Genetic Syndromes and Skeletal Dysplasia Associated with Short Stature – A Case Series : Apollo Medicine

Secondary Logo

Journal Logo

Original Article

Genetic Syndromes and Skeletal Dysplasia Associated with Short Stature – A Case Series

Agarwal, Divya; Kochar, I. P. S.1; Gupta, Vineet Bhushan2; Menon, Kriti

Author Information
Apollo Medicine 20(2):p 93-100, Apr–Jun 2023. | DOI: 10.4103/am.am_59_23
  • Open



Stature has a very high heritability index of about 80%. There are multiple genes which regulate the chondrogenesis at the growth plate. It is but natural that mutations or defects involving these genes lead to normal variant short stature in case of mild defects and severe pathologic short stature in case of strong defects. Genetic syndromes, primordial short stature syndromes, and skeletal dysplasia form the majority of genetic causes of pathologic short stature.

Materials and Methods: 

Here, we present 25 patients evaluated in the genetic clinic and a genetic cause could be identified in 20 of them.


Systematic approach to the evaluation of short stature – differentiating proportionate and disproportionate, differentiating primordial from postnatal onset short stature along with appropriate genetic tests can delineate the definite cause in up to 80% of patients with short stature. The common genetic syndromes diagnosed included Noonan syndrome, Kabuki syndrome and common skeletal dysplasia diagnosed were achondroplasia and epiphyseal dysplasia. Some of the rare syndromes diagnosed were Kenny-Caffey syndrome, 12p-deletion syndrome, and Dyggve–Melchior–Clausen syndrome.


This series of short-stature cases with phenotype-genotype delineation strengthens the need for structured evidence-based protocol for the multi-disciplinary management of short stature.


Short stature is one of the commonest conditions in pediatric and endocrinology outpatient clinics. The most common type of short stature is constitutional without any identifiable cause. There is a direct correlation with chondrogenesis at the growth plate. Linear growth or height is a result of chondrogenesis at the growth plate and all forms of short stature are, therefore, due to decreased chondrogenesis at the growth plates.[1]

Normal growth/stature is modulated by several thousands of genes that affect growth plate function and hence genetic defects in these local growth plate systems result in short stature. Polymorphisms and mild mutations in these genes modulate height within the normal range and cause mild polygenic short stature, also called normal variant short stature (constitutional delay and familial short stature).[2]

Mutations with a strong effect on protein function cause significant stunting of height or pathological short stature with or without other systemic features, these could be short stature syndromes or skeletal dysplasia.

Exome sequencing and other readily available genetic tests have become powerful diagnostic as well as research tools to identify the etiology of such pathologic short stature.

As more and more definitive underlying molecular cause is identified, the number of patients who receive the unhelpful diagnosis of “idiopathic” short stature is decreasing.[3]

It is important to identify and understand the underlying cause or molecular genetic basis of short stature in patients as it has a significant impact on their care. It will not just guide management and recognize associated health risks, it will help limit other expensive/invasive/cumbersome testing or treatments. It will also enable genetic counseling with regard to the risk of recurrence and definitive prenatal tests in the family. Most importantly, it will improve a basic understanding of skeletal development and growth which paves the way to the development of new molecular-based treatment approaches.

We present here retrospective analyses of genetic evaluation and genetic diagnosis in a cohort of patients with suspected pathologic short stature, referred to the genetic clinic, within a span of 1 year. The article showcases the utility and power of genetic services and genetic testing in providing a definitive diagnosis and optimal management in cases of pathologic short stature.


This is a retrospective analysis of patients who were referred for evaluation of the cause of pathologic short stature to the genetic clinic after initial workup in pediatrics or pediatric endocrinology and underwent detailed genetic testing in a tertiary care genetic center during a 1-year period from December 2021 to December 2022. Short stature was defined by height <3 standard deviation (SD) for age by using WHO charts for height for age. Normal variant short stature and the most common causes of pathologic short stature such as Turner syndrome and hormonal causes such as hypothyroidism and growth hormone deficiency were already screened for in these patients by karyotype and relevant hormone studies before referral. Undiagnosed cases were then referred to the genetics clinic.

