was +0.3 at the first year and +0.6 SDS at the second year. Patients with heterozygous IGF1R variants may respond to rhGH treatment, aligning with previous reports. However, the response remains variable (26). Çelik et al. (27) concluded in their recent review that rhGH has a partial beneficial effect in cases with IGF1R defects, particularly when initiated early and administered long-term. Nearly half of the patients achieved a height gain of more than 1 SDS over the long term (26). Walenkamp et al. (18) suggested that higher IGF1 levels may need to be tolerated during the treatment to achieve a clinically significant increase in height SDS due to the partial insensitivity to IGF1 in these patients. The reluctance to increase the rhGH due to elevated IGF1 SDS levels may have contributed to suboptimal treatment response in our case. Higher IGF1 levels after rhGH therapy may indicate IGF1R gene variants (18).

The correlation between IGF1R defects and clinical presentation remains unclear, and the wide phenotypic variability complicates the selection of patients for IGF1R gene sequencing. However, advances in NGS technologies have enabled massively parallel sequencing of multiple genes and genomic regions with high precision, significantly enhancing diagnostic yield. By capturing both coding and non-coding regions, NGS facilitates the comprehensive identification of pathogenic variants, including SNVs, small in/dels, and CNVs, thereby revolutionizing the diagnostic approach to genetically heterogeneous disorders (28).

In conclusion, uncovering the genetic causes of idiopathic growth failure is important, as it facilitates more precise diagnoses, reduces unnecessary testing, and potentially enables targeted therapies. Our experience with rhGH therapy in one patient suggests a modest growth response, consistent with previous studies. A +0.6 SDS gain over two years aligns with prior reports of partial responsiveness in IGF1R variant carriers. However, elevated IGF1 levels during treatment highlight the importance of balancing therapeutic doses to optimize height gains without causing side effects.