Invitae Holoprosencephaly Panel


Test description

The Invitae Holoprosencephaly Panel analyzes up to seven genes that are associated with holoprosencephaly, a wide spectrum of brain malformations that are a result of incomplete development of the brain early in gestation. These genes were selected based on the available evidence to date to provide Invitae’s broadest test for holoprosencephaly.

Genetic testing of these genes may confirm a diagnosis and help guide treatment and management decisions. Identification of a disease-causing variant can inform recurrence-risk assessment and guide genetic counseling.

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Primary panel (5 genes)


Add-on preliminary-evidence genes (2 genes)

Preliminary-evidence genes currently have early evidence of a clinical association with the specific disease covered by this test. Some clinicians may wish to include genes which do not currently have a definitive clinical association, but which may prove to be clinically significant in the future. These genes can be added at no additional charge. Visit our Preliminary-evidence genes page to learn more.


Holoprosencephaly (HPE) encompasses a spectrum of cerebral and facial malformations that occur when the forebrain fails to divide along the midline into distinct hemispheres during early embryonic development. HPE severity ranges from partial division of the forebrain to complete absence of the midline and accompanying clinical presentation, which is typically correlated with the degree of cerebral malformation and ranges from closely spaced eyes or a single central maxillary incisor to a single cyclopic eye and the presence of a proboscis (nose-like appendage). The majority of individuals with HPE have intellectual disability. Incomplete penetrance and widely variable expressivity, even within the same family, are observed.

The clinical sensitivity is up to 47% with a positive family history and 7% in cases with no family history.

Holoprosencephaly is inherited in an autosomal dominant pattern. De novo variants have been well-described in SHH (10%–30%), SIX3 (10%–20%), and ZIC2 (70%–80%).

Incomplete penetrance and widely variable expressivity, even within the same family, have been observed in cases of holoprosencephaly.

The incidence of holoprosencephaly is 1 in 10,000 live births.

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
CDON NM_016952.4
GLI2 NM_005270.4
PTCH1 NM_000264.3
SHH NM_000193.2
SIX3 NM_005413.3
TGIF1 NM_173208.2
ZIC2 NM_007129.3