Homozygous noncanonical splice variant in LSM1 in two siblings with multiple congenital anomalies and global developmental delay

Abstract

Two siblings, one male and one female, ages 6 and 13 yr old, have similar clinical features of global developmental delay, multiple congenital anomalies affecting the cardiac, genitourinary, and skeletal systems, and abnormal eye movements. Whole-genome sequencing revealed a homozygous splice variant (NM_014462.3:c.231+4A>C) in LSM1 that segregated with the phenotype in the family. LSM1 has a role in pre-mRNA splicing and degradation. Expression studies revealed absence of expression of the canonical isoform in the affected individuals. The Lsm1 knockout mice have a partially overlapping phenotype that affects the brain, heart, and eye. To our knowledge, LSM1 has not been associated with any human disorder; however, the tissue expression pattern, gene constraint, and the similarity of the phenotype in our patients and the knockout mice models suggest it has a role in the development of multiple organ systems in humans.

Keywords: bicuspid aortic valve; bilateral cryptorchidism; congenital mitral stenosis; congenital strabismus; craniofacial asymmetry; cupped ear; hydronephrosis; hydroureter; inguinal hernia; intellectual disability, moderate; intermittent microsaccadic pursuits; lumbar hemivertebrae; moderate global developmental delay; penile hypospadias; perimembranous ventricular septal defect; primum atrial septal defect; triphalangeal thumb.

Figure 1.

Pedigree. Affected individuals, unaffected siblings, and parents were tested for segregation analysis of noncanonical splice variant in LSM1. (+) Wild-type allele.

Figure 2.

Two percent agarose-gel electrophoresis image of the cDNA studies performed with two sets of primers. Peripheral blood samples were collected from one affected individual (II-6), unaffected carrier parents (I-2 and I-1), and a control. (A) Two different sets of primers were designed, given the lack of exon 3 in one noncoding isoform (NR_045492.1). Forward primer of set 1 (LSM1splice1F; yellow-filled, red outlined right arrow) maps to first exons of NM_014462.2 and NR_045492.1 only. Forward primer of set 2 (LSM1splice2F; yellow-filled, black outlined right arrow) maps to exon 3 of NM_014462.2 and NR_045493.1 only. Reverse primers of both sets (LSM1splice1R and LSM1splice2