Associated disorders

The CTNNA1 gene has preliminary evidence supporting a correlation with hereditary diffuse gastric cancer (HGDC).

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Invitae tests that include this gene:

The CTNNA1 gene encodes alpha-1 catenin, one of three cytoplasmic proteins that anchor E-cadherin to the cytoskeleton. Dysfunction of this process allows cancer cells to separate from the primary tumor nodules, which may contribute to cancer invasion and metastasis.

CTNNA1 heterozygote
OMIM: 116805

Clinical condition
The CTNNA1 gene currently has no well-established disease association; however, there is preliminary evidence supporting a correlation with autosomal dominant hereditary diffuse gastric cancer (PMID: 23208944, 26182300, 26364057, 26380059). These data, however, are currently insufficient to make a clear determination regarding this association. Therefore, CTNNA1 is considered a “ preliminary-evidence” gene and is available on Invitae’s Gastric Cancer Panel. Preliminary-evidence genes are selected from an extensive review of the literature and expert recommendations, but the association between the gene and the specific condition has not been completely established. This uncertainty may be resolved as new information becomes available, and therefore clinicians may continue to order these preliminary-evidence genes.

Gene information
CTNNA1 associates with the cytoplasmic domain of a variety of cadherins; however, the precise function of the encoded protein is uncertain. It has been suggested that CTNNA1 may play a crucial role in cell differentiation, regulating actin filament assembly, and inhibiting actin branching (UniprotKB – P35221 (CTNA1_HUMAN) http://www.uniprot.org/uniprot/P35221. Accessed March 2016).

Variants in CTNNA1 have autosomal dominant inheritance. This means that an individual with a pathogenic variant has a 50% chance of passing that variant on to their offspring.

Because the evidence regarding CTNNA1 and hereditary diffuse gastric cancer is limited and preliminary, there are no guidelines or recommendations to suggest alteration to medical management based solely on the presence of a CTNNA1 variant. However, an individual’s cancer risk and medical management are not determined by genetic test results alone. Overall cancer risk assessment incorporates additional factors including personal medical history, family history, and any available genetic information that may result in a personalized plan for cancer prevention and surveillance.

Even though data regarding CTNNA1 are preliminary, knowing if a pathogenic variant is present is advantageous. At-risk relatives can be identified, allowing pursuit of a diagnostic evaluation. In addition, the available information regarding hereditary cancer susceptibility genes is constantly evolving and clinically relevant CTNNA1 data is likely to become available in the near future. Awareness of this variant encourages patients and their providers to inform at-risk family members, to consider implementing established screening protocols, and to be vigilant in maintaining close and regular contact with their local genetics clinic in anticipation of new information.

Review Date: March 2016

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
CTNNA1 NM_001903.3