We have included here the cases where the primary concern was short stature with or without other concerns and not the cases where shortness was recorded only during the examination of the patient.

Out of all cases referred, a total of 25 cases underwent detailed genetic testing and are presented here. Patients who did not undergo genetic testing as advised have been excluded from this cohort. All these 25 patients underwent detailed head-to-toe examination, record of all dysmorphic features, detailed anthropometry with the calculation of upper-lower segment ratios, and plotting of anthropometric measurements on WHO charts along with mid-parental height (wherever both parents were available). Detailed prenatal history, past history, developmental history, and family history were recorded. Most of the patients already had X-ray hands with wrist, thyroid profile which was recorded.

All patients with proportionate short stature patients underwent X-ray thoracic and lumbar spine (Anteroposterior and lateral views) and, those with disproportionate short stature, underwent a detailed skeletal survey. Further genetic investigations such as chromosomal microarray, methylation-sensitive multiplex ligation probe amplification (MS-MLPA), or next-generation sequencing (NGS) were done based on the overall evaluation and clinical diagnosis. Genetic testing was done with proper pretest counseling and informed consent. The data prioritization, filtering, and reporting on NGS were done as per standard American College of Medical Genetics guidelines.


Out of 25 patients, 17 were males and 8 were females. The age range of the cohort was 10 months–20 years. Overall, 20 out of 25 patients received a definitive diagnosis after genetic evaluation and testing.

Amongst 25, 20 patients were observed to have proportionate short stature where upper segment lower segment (US: LS) body ratios were within the normal range for age and five patients had disproportionate short stature, pointing towards the presence of skeletal dysplasia.

Out of 20, inspite of having proportionate body segments, 6 were suspected to be having skeletal dysplasia due to acromelia (small hands and feet) and associated skeletal abnormalities.

Among the remaining 14, genetic chromosomal or single gene syndromes were suspected in nine patients [Table 1-Case 1–9] and they underwent chromosomal microarray or exome sequencing. Two patients were confirmed to have Noonan syndrome and 2 children with Kabuki syndrome by exome sequencing. One child was suspected to have Prader–Willi syndrome and was confirmed to be having the same on methylation-specific MLPA.

Table 1:
Salient clinical features, genetic test/final diagnosis and management of cases 1–9 with proportionate short stature-genetic syndromic cause

Primordial short stature syndrome was suspected in four patients [Figure 1, Case 10–13]. One patient (Case 10) was confirmed to be having a chromosomal microdeletion disorder and the other was diagnosed to be having microcephalic osteodysplastic primordial short stature syndrome (MOPD) (case-11).

Figure 1:
Cases 10–13 with Primordial short stature

Familial short stature was the final diagnosis for a patient father affected duo (case 14) where genetic test ruled out autosomal dominant genetic syndrome of short stature.

In 5 cases with disproportion of upper and lower segment [Table 2-Cases 15–19], there were short limbs in 4 and short spine in 1.

Table 2:
Cases 15–25-Suspected skeletal dysplasia-salient clinical features, genetic testing, diagnosis and management

In these 5 cases along with another six patients with proportionate short stature, skeletal dysplasia was suspected due to the presence of acromelia (small hands/feet) or associated skeletal findings. The 11 patients underwent detailed X-rays and exome sequencing and skeletal dysplasia were confirmed in 7 out of these 11 patients [Table 2].

