IntroductionNevoid basal cell carcinoma syndrome (NBCCS) is a rare autosomal dominant disorder classically associated with multiple basal cell carcinomas, odontogenic keratocysts and skeletal anomalies. However, its significant phenotypic heterogeneity often delays the diagnosis. Here, we undertake the first comprehensive characterisation of NBCCS and congenital urinary tract anomalies.MethodsClinical evaluation followed by genetic testing was performed on a proband with congenital hydronephrosis due to ureteropelvic obstruction. Then, a cohort of patients with molecularly confirmed NBCCS evaluated at a single institution was analysed, followed by a comprehensive review of the literature.ResultsThe novel, non-canonical splice-site variant c.349+4 delA inPTCH1was detected in a proband, with RNA analysis confirming exon 2 skipping. Of the additional nine NBCCS cases examined at our institution, a second proband with a nonsense variant inPTCH1was identified with renal agenesis and a bladder diverticulum. A literature review then yielded 11 case reports of patients with congenital urinary tract anomalies, most frequently renal agenesis.DiscussionCongenital urinary tract anomalies are a variable finding in NBCCS. Renal ultrasound may be warranted at the time of initial diagnosis, if not previously performed. Moreover,PTCH1should be included in multigene panels that assess for congenital urinary tract disorders.

Supplementary Table 5: Summary of the hereditary cancer germline sequencing performed for each patient in the MPC cohort

Supplementary Table 6: Sensitivity analysis comparing treatment received for each cancer diagnosis, with the exclusion of all skin cancer cases.

Supplementary Table 2: Summary of patients with pathogenic variants identified in the MPC cohort

Supplementary Table 3: Summary of patients without hereditary cancer susceptibility identified in the MPC cohort

Bryant-Li-Bhoj syndrome (BLBS), which became OMIM-classified in 2022 (OMIM: 619720, 619721), is caused by germline variants in the two genes that encode histone H3.3 (H3-3A/H3F3A and H3-3B/H3F3B) [1-4]. This syndrome is characterized by developmental delay/intellectual disability, craniofacial anomalies, hyper/hypotonia, and abnormal neuroimaging [1, 5]. BLBS was initially categorized as a progressive neurodegenerative syndrome caused by de novo heterozygous variants in either H3-3A or H3-3B [1-4]. Here, we analyze the data of the 58 previously published individuals along 38 unpublished, unrelated individuals. In this larger cohort of 96 people, we identify causative missense, synonymous, and stop-loss variants. We also expand upon the phenotypic characterization by elaborating on the neurodevelopmental component of BLBS. Notably, phenotypic heterogeneity was present even amongst individuals harboring the same variant. To explore the complex phenotypic variation in this expanded cohort, the relationships between syndromic phenotypes with three variables of interest were interrogated: sex, gene containing the causative variant, and variant location in the H3.3 protein. While specific genotype-phenotype correlations have not been conclusively delineated, the results presented here suggest that the location of the variants within the H3.3 protein and the affected gene (H3-3A or H3-3B) contribute more to the severity of distinct phenotypes than sex. Since these variables do not account for all BLBS phenotypic variability, these findings suggest that additional factors may play a role in modifying the phenotypes of affected individuals. Histones are poised at the interface of genetics and epigenetics, highlighting the potential role for gene-environment interactions and the importance of future research.

Supplementary Table 4: Number of genes tested over time in the MPC patient cohort and its effect on hereditary cancer sequencing results

Supplementary Table 1: Summary of occupational exposures and modifying chronic health conditions in the MPC patient cohort

Supplementary Figure 1: Flow diagram of patients evaluated with the selection criteria sequentially applied in order to define the triple primary cancer cohort for further analysis.

Raine syndrome (RS) is an autosomal recessive disorder characterized by distinctive facial dysmorphisms and generalized osteosclerosis of periosteal bone causing exophthalmos, choanal atresia or stenosis, osteosclerosis and intracranial calcifications. The syndrome is caused by biallelic loss-of-function variants in FAM20C located on chromosome 7p22.3. FAM20C is an ubiquitously expressed protein kinase. that contains five functional domains including a catalytic domain, a binding pocket for FAM20A and three distinct N-glycosylation sites. With an estimated prevalence of one in a million, Raine syndrome is exceptionally rare, with fewer than 50 cases reported in the literature to date with both lethal and non-lethal outcomes in affected neonates. Identification of mutations in FAM20C are paramount to understanding the various phenotypic presentations of RS and understanding the disease pathology and to establish genotype-phenotype correlations. Monozygotic diamniotic female twins were born to non-consanguineous parents with craniofacial dysmorphisms including proptosis, hypertelorism, absent nasal bridge, anteverted nares, midface hypoplasia, microretrognathia, frontal bossing, and craniosynostosis. The twins were born prematurely at 28 weeks due to pregnancy complications of polyhydramnios and premature rupture of membrane. Rapid exome sequencing of Twin A confirmed he was homozygous for the pathogenic variant FAM20C c.1007T>C, p.Met336Arg. The same variant was confirmed to be present on both alleles for Twin B and phenotype was identical. Review of the literature found that the variant was previously reported in the literature in a infant born with a very similar phenotype, specially the craniofacial abnormalities as our institution's twin cases. Both twins passed away at four weeks post-delivery due to respiratory failure. We report on the first case of twin newborns with pathogenic mutations in FAM20C resulting in lethal RS. Syndromic features, including choanal atresia, micrognathia, exophthalmos, and generalized osteosclerosis, align with the previously reported RS phenotype associated with the same variant. This suggests a genotype-phenotype correlation that is very complex in a rare disease like RS. n silico analysis and mapping of the variant on a three-dimensional (3D) model of FAM20C it is predicted to be deleterious and to affect N-glycosylation, protein folding, and subsequent secretion of FAM20C. Discovering new variants in FAM20C is crucial for understanding the diverse phenotypic manifestations of RS and gaining insights into the pathology of the disease.

