Genetics of idiopathic short stature: Insights into growth regulation

Case 1

An 8-year-old male child was brought to outpatient department with the complaint of poor growth from the age of 4 years. He was born at term, appropriate for gestational age (birth weight 3 kg). There was no history indicative of any systemic illness, previous hospitalizations, or long-term medication use, such as steroids. On examination, the child exhibited short stature with no signs of dysmorphism or micronutrient deficiency. Anthropometric measurements revealed a weight of 15.2 kg (−2.45 SDS), height of 102.6 cm (−3.36 SDS), upper segment to lower segment ratio (US: LS) of 0.9:1, body mass index (BMI) of 14.47 kg/m² (−0.39 SDS), and mid-parental height of 160 cm (−1.78 SDS). The baseline workup, including hemogram, liver and kidney function tests, celiac serology, and thyroid profile, was within normal limits. Skeletal maturity was assessed to be 5 years. GH stimulation tests demonstrated normal peak responses (15 ng/mL with insulin and, 18 ng/mL with clonidine) with two agents. The child was diagnosed with ISS and offered GH replacement therapy; however, the family was unable to afford the treatment.

Case 2

A 10-year-old girl presented with short stature relative to her peers. She has consistently been shorter than her age-matched peers since early childhood, with a height below the 3^rd percentile (−2.5 SDS) for her age and gender. Her weight was within the normal range for her height. Both parents exhibited short stature, with heights below the 5^th percentile for their respective genders. There was no significant medical history, chronic illnesses, or genetic disorders in the family. Physical examination revealed no dysmorphic features or signs of chronic illness, and her development and cognitive function were within normal limits. Routine tests such as complete blood count (CBC) and hormonal evaluations were all within normal ranges. A bone age assessment was consistent with her chronological age. Based on her growth trajectory, familial background, and unremarkable laboratory findings, the patient was diagnosed with FSS. The parents were counseled that children with FSS generally attain a final adult height within their genetically determined potential. However, in cases where height is markedly low (below −2.25 SDS) as in this case, the predicted adult height may fall significantly below the mid-parental height (MPH) range. GH stimulation testing revealed a peak GH level of 11 ng/mL. Consequently, GH therapy was initiated at a dosage of 33 µg/kg/day.

Case 3

A 13-year-old male child initially presented at 8 years of age with the parental concerns of inadequate weight and height gain since past 3 years. He also had complaints of chronic constipation at presentation; however, his intellect was average for his age. He had no other systemic complaints and had normal head circumference and attained all milestones slightly delayed for age. He was born by normal vaginal birth at term at home; appearance was “small”; however, exact birth weight was not documented; cried immediately after birth; and had normal perinatal transition. According to parents, child attained all milestones with a delay of around 5–6 months as compared to elder sibling. At initial presentation, he had weight of 14 kg (−4.4 Z score), height of 106 cm (−6.4 Z score), and head circumference of 47.5 cm (<−2 standard deviation [SD] for population) and sexual maturity rating (SMR) stage-1. He had no affected sibling and parents had normal height (MPH 164.2 cm), with thyroid function tests (TFT), and tissue transglutaminase IgA (tTg-IgA) of 2 U/mL. In the baseline investigations, he had microcytic hypochromic anemia, hypocalcemia secondary to vitamin D deficiency and was started on supplements. Wrist X-ray had shown delayed bone age at this point of 2–3 years. TFT and tTg-IgA were normal; and GH stimulation test showed a peak value of 14.84 ng/mL at 90 min, and hence, child was classified as ISS. GH therapy was also started at that time.

At the time of enrolment, he was 13 years-old on follow-up assessment with weight of 28 kg (3^rd–10^th centile, −1.99 SDS), height of 128.5 cm (<−3 centile, −3.29 SDS) attained while on GH therapy and BMI of 17.08 kg/m² (25^th–50^th centile, −0.43 SDS). However, there was no significant phenotypic trait and X-rays were also normal. This child had significant arm span (AS): height difference of 3.5 cm between the two and abnormal US: LS ratio for age. On genetic analysis for short stature, he was found to have a heterozygous deletion of exon 5, 6 of SHOX gene on Xp22.

