Invitae Legius Syndrome Test


Test description

The Invitae Legius Syndrome Test analyzes SPRED1, a gene that is associated with Legius syndrome. Legius syndrome is one of the RASopathies, which are a class of pediatric disorders associated with genes that are members of the mitogen-activated protein kinase (Ras/MAPK) pathway. This pathway is involved in a signal transduction cascade that is necessary for the proper formation of several types of tissue during embryonic and postnatal development.

Legius syndrome is characterized by café-au-lait macules, axillary and inguinal freckling, macrocephaly, and lipomas. Genetic testing of this gene may establish or confirm a diagnosis and help guide treatment and management decisions. Identification of a disease-causing variant would also enable testing and diagnosis of at-risk relatives.

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Primary panel (1 gene)


Add-on neurofibromatosis type 1 gene (1 gene)

The RASopathies exhibit numerous overlapping phenotypic features due to their common underlying Ras/MAPK pathway dysregulation. Legius syndrome overlaps clinically with neurofibromatosis type 1 (NF1): Both are characterized by the presence of multiple café-au-lait spots and axillary and inguinal freckling, but Legius syndrome lacks NF1-specific features like neurofibromas, Lisch nodules, and optic gliomas. For this reason (and depending on the clinical presentation of the patient), clinicians may wish to include NF1 in this test for a broader analysis.


Alternative tests to consider

The RASopathies are multisystemic disorders whose expressions are highly variable, even among family members. Many of the clinical features that can differentiate RASopathy conditions manifest later in childhood or change with age, making accurate clinical diagnosis difficult. The phenotypes of many RASopathy conditions are expanding: Individuals are being discovered with a molecular genetic finding in a RASopathy gene but clinical findings that are not typically described in the specific condition associated with that gene. Additionally, some genes are associated with more than one RASopathy syndrome.

Testing for Legius syndrome is also included in the broader Invitae RASopathies Comprehensive Panel. Depending on the individual’s clinical and family history, this broader panel may be appropriate and can be ordered for no additional charge.

Legius syndrome

Legius syndrome is characterized by the presence of multiple café-au-lait spots and axillary and inguinal freckling. The disorder is quite similar to and may be misdiagnosed as neurofibromatosis type 1; however, individuals with Legius syndrome have a notable absence of neurofibromas, Lisch nodules, and optic gliomas. Variable features of the disorder may include macrocephaly, learning disabilities, hyperactivity, and lipomas. Individuals with Legius syndrome often have normal intelligence.

Diagnosing Legius syndrome based solely on clinical findings is difficult. Detecting a pathogenic variant in SPRED1 is necessary to make a diagnosis. To date, only approximately 200 individuals have been identified as having pathogenic SPRED1 variants. The majority of these data reflect groups of patients who tested negative for NF1. An estimated 3%-8% of patients who have clinical characteristics consistent with NF1 but do not have an identifiable pathogenic variant in the NF1 gene will carry a pathogenic SPRED1 variant. Based on the SPRED1 mutation database (accessible online at, an estimated 90% of variants would be detected by sequence analysis and approximately 9% would be detected by deletion/duplication analysis.

Legius syndrome is inherited in an autosomal dominant pattern.

Legius syndrome is completely penetrant with variable expressivity. The majority of individuals with Legius syndrome have abnormal pigmentation, but the age of onset for café-au-lait spots and freckling is not well established.

The prevalence of Legius syndrome is not directly known. Pathogenic variants in SPRED1 have been identified in approximately 200 individuals with a clinical diagnosis of Legius syndrome. An estimated 1%-4% of individuals with multiple café-au-lait spots have Legius syndrome.

Genetic testing for Legius syndrome should be considered in individuals with abnormal pigmentation (multiple café-au-lait spots with or without axillary and inguinal freckling) and a lack of other features related to neurofibromatosis type 1 (neurofibromas, Lisch nodules, and optic gliomas). Testing can also be considered for individuals who have a family history in which multiple family members have numerous café-au-lait spots or axillary and inguinal freckling.

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
NF1 NM_000267.3
SPRED1 NM_152594.2