ATP1A1 encodes a sodium-potassium ATPase that has been linked to several neurological diseases. Using exome and genome sequencing, we identified the heterozygous ATP1A1 variant NM_000701.8: c.2707G>A;p.(Gly903Arg) in two unrelated children presenting with delayed motor and speech development and autism. While absent in controls, the variant occurred de novo in one proband and co-segregated in two affected half-siblings, with mosaicism in the healthy mother. Using a specific ouabain resistance assay in mutant transfected HEK cells, we found significantly reduced cell viability. Demonstrating loss of ATPase function, we conclude that this novel variant is pathogenic, expanding the phenotype spectrum of ATP1A1.

Sex chromosome aneuploidies (SCA) such as Turner, Klinefelter, Jacobs, and Trisomy X syndromes are prevalent genetic disorders with well-established phenotypes. Challenges persist, however, in determining the need for further genetic evaluation in cases of affected individuals exhibiting atypical symptoms. The present study retrospectively examined 54 pediatric patients with an SCA diagnosis at a single institution between January 2015 and December 2023. Twelve patients (22.2%) exhibited a discordant phenotype, of which five were confirmed to have a distinct monogenic disorder, a diagnostic rate of 41.7%. The monogenic conditions identified included DNAH5-related primary ciliary dyskinesia, Burn-McKeown syndrome, Tatton-Brown-Rahman syndrome, SETD1B-related neurodevelopmental disorder, and SET-related disorder. The median age at SCA diagnosis was 3.5 months versus 7.0 years for the second genetic condition, indicating significant diagnostic delays. Our findings highlight the importance of comprehensive genetic evaluation in pediatric patients with SCA who exhibit atypical phenotypes.

KIF21A encodes a kinesin motor protein associated with isolated congenital fibrosis of the extraocular muscles (CFEOM), which occurs when the autoinhibitory interaction between its motor and third coiled-coil domains is disrupted. In this study, we describe a female child who is heterozygous for a novel de novo missense variant in KIF21A p.Leu664Pro, located in the second coiled-coil domain that was absent in her unaffected parents and in healthy population cohorts. She presented with progressive peripheral neuropathy, hypoplasia of the corpus callosum and strabismus in the absence of CFEOM. Protein modelling predicts that the KIF21A variant leads to significant alterations in its structure as well as binding with TUBB3. Co-immunoprecipitation data was consistent with decreased binding of KIF21A p.Leu664Pro to TUBB3 in vitro compared with reference. Taken together, we delineate a KIF21A-related phenotype defined by progressive peripheral neuropathy, brain anomalies, developmental delay and comitant strabismus potentially stemming from the disruption of the interaction between KIF21A and TUBB3.

Rare diseases affect 6%-8% of the population and present diagnostic challenges, particularly for historically marginalized ethnic and racial groups. The Undiagnosed Diseases Network (UDN) aims to enhance diagnosis rates and research participation among such minoritized groups. A retrospective review was conducted from 2015 to 2023, analyzing 2235 UDN participants to evaluate its progress toward this objective. Data on demographics, disease phenotypes, diagnostic outcomes, and socioeconomic factors were collected and statistical analyses assessed differences among ethnic and racial groups. This demonstrated that Hispanic and Black non-Hispanic groups were underrepresented, while White non-Hispanic participants were overrepresented in the UDN compared to the US population. Individuals whose primary language was not English were also significantly underrepresented. Diagnosis rates varied, with the highest rates among Asian non-Hispanic (39.5%) and Hispanic (35.3%) groups and the lowest rate in the White non-Hispanic group (26.8%) (p < 0.001). Binomial logistic regression found, however, that only participant age and disease phenotype predicted the likelihood of receiving a diagnosis (p < 0.001). Persistent ethnic and racial disparities in UDN participation appear to be associated with major differences in application rates. Under-enrollment of historically marginalized ethnic and racial groups may be due to economic hardships and language barriers. No differences in the diagnostic yield among ethnic and racial groups were observed after controlling for other factors. This work highlights the value of comprehensive genetic evaluations for addressing healthcare disparities and suggests priorities for advancing inclusion in rare disease research.