After definitive diagnosis, specific, targeted, and optimal patient management could be done. In 7 out of 25 cases, the children could be confidently started on growth hormone trial after diagnosis based on previous evidence of response in the particular genetic syndrome. Two patients with achondroplasia and 1 of hypochondroplasia were advised the recently Food and Drug Administration approved drug Vosoritide, which inhibits the overactive fibroblast growth factor receptor 3 (FGFR3) gene pathway in the disorder. Almost all patients needed supportive multidisciplinary management and advice from various specialists based on the diagnosis. Reproductive counseling, definite risk of recurrence, and option of prenatal test could be given in all 22 cases where an underlying variant/mutation was identified.

Case illustrations

Case-2: Proportionate short stature with dysmorphism

A 1-year-old female, 1st born to nonconsanguineous couple was referred in view of short stature, failure to thrive, and mild global developmental delay. Her parents noticed not gaining height and weight from 6 months of age in spite of her having a good appetite and no intercurrent illnesses. There was a mild delay in attaining milestones which were more in the motor domain than speech and cognition. At 1 year, she could sit, babble, respond to names and play with toys. At birth, length and weight were historically normal although there was no record available. There was a history of polyhydramnios during the third trimester of pregnancy in the mother. Her length was 64 cms (−3 to −4 SD for age), US: LS ratio was 1.6 (normal), head circumference was 47.5 cms (−1 to −2 SD), weight −6.3 kgs (−2 to −3 SD for age). Facial dysmorphism was noted [Figure 2] along with hyperpigmentation of skin over arms and legs and sparse scalp hair. Systemic examination was normal except mild hypotonia and brisk deep tendon reflexes (DTRs) in both legs.

Figure 2:
Case 2: (a) Dysmorphism- Downslant of eyes, Mild ptosis both eyes, hypertelorism, sparse hair, prominent tip of nose, long philtrum. (b) Skin Hyperpigmentation of legs

She had been extensively investigated before the referral to medical genetics. Magnetic resonance imaging brain and magnetic resonance angiography brain done at 7 months of age were normal. Metabolic profile including tandem mass spectrometry/urine gas chromatography–mass spectroscopy was done which was normal. Echocardiography had shown mild pulmonic stenosis. In view of short stature, polyhydramnios in the antenatal period with distinct facial features and mild pulmonic stenosis, we suspected Noonan syndrome or a Noonan-like genetic syndrome.

Whole exome sequencing was ordered after discussion of clinical differentials. Relevant human phenotype ontology (HPO) terms correlating with the main clinical features of the child were provided to the genetic test analyses team. A heterozygous missense variant c.146C > G (p. Pro49Arg) in the PPP1CB gene which has been previously reported in patients with “Noonan-like disorder with loose anagen hair 2-NSLAH” was found. This is a rare disorder with short stature, failure to thrive, mild developmental delay, characteristic facial features, right-sided congenital heart lesions (in 50%), and ectodermal abnormalities, particularly of hair and skin. Mild ventriculomegaly and cerebellar tonsillar herniation or Arnold chiari malformation have been reported before. In view of brisk DTRs and in the light of the diagnosis, the child was evaluated thoroughly for the Chiari malformation. On the basis of review of previous reported similar cases, we were able to provide definitive multidisciplinary management and guide the parents about an increased risk of some complications and prognosis. We could counsel and reassure parents about the low risk of recurrence in future offspring and could offer them a definitive prenatal test by fetal targeted mutation analysis.

Case 11-Severe proportionate primordial short stature

A 10-month-old girl, 1st born to nonconsanguineous couple, was referred in view of growth restriction noticed from 5 months of intrauterine period (Primordial). She was born at near term with birth weight of 1.1 kg. At 10 months, she weighed 2.9 kgs (−6 SD for age), and was 50.5 cms. long (−8 SD for age) and head size was 35.5 cms (−7SD) i.e., had the growth parameters of a neonate. There were no neonatal complications and there had been no health concerns other than the severe lag of growth. She had been gaining developmental milestones normally.

