Associated disorders

The GALNT12 gene has preliminary evidence supporting a correlation with colorectal cancer (MedGen UID: 324734).

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The GALNT12 gene encodes an enzyme that attaches sugars to proteins. These sugars are important for regulating the signaling of the Wnt and TGF-beta signaling pathways, which are known to be involved in colorectal carcinogenesis.

GALNT12 heterozygote
MedGen UID: 324734

Clinical condition
While there is currently no well-established data to associate the GALNT12 gene with a specific disease or condition, there is preliminary evidence suggesting variants in this gene may be associated with a predisposition to colorectal cancer (PMID: 22461326 19617566 ). These data, however, are currently insufficient to make a clear determination regarding this association. The risk for other cancers may be elevated in individuals with GALNT12 variants; however, this evidence is also limited and emerging.

GALNT12 is considered a “preliminary-evidence” gene by Invitae. 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
GALNT12 encodes a member of a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases, which catalyze the transfer of N-acetylgalactosamine (GalNAc) from UDP-GalNAc to a serine or threonine residue on a polypeptide acceptor in the initial step of O-linked protein glycosylation (NCBI Gene. Gene ID: 79695. Accessed October 2015).

Variants in GALNT12 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.

Medical management and surveillance protocols for individuals with a pathogenic variant in GALNT12 have been developed by the National Comprehensive Cancer Network (NCCN) (NCCN Clinical Practice Guidelines in Oncology: Genetic/Familial High-Risk Assessment: Colorectal. Version 1.2016):

  • If no personal history of colorectal cancer but there is a diagnosis of colorectal cancer in a first-degree relative, colonoscopy is recommended every 5 years beginning at age 40, or 10 years prior to the first-degree relative’s age at diagnosis.
  • If there is no personal history of colorectal cancer and no diagnosis of colorectal cancer in a first-degree relative, colonoscopy is recommended every 5 years beginning at age 40.

Knowing if a pathogenic GALNT12 variant is present is advantageous. At-risk relatives can be identified, enabling pursuit of a diagnostic evaluation. Further, the available information regarding hereditary cancer susceptibility genes is constantly evolving and more clinically relevant data regarding GALNT12 are likely to become available in the near future. Awareness of this cancer predisposition encourages patients and their providers to inform at-risk family members, to diligently follow published screening protocols, and to be vigilant in maintaining close and regular contact with their local genetics clinic in anticipation of new information.

Review Date: July 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
GALNT12 NM_024642.4