New mutations and an updated database for the patched‐1 (PTCH1) gene

Abstract Background Basal cell nevus syndrome (BCNS) is an autosomal dominant disorder characterized by multiple basal cell carcinomas (BCCs), maxillary keratocysts, and cerebral calcifications. BCNS most commonly is caused by a germline mutation in the patched‐1 (PTCH1) gene. PTCH1 mutations are also described in patients with holoprosencephaly. Methods We have established a locus‐specific database for the PTCH1 gene using the Leiden Open Variation Database (LOVD). We included 117 new PTCH1 variations, in addition to 331 previously published unique PTCH1 mutations. These new mutations were found in 141 patients who had a positive PTCH1 mutation analysis in either the VU University Medical Centre (VUMC) or Maastricht University Medical Centre (MUMC) between 1995 and 2015. Results The database contains 331 previously published unique PTCH1 mutations and 117 new PTCH1 variations. Conclusion We have established a locus‐specific database for the PTCH1 gene using the Leiden Open Variation Database (LOVD). The database provides an open collection for both clinicians and researchers and is accessible online at http://www.lovd.nl/PTCH1.

In 1996, the patched-1 (PTCH1) gene (MIM#601309) was first reported as a candidate gene for BCNS. Two different heterozygous mutations in the PTCH1 gene were identified in two patients with Gorlin syndrome (Johnson et al., 1996). Another disorder that is caused by a germline mutation in the PTCH1 gene is holoprosencephaly-7 (MIM#610828), a structural anomaly of the brain in which there is failed or incomplete separation of the forebrain early in gestation. In addition, the vast majority of sporadic BCCs have somatic mutations in PTCH1 (Bonilla et al., 2016;Reifenberger et al., 2005).

| The PTCH1 gene
PTCH1 (NCBI Reference Sequence NM_000264.3) is the human homolog of the Drosophila patched-1 gene and is located on chromosome 9q22.3. It contains 24 exons with the transcriptional start site in exon 1 and the termination site in exon 23. PTCH1 encodes a 1447-amino acid transmembrane glycoprotein, which is part of the hedgehog (Hh) pathway. The Hh pathway is a key regulator in embryonic development and tumorigenesis controlling cell differentiation, tissue polarity, and cell proliferation.
The function of the PTCH1 protein is inhibition of the transmembrane protein Smoothened (SMO). Extracellular Hh ligands can bind to the PTCH1 receptor, releasing this inhibition, allowing SMO to signal downstream and activate GLI transcription factors. Based on this role in preventing cells from uncontrolled proliferation, PTCH1 is seen as a tumor suppressor gene. SMO on the other hand acts as an oncogene (Kogerman et al., 2002).
The typical congenital features of BCNS seem to occur due to haploinsufficiency (Wicking et al., 1997), while tumors in BCNS are believed to develop according to the two-hit hypothesis described by Knudson, (2001)and Pan, Dong, Sun, & Li, (2010. In the latter, either both alleles of the gene harbor a mutation, or one mutated allele is accompanied by allelic loss of the remaining wild-type allele. Recent mouse model studies show that haploinsufficiency of PTCH1 may be sufficient for the development of medulloblastoma and rhabdomyosarcoma, so tumor formation not always follows the two-hit hypothesis (Calzada-Wack et al., 2002;Zurawel, Allen, Wechsler-Reya, Scott, & Raffel, 2000). With DNA sequencing analysis of the PTCH1 gene, mutation detection frequency ranges from 50% to 85% in individuals with typical findings of BCNS (Lam, Ou, & Billingsley, 2013). Mosaic presentations of BCNS can occur (Reinders et al., 2016;Torrelo et al., 2013).

| Ethical compliance
Our study was approved by the independent ethics committee of our hospital.

| The PTCH1 database
We have established a database for PTCH1 using the Leiden Open Variation Database (LOVD) version 3.0 (Variants of patched 1 (PTCH1), 2004). The purpose of this database is to assemble molecular variants of the PTCH1 gene in a standardized format. The database provides an open collection for both clinicians and researchers containing published and unpublished PTCH1 mutations.
For each mutation, information is provided at the molecular level: DNA change, predicted protein change, RNA change, exon, type of mutation, reported pathogenicity, technique used, and source of material, and phenotype information if available. The Sequence Variant Nomenclature of all mutations (new and published) is updated according to the latest guidelines of the Human Genome Variation Society (HGVS) version 15.11 and based on NCBI Reference Sequence NM_000264.3. T A B L E 1 Diagnostic criteria for basal cell nevus syndrome (Bree & Shah, 2011). Two major criteria, one major criterion and two minor criteria, or one major and genetic confirmation is required for diagnosis
The majority of patients were from the Netherlands (68%, 76/110). The age of DNA test ranged from 0 to 70 years, with a mean age of 26.5 years. Motivations for genetic testing written on the application forms were: (1) clinical suspicion of BCNS (47.4%); (2) clinical diagnosis of BCNS (32.6%); (3) first-degree family member with BCNS (16.8%); and (4) family members with symptoms of BCNS (3.2%). In total, four individuals were prenatally screened for BCNS, because of a first-degree family member or a clinical suspicion based on ultrasonography.

DATABASE AVAILABILITY
The data are accessible to the public at http://www.lovd.nl/ PTCH1. Contributors will have to register for a login and password.