Benign Tumors Associated With Heterozygous NTHL1 Variant

NTHL1 is a tumor suppressor gene involved in base excision repair. It is associated with an increased risk for colorectal and breast cancer when two variant gene copies are inherited. However, inheriting one variant NTHL1 copy is not associated with increased tumor risk. Genetic counselors report heterozygous NTHL1 mutations as benign. We present the case of a 22-year-old patient with a heterozygous NTHL1 variant who developed an arm schwannoma, spinal schwannoma, and hepatic hemangioma. The patient also reported feeling multiple other bumps on his body but did not seek medical care due to a lack of symptoms. This case suggests that heterozygous NTHL1 variants may be implicated in tumor development.

Rare loss of function variants in candidate genes and risk of colorectal cancer

Although ~ 25% of colorectal cancer or polyp (CRC/P) cases show familial aggregation, current germline genetic testing identifies a causal genotype in the 16 major genes associated with high penetrance CRC/P in only 20% of these cases. As there are likely other genes underlying heritable CRC/P, we evaluated the association of variation at novel loci with CRC/P. We evaluated 158 a priori selected candidate genes by comparing the number of rare potentially disruptive variants (PDVs) found in 84 CRC/P cases without an identified CRC/P risk-associated variant and 2440 controls. We repeated this analysis using an additional 73 CRC/P cases. We also compared the frequency of PDVs in select genes among CRC/P cases with two publicly available data sets. We found a significant enrichment of PDVs in cases vs. controls: 20% of cases vs. 11.5% of controls with ≥ 1 PDV (OR = 1.9, p = 0.01) in the original set of cases. Among the second cohort of CRC/P cases, 18% had a PDV, significantly different from 11.5% (p = 0.02). Logistic regression, adjusting for ancestry and multiple testing, indicated association between CRC/P and PDVs in NTHL1 (p = 0.0001), BRCA2 (p = 0.01) and BRIP1 (p = 0.04). However, there was no significant difference in the frequency of PDVs at each of these genes between all 157 CRC/P cases and two publicly available data sets. These results suggest an increased presence of PDVs in CRC/P cases and support further investigation of the association of NTHL1, BRCA2 and BRIP1 variation with CRC/P.