On examination-she had a triangular face, [Figure 3a] a prominent nose with overhanging columella. The voice was noticeably squeaky and high-pitched. An X-ray of the hand with wrist showed no carpal (capitate or hamate) bones suggesting severely delayed bone age. In view of severe intrauterine and infantile growth restriction, microcephaly, relatively preserved cognitive development, characteristic facial features, and typical voice, MOPD was suspected. Accordingly, exome sequencing was done to confirm the clinical suspicion and delineate the molecular defect. This identified pathogenic mutations in the PCNT gene [Figure 3b] consistent with Microcephalic osteodysplastic primordial dwarfism type II (MOPD-Type II). This is the most common form of primordial short stature syndrome and features which differentiate it from other forms of primordial dwarfism and that may necessitate treatment include abnormal dentition, a slender bone skeletal dysplasia with hip deformity and/or scoliosis, insulin resistance/diabetes mellitus, chronic kidney disease, cardiac malformations, and global vascular disease. The patient was advised to be followed and observed for these complications. MOPDII is an autosomal recessive condition with 25% risk of recurrence in offspring. Hence, the parents were counseled about prenatal tests in their subsequent pregnancy by fetal sampling and targeted testing for the mutations identified in this child.

Figure 3:
Case 11: (a) Facial features-Case 11-Triangular face, prominent nose and overhanging columella. (b) Mutations identified in PCNT gene

Case 19-Severe disproportionate short stature with short spine in 2 brothers

Two brothers 17 and 15 years old, born to consanguineous marriage, were referred for severe short stature and intellectual disability. The children were born with normal weight and height and lag of growth as compared to the peer group was noticed in 2nd year of life. By the time it was noticed in the first child, the mother was already pregnant with the second child. Slowly both children were lagging behind severely and at present, the height of the elder one was 99.5 cm and that of the younger one was 101 cm (average height of a 4-year-old boy) [Figure 4a]. They started having joint movement restriction and gradually progressive long bone deformities as well as curving of back from 4 years of age. There was a global developmental delay and at present both have mild to moderate intellectual disabilities.

Figure 4:
Case 19: (a) Affected brothers, 17 and 15 years old with nonaffected father. (b) short spine short stature, prominent joints, joint restriction. (c) X Ray Thoracolumbar spine, Lateral- Platyspondyly and double hump vertebrae (shown by arrow). (d) X ray Pelvis AP-Extreme irregularity of iliac crests- lacy appearance

On examination, they were observed to have disproportionate short stature. The US: LS ratio was 0.78 - normal 0.9, suggestive of short spine [Figure 4b]. Facial features were coarse with largemouth, abnormal dentition, and low anterior hairline. No corneal clouding was seen. Joint movement restriction can be noted [Figure 4b]. There was no organomegaly and the rest systemic examination was normal. The clinical differentials included genetic conditions of spondyloepiphyseal skeletal dysplasia with intellectual disability with coarse facial features. Mucopolysaccharidosis (esp. type IV) was screened for by urine chromatography for glycosaminoglycans and was found to be negative.

Skeletal survey revealed pathognomonic findings of Dyggve–Melchior–Clausen (DMC) syndrome, a Spondyloepiphyseal dysplasia with microcephaly, and intellectual disability with coarse facies. [Figure 4c and d].

Exome sequencing confirmed the diagnosis by revealing homozygous mutation in DYM gene c.1460 + 2T>C, Splice site donor/null variant, and loss of function consistent with the diagnosis of DMC syndrome.

Dyggve–Melchior–Clausen is a severe autosomal recessive spondyloepiphyseal skeletal dysplasia caused due to biallelic mutations in the DYM gene. The risk of recurrence in each subsequent pregnancy is 25%. In the reported family, the couple was desirous of a disease-free child but were very reluctant to plan pregnancy in view of both affected children. With the help of a definitive molecular cause, we were able to offer the family a definite risk of recurrence and the option of prenatal tests to detect the disease in the fetus at 12 weeks of pregnancy.