Abstract The occurrence of multiple primary cancers (MPC) is thought to reflect increased cancer susceptibility in patients due to a combination of genetic and environmental factors. Here we conducted a retrospective review of 2,894 consecutive patients evaluated at a single institution and identified 31 (1.14%) individuals with a history of three or more primary cancers, then analyzed the genetic and environmental influences associated with their propensity for developing malignancies. We found that 35.5% of patients had a hereditary cancer syndrome (HCS), with high penetrance HCS in 72.7% of cases, suggesting that monogenic causes underly a significant proportion of triple primary cancer risk. Analysis of cancer frequencies found that the diagnosis of breast cancer was associated with a significantly lower likelihood of HCS, while the diagnosis of colorectal, prostate, and pancreas cancer was associated with a significantly higher likelihood of HCS. Comparison of HCS-positive and HCS-negative patients revealed similar demographic characteristics, mean age at first diagnosis, and family history of cancer. Moreover, no significant differences in lifestyle behaviors, occupational exposures, chronic health conditions, or treatment with chemotherapy and radiation were observed between HCS-positive and -negative groups, though outliers in tobacco smoking, as well as systemic treatment after both first and second primary cancers were observed. These findings indicate a robust contribution of HCS to cancer susceptibility among patients with triple primary cancers while environmental influences were less evident. This emphasizes the need for larger MPC cohorts incorporating additional genetic and environmental factors to more comprehensively characterize drivers of cancer risk. Prevention Relevance: In patients with three or more primary cancers, genetic predisposition explained a significant proportion of cases; however, treatment history, lifestyle habits, and other exposures appeared to play a less significant role. This highlights the value of early genetic screening and the need to develop more sensitive markers of cancer susceptibility. See related Spotlight, p. 193

American Journal of Medical Genetics Part AVolume 191, Issue 7 p. 1681-1686 ISSUE INFORMATIONFree Access Table of Contents, Volume 191A, Number 7, July 2023 First published: 07 June 2023 https://doi.org/10.1002/ajmg.a.62813AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat Volume191, Issue7July 2023Pages 1681-1686 RelatedInformation

Coffin-Siris syndrome (CSS) is a rare neurodevelopmental disorder that is associated with multiple congenital anomalies and caused by de novo monoallelic germline pathogenic variants in BAF-complex genes. Despite their function as tumor suppressors, the cancer risk in patients with CSS remains unclear. We analyzed cancer sequencing data sets, conducted a comprehensive literature review of patients with CSS diagnosed with malignancies, and examined a cohort of 376 CSS registry patients to estimate cancer frequency. A review of the literature identified several reports of patients with CSS diagnosed with a malignancy, with ARID1A being the most frequent causative gene and associated with hepatoblastoma in 3 cases. Although no cases of malignancy were reported among the patients in the CSS registry, only 26 patients with ARID1A-CSS were available for analysis. Combining these patients with all cases reported in the literature led to the estimate of hepatoblastoma prevalence in ARID1A-CSS of 3.6% (95% CI 0.79%-10.4%). Our findings suggest the hepatoblastoma risk among patients with ARID1A-CSS may exceed the established 1% risk threshold and therefore warrant surveillance. There remains insufficient evidence to support any other CSS gene-cancer association, emphasizing the need for further systematic study.

Heterozygous, loss-of-function germline variants in ATM have been associated with an increased lifetime risk of breast, pancreas, prostate, stomach, ovarian, colorectal, and melanoma cancers. We conducted a retrospective review of thirty-one unrelated patients found to be heterozygous for a germline pathogenic variant in ATM and identified a significant proportion of patients in this cohort with cancers not currently associated with the ATM hereditary cancer syndrome, including carcinomas of the gallbladder, uterus, duodenum, kidney, and lung as well as a vascular sarcoma. A comprehensive review of the literature found 25 relevant studies where 171 individuals with a germline deleterious ATM variant have been diagnosed with the same or similar cancers. The combined data from these studies were then used to estimate the prevalence of germline ATM pathogenic variants in these cancers, which ranged between 0.45% and 2.2%. Analysis of tumor sequencing performed in large cohorts demonstrated that the frequency of deleterious somatic ATM alterations in these atypical cancers equaled or exceeded the alteration frequency in breast cancer and occurred at a significantly higher rate than in other DNA-damage response tumor suppressors, namely BRCA1 and CHEK2. Furthermore, multi-gene analysis of somatic alterations in these atypical cancers demonstrated significant co-occurrence of pathogenic alterations in ATM with BRCA1 and CHEK2, while there was significant mutual exclusivity between pathogenic alterations in ATM and TP53. This indicates that germline ATM pathogenic variants may play a role in cancer initiation and progression in these atypical ATM malignancies, potentially influencing these cancers to be driven toward DNA-damage repair deficiency and away from loss of TP53. As such, these findings provide evidence for broadening of the ATM-cancer susceptibility syndrome phenotype to improve the recognition of affected patients and provide more efficacious, germline-directed therapies.