Monogenic causes

GH/IGF-1 axis

The GH receptor (GHR), a transmembrane protein, belongs to the cytokine-GH-prolactin receptor family. Mutations in the GH1 gene can cause GH deficiency or impaired signaling. Defects in GHR, signal transducer and activator of transcription 5B (STAT5B), and inhibitor of nuclear factor are considered disorders of the “proximal” GH-IGF-1 axis, while mutations in IGF1 and insulin-like growth factor-binding protein, acid-labile subunit (IGFALS) affect the “distal” part [Figure 1]. STAT5B and IKBKB mutations can also lead to GH resistance and immune dysfunction. A peak GH concentration below 7 ng/mL has been linked to GH deficiency. Measuring IGF-1 levels is strongly recommended in the evaluation of short stature. GH insensitivity is suggested in patients with low GH-binding protein (GHBP) levels, low IGF-1, and elevated GH levels. Other gene mutations, such as those in the transcription factors PROP1 and POU domain, class I, transcription factor 1 (POU1F1), are associated with severe growth failure and classical GH deficiency.^[11] Mild mutations in the GHR gene contribute to approximately 5% of ISS^[12] cases with abnormal GHR signaling also implicated. IGF-1 haploinsufficiency and mutations in the IGFALS and insulin-like growth factor I receptor (IGF1R) genes are linked to ISS.^[13] IGF1 defects manifest as low IGF-1 levels with normal IGFBP-3. IGFALS mutations result in very low IGF-1 and IGFBP-3. IGF1R mutations are associated with microcephaly, cardiac defects, and developmental delays.^[14]

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Figure 1:

Growth hormone-insulin-like growth factor 1 axis pathway.

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Recent studies have identified variations in the pregnancy-associated plasma protein A2 (PAPP-A2) gene, leading to severe short stature due to reduced IGF-1 availability [Table 2]. PAPP-A2 mutations result in high GH, IGF-1, IGF-2 IGFBP-3, and IGFBP-5 levels but low or undetectable PAPP-A2.^[15]

Table 2: Common syndromes presenting with short stature.

Syndromes	Salient clinical features	Genetic etiology
Turner syndrome	Short stature, delayed puberty, amenorrhea, webbed neck, renal and cardiac anomalies	Monosomy X
Floating harbor syndrome	Short stature, early puberty, intellectual disability, and brachydactyly	SRCAP, AD
Noonan syndrome	Short stature, pulmonary stenosis, pectus deformity, and dysmorphism	RAS-MAPKgenes, AD
Silver-Russell syndrome	Short stature, SGA at birth, body asymmetry, and feeding difficulties	Hypomethylation of the paternally inherited allele (ICR1) at chromosome 11p15 (30–60% cases) Maternal uniparental disomy of chromosome 7 (5–10% of cases)
Prader–Willi syndrome	Short stature, hypotonia, cryptorchidism, feeding difficulty in infancy followed by hyperphagia and obesity later on	Deletion of the paternally inherited 15q11.2-q13 region Uniparental disomy of the maternal chromosome 15q11.2-q13 region (UPD 15) Imprinting center deletion or epimutation
Pseudohypoparathyroidism	Short stature, cataract and dental anomalies	Methylation abnormalities, maternal deletions, uniparental disomy of chromosome 20
Laron syndrome	Short stature, delayed bone age, delayed puberty, low IGF-1, increased GH	GHR, AR
ASS	Short stature, delayed puberty, and shawl scrotum	FGD1, XLR
Bloom syndrome	Short stature, photosensitivity, intellectual disability, microcephaly and malignancies	RECQL3, AR

SGA: Small for gestational age, IGF: Insulin-like growth factor, GH: Growth hormone, GHR: Growth hormone receptor, ASS: Aarskog–Scott syndrome, RECQL3: recq protein-like 3, FGD1: fyve, rhogef, and ph domain-containing protein 1, XLR: X-linked recessive, SRCAP: snf2-related cbp activator protein, AD: autosomal dominant, Ras-MAPK: mitogen-activated protein kinase, AR: autosomal recessive

Copy number variations (CNV)

CNVs are implicated in approximately 10% of ISS cases.^[8] A study of 119 Chinese ISS children detected five pathogenic or potentially pathogenic CNVs, yielding a diagnostic rate of 2.5%.^[25] Another study of 19 patients (height < −2 SD) identified three patients having CNVs associated with genes linked to short stature.^[26] These findings suggest that CNVs contribute to a small but significant proportion of ISS cases. Dauber et al. (2011) found high incidence of CNVs in short stature patients, particularly for deletions with a frequency below 5%, with rare deletions being significantly more common in these individuals.^[27]

Epigenetic factors

Epigenetic modifications, including imprinting disorders, are important in the context of ISS. Silver-Russell syndrome, caused by chromosome 7 maternal uniparental disomy (UPD) or hypomethylation of paternal allele at 11p15, leads to suppressed IGF-2 transcription.^[28] Prader-Willi syndrome, resulting from deletions or UPD of chromosome 15,^[29] and pseudohypoparathyroidism, caused by methylation or UPD of chromosome 20, are also associated with short stature.^[30] Temple syndrome, due to maternal UPD of chromosome 14, presents with features such as short stature and early puberty.^[31] In addition, epigenetic changes, such as DNA methylation and histone modification, can alter growth-determining genes and should be considered in ISS diagnosis.