The prevalence of short stature is estimated to be varying from 2.8% to 3.7% in India.[4]

It is a common concern in parents during the growing age of children, as comparison with peers of similar age is inevitable in school, family, or neighborhood. Advice from pediatricians and referrals to pediatric endocrinologists is common and has remained stable over years to look for treatable causes. The gender difference in our small cohort of short stature (male: female ratio of 2:1), reflects the social fabric in the country for taking medical help and is depicted in other studies on short stature from India.[2]

The main determinant of height is chondrogenesis at the growth plate of bones which is regulated by multiple systemic factors as well as local factors. The systemic factors include nutritional intake, hormones, and inflammatory cytokines. Systemic diseases, such as hypothyroidism, celiac disease, and other chronic disorders can hence, impair growth.[5,6] Local factors regulating the growth plate in the bones include intracellular regulatory mechanisms in the growth plate chondrocytes, cartilage extracellular matrix components, and paracrine factors in the growth plate.

Polymorphism and mild mutations in the genes which regulate these functions in the growth plate, modulate height within the normal range and cause mild polygenic short stature. The mild mutations cause mild inhibition of a particular function in the growth plate and they can be inherited from one generation to the next. This forms part of the spectrum of normal variant short stature, including constitutional and familial short stature.[3] Mutations with a strong effect and thus affecting chondrogenesis significantly, cause relatively severe or pathologic short stature. With the advent of advanced genetic tests in clinics, the etiologic profile of short stature is undergoing a dynamic shift.[7]

Most of the etiologic studies on short stature till now, have found constitutional/familial short stature and hormonal causes such as hypothyroidism, type 1 diabetes, growth hormone deficiency, and chronic illnesses such as celiac disease as the most common cause followed by, skeletal diseases and genetic syndromes as less common causes.[6,8] However, with chronic diseases getting diagnosed earlier, thereby leading to less long-term complications such as short stature and increased genetic understanding of normal variant short stature such as familial short stature, the etiologic shift is happening toward the diagnosis of more genetic causes.

Among the genetic syndromic causes of short stature, the most common are Turner syndrome, Noonan syndrome, Neurofibromatosis type 1, Silver Russel syndrome, and Prader–Willi syndrome.[7] The present report lists the genetic diagnoses of short stature in the genetic clinic after initial evaluation by the primary physician and has a bias because of the exclusion of cases which were diagnosed and managed at the primary level and not referred.

Hence, the probable absence of Turner syndrome and Russel Silver syndrome in this cohort is because of their easily recognizable distinct clinical features and easily interpretable diagnostic genetic tests of karyotype and methylation study. The patients of Noonan syndrome, Kabuki syndrome as well as primordial short stature syndromes diagnosed had mild systemic features, subtle dysmorphism, or mild ID which can be easily missed in the eyes of a nonexpert.

Among the skeletal dysplasia group, achondroplasia and hypochondroplasia were diagnosed by the characteristic presentation of short limb short stature, typical radiographic features, and targeted mutation analysis of the FGFR3 gene. Dyggve–Melchior–Clausen syndrome, Geleophysic dysplasia, Kenny

Caffey syndrome, and Brachytelephalangic Chondrodysplasia punctata were suspected after careful analysis of clinical features and radiographs, followed by confirmation by genetic test.

The yield of genetic tests for etiologic diagnosis of short stature has varied from 30% to 50% in various studies.[9–11] The provision of appropriate HPO terms to the laboratory/clinical differentials can increase the yield of genetic tests such as exome sequencing. In the present cohort, a diagnosis was reached in 20 out of 25 patients (80%). A systematic approach [Figure 5] with identification of proportionate and disproportionate, primordial and postnatal cases, careful study of radiographic features as well as ordering and using genetic tests in an appropriate manner helps in achieving a high diagnostic yield. Exome sequencing reanalysis was done in two patients where clinical features were re-evaluated to suggest the differentials and genes to the laboratory, thus showcasing the importance of deep phenotyping and providing sufficient details to the genetic test analysis team to be able to optimally use these powerful technologies.

