Invitae ARSE-Related Chondrodysplasia Punctata Test


Test description

The Invitae ARSE-Related Chondrodysplasia Punctata Test analyzes the ARSE gene, which is associated with a bone-and-cartilage-development disorder, X-linked chondrodysplasia punctata 1 (CDPX1). Genetic testing of this gene may confirm a diagnosis and help guide treatment and management decisions. Identification of a disease-causing variant can inform recurrence-risk assessment and genetic counseling.

Order test

Primary panel (1 gene)


Add-on NSDHL-related congenital hemidysplasia with ichythyosiform erythroderma and limb defects (CHILD) syndrome (1 gene)

NSDHL-related congenital hemidysplasia with ichthyosiform erythroderma and limb defects (CHILD) syndrome has clinical findings that overlap with chondrodysplasia punctata (CDP). In addition to CDP, individuals with CHILD syndrome have ichthyosis, limb defects, and visceral anomalies. Depending on the clinical presentation of the patient, clinicians may wish to broaden the analysis by including NSDHL. This gene can be added at no additional charge.


X-linked chondrodysplasia punctata (CDPX1) is characterized by stippled epiphyses that typically involve the ankle, toes, and fingers, although other bones may be affected. Males have shortened fingers and distinct facial features that include a flattening of the nasal bridge and nose. Calcifications of cartilage, particularly in the trachea, larynx, and bronchi, can cause breathing problems. Less commonly, features of developmental delay, hearing loss, vision abnormalities, or heart defects have been reported. Carrier females are not affected; however, some carrier females have been noted to have short stature.

Approximately 60%–75% of males with CDPX1 have a pathogenic sequence variant in ARSE. Contiguous Xp gene deletions that include ARSE may account for up to 25% of patients with CDPX1; however, the deletions can extend through to STS, XG, and MIC2X and present with additional features including ichthyosis, intellectual disability, anosmia, and hypogonadotropic hypogonadism.

Chondrodysplasia punctata 1 (CDPX1) is inherited in an X-linked dominant pattern.

CDPX1 is highly penetrant and exhibits clinical variability. While most male individuals have some features of varying severity, unaffected carrier males have also been described.

In one study, the prevalence of chondrodysplasia punctata was estimated at 1 in 500,000.

This test may be considered for male patients presenting with chondrodysplasia punctata, brachytelephalangy, and nasomaxillary hypoplasia.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence, and select noncoding variants. Our assay provides a Q30 quality-adjusted mean coverage depth of 350x (50x minimum, or supplemented with additional analysis). Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods, except individual variants that have high quality scores and previously validated in at least ten unrelated samples.

Our analysis detects most intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. If you are requesting the detection of a specific single-exon copy number variation, please contact Client Services before placing your order.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
ARSE NM_000047.2
NSDHL NM_015922.2