Chromosomal microarray (CMA)

CNVs are gains or losses of genomic DNA segments, ranging from kilobases to megabases in size. CMA can be an essential tool for evaluating children with ISS, as they may uncover a more specific genetic diagnosis, such as a deletion of a chromosomal segment that houses a critical gene. American College of Medical Genetics and Genomics recommends CMA analysis as a first-tier diagnostic test for children with short stature especially in cases where phenotypic evaluation does not reveal any recognizable syndrome.^[32] The diagnostic yield for identifying CNVs associated with short stature is estimated at 5–10%.^[33] CMA is a high-resolution genetic testing technique that detects CNVs. The process begins with the extraction of DNA from a patient’s blood or tissue sample, which is then labeled with fluorescent tags. This labeled DNA is hybridized onto a microarray chip, which contains thousands of probes that correspond to various regions of the genome. After hybridization, the microarray is scanned to measure the fluorescence intensity at each probe. This intensity reflects the presence or absence of specific genomic sequences, helping identify regions of gain (duplication) or loss (deletion) in the patient’s DNA compared to a reference genome. The data are then analyzed using various bioinformatic tools and databases. As a result, CMA is an effective method for diagnosing genetic disorders, including those associated with ISS, developmental delays, and other syndromes related to CNVs. A study by Dauber et al. found that individuals with short stature (height SD score <−2) had a 1.26-fold increase in copy number variant length, particularly for deletions, with rare deletions being 2.3 times more frequent in this group.^[27] In a cohort of 200 individuals with short stature, 20 patients (10%) with presumed pathogenic CNVs, including duplications and deletions, some linked to known syndromes and genes related to stature were identified.^[8]

Next-generation sequencing (NGS)

NGS could serve as an important and advanced diagnostic tool in the evaluation of children with ISS, though results may vary depending on the clinical context and phenotype. NGS testing in the evaluation of short stature is indicated for patients with profound short stature (<−3 SD), SGA without catch-up growth, FSS (parental height < −2 SD), or cases where ISS is associated with additional syndromic features or suspected monogenic causes.^[34] It is also considered in cases of parental consanguinity or when associated with intellectual disability, microcephaly, skeletal abnormalities, or facial dysmorphism. The process begins by extracting DNA from a sample, which is then fragmented into small pieces. These fragments are ligated with adapters and amplified, creating a library. The library is loaded onto a sequencing platform, where each fragment is sequenced in parallel, generating millions of short DNA sequences. Bioinformatic tools are used to align these sequences to a reference genome, enabling the identification of genetic variations such as mutations, insertions, deletions, and CNVs. NGS is widely used for genetic testing, allowing for comprehensive analysis of gene panels, exomes, or the entire genome in conditions such as short stature, where genetic causes may be suspected. WES offers the advantage of focusing on the coding regions of DNA, thereby narrowing the data set. The diagnostic yield of WES was found to be 36% in a cohort of 14 patients with severe ISS. Subsequent studies have demonstrated the utility of WES, with diagnostic yields ranging from 16.5% in patients with isolated SS to 21% in those with associated syndromic features.^[35] A key limitation is the identification of variants of uncertain significance (VUS), making interpretation challenging.

Genome-wide approach

Genome-wide association studies (GWAS) typically focus on identifying genetic variations associated with specific traits by comparing the genomes of individuals with short stature to those of healthy controls. These studies use statistical methods to detect associations between genetic variants, such as single-nucleotide polymorphisms (SNPs), and the phenotype of interest. The EPIGROW study examined 232 candidate genes related to growth using NGS in a cohort of 263 patients with ISS and SGA. This study identified specific SNPs in genes like ZBTB38, which were significantly associated with short stature.^[36]

Epigenetic studies

These studies explore how gene expression is regulated by factors such as DNA methylation, histone modifications, and non-coding ribonucleic acid (RNA), without changes in the DNA sequence. In ISS, these studies can reveal how growth-related genes, such as IGF1 and SHOX, may have altered expression through epigenetic mechanisms. Common tests include DNA methylation, histone modification analysis, non-coding RNA profiling, and chromatin immunoprecipitation, which help identify epigenetic influences on growth regulation and potential causes of short stature.^[37]

Treatment and management

The landscape of ISS treatment is evolving with advances in genetics, molecular biology, and targeted therapies. While GH therapy remains the standard, newer approaches such as CNP analogs, gene editing, and endocrine modulators hold promise for personalized and more effective interventions. Future research and clinical trials will be critical to validating these emerging therapies and integrating them into clinical practice.