Figure 5:
Clinical pathway for the evaluation of a child with short stature. MPH: Mid parental height, US: LS: Upper segment: Lower segment

A definite molecular diagnosis helps in the personalized management of patients as enumerated in the result. Genetic testing sometimes is also essential for differentiation between normal variants and pathologic short stature. Familial short stature is increasingly being classified as a pathological variant with the recognition of hitherto undiagnosed genetic conditions such as GH resistance, collagenopathies, RASopathies, and aggrecan gene mutations.[2] Case 14 in our cohort was such a father–son duo who underwent genetic testing but were not found to harbor any definitive genetic mutation in known genes of short stature.


The cases described give a glimpse of genetic conditions in patients with short stature. It is imperative for clinicians to have a systematic detailed clinical approach as well as a clear understanding of the genetic tests to be able to use these new technologies to the fullest. There are several clinical pathways and protocols recommended by leading pediatric and genetic groups. Each clinic or hospital may develop its own protocol depending upon the clinical, radiologic, orthopedic, and laboratory facilities. The aim should be to have in place properly balanced and functional multi-disciplinary evidence-based short stature clinical service.

Conflicts of interest

There are no conflicts of interest.

Declaration of patient consent

The authors certify that they have obtained all appropriate patient consent forms. In the form, the patients have given their consent for their images and other clinical information to be reported in the journal. The patients understand that their names and initials will not be published and due efforts will be made to conceal their identity, but anonymity cannot be guaranteed.



Authors and contributions


1. Jee YH, Baron J. The biology of stature. J Pediatr 2016;173:32–8.
2. Raviteja KV, Das L, Malhotra B, Marwaha RK, Dutta P. Readdressing short stature in India:The “long and the short”of it. Indian J Endocrinol Metab 2021;25:389–91.
3. Jee YH, Andrade AC, Baron J, Nilsson O. Genetics of short stature. Endocrinol Metab Clin North Am 2017;46:259–81.
4. Pedicelli S, Peschiaroli E, Violi E, Cianfarani S. Controversies in the definition and treatment of idiopathic short stature (ISS). J Clin Res Pediatr Endocrinol 2009;1:105–15.5.
5. Nilsson O, Marino R, De Luca F, Phillip M, Baron J. Endocrine regulation of the growth plate. Horm Res 2005;64:157–65.
6. Rajput R, Rani M, Rajput M, Garg R. Etiological profile of short stature in children and adolescents. Indian J Endocrinol Metab 2021;25:247–51.
7. Polidori N, Castorani V, Mohn A, Chiarelli F. Deciphering short stature in children. Ann Pediatr Endocrinol Metab 2020;25:69–79.
8. Gutch M, Sukriti K, Keshav GK, Syed MR, Abhinav G, Annesh B, et al. Etiology of short stature in Northern India. J ASEAN Fed Endocr Soc 2016;31:23.
9. Andrade NL, Funari MF, Malaquias AC, Collett-Solberg PF, Gomes NL, Scalco R, et al. Diagnostic yield of a multigene sequencing approach in children classified as idiopathic short stature. Endocr Connect 2022;11:e220214.
10. Hauer NN, Popp B, Schoeller E, Schuhmann S, Heath KE, Hisado-Oliva A, et al. Clinical relevance of systematic phenotyping and exome sequencing in patients with short stature. Genet Med 2018;20:630–8.
    11. Kim YM, Lee YJ, Park JH, Lee HD, Cheon CK, Kim SY, et al. High diagnostic yield of clinically unidentifiable syndromic growth disorders by targeted exome sequencing. Clin Genet 2017;92:594–605.

    Achondroplasia; Noonan; Primordial dwarfism; Short stature; Skeletal dysplasia

    Copyright: © 2023 Apollo Medicine