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FGFR3 N540S variant exhibits phenotypic heterogeneity between proportionate short stature and hypochondroplasiaGenetic Testing Reveals New Variety of Short Stature Cause

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Key Takeaway
Note that the FGFR3 N540S variant can present as proportionate short stature rather than typical hypochondroplasia.

This case report describes the identification of the FGFR3 variant (c.1619A>G, p.N540S) in a 3-year-old male with proportionate short stature. The study involved a small sample size of 3 individuals, including the proband, his mother, and his maternal grandfather, all of whom harbored the heterozygous variant. The variant was classified as likely pathogenic by ACM1 guidelines.

A key finding is the phenotypic heterogeneity associated with the FGFR3 N540S variant. While the proband presented with proportionate short stature and no dysmorphic features, previous cases of this specific variant were associated with hypochondroplasia (HCH) and abnormal radiographic features.

The authors note the limitations of the study due to the small sample size inherent in a case report. Clinical practice relevance includes the importance of genetic investigation in cases of idiopathic short stature to identify specific variants and understand the diversity of clinical presentations associated with those variants.

How this fits prior evidence

This case report addresses a gap in the clinical characterization of the FGFR3 N540S variant. While previous coverage noted that growth hormone therapy in idiopathic short stature shows no significant ocular biometric changes, this report highlights the importance of genetic investigation to differentiate between idiopathic short stature and conditions like hypochondroplasia, where other treatments like Vosoritide may be relevant.

Doctors studied a 3-year-old boy and his relatives who all had short stature. They used whole-exome sequencing to look at the family's DNA. They found a specific genetic variant in the FGFR3 gene. This variant was also found in the boy's mother and his maternal grandfather.

While this specific genetic variant usually causes a condition called hypochondroplasia, it appeared differently in this family. The young boy had proportionate short stature without the typical physical features usually seen with this mutation. This shows that the same genetic change can look different in different people.

Because this is a single case report involving only three people, the findings are limited. It does not provide a broad conclusion for all patients. However, it highlights why genetic testing is important for children with unexplained short stature. It shows that one gene can have different effects, making personalized testing a useful tool for doctors.

What this means for you:
A specific gene variant can cause different types of short stature in different people, highlighting the need for genetic testing.

Common questions

What did the genetic test reveal about the child's growth?

The test identified a specific variant in the FGFR3 gene. While this variant usually causes a condition called hypochondroplasia, it caused proportionate short stature in this 3-year-old boy. This finding shows that the same genetic mutation can result in different physical appearances in different patients.

How many people were involved in this study?

This was a case report involving a small group of three people: a 3-year-old boy and his mother and maternal grandfather. Because the sample size is very small, these results are specific to this family and do not represent a large population.

Why is this finding important for children with short stature?

This case shows that genetic testing is important for children with idiopathic short stature. It demonstrates that one specific gene can cause different types of growth issues. This helps doctors understand that different symptoms can stem from the same underlying genetic cause.

Study Details

Study typeSystematic review
EvidenceLevel 1
PublishedSep 2026
View Original Abstract ↓
ObjectiveTo report the identification of a FGFR3 gene variant in a family with idiopathic short stature, characterized by proportionate stature and the absence of dysmorphic features, and to highlight the importance of genetic investigation in ISS as well as the clinical heterogeneity of the FGFR3 N540S variant.MethodsBased on clinical and genetic data collected from the proband and short-statured relatives, we analyzed the clinical characteristics of the pedigree and the pathogenicity of the genetic variant.ResultsA 3-year-old male presented with proportionate short stature and no dysmorphic features. Imaging studies revealed no significant skeletal abnormalities. Combined with the short stature observed in multiple family members, a clinical diagnosis of FSS was established. Whole-exome sequencing identified a maternally inherited heterozygous FGFR3 variant (c.1619A>G, p.N540S) in the proband. The mother and maternal grandfather also harbored this variant. ACMG classification deemed it likely pathogenic. Literature review revealed that all previously reported patients with the FGFR3 N540S variant exhibited clinical manifestations of HCH with abnormal radiographic features.ConclusionThis is the first report of proportionate short stature associated with the FGFR3 N540S variant, demonstrating substantial phenotypic heterogeneity at this site. Genetic testing is strongly recommended for patients with FSS, particularly those with severe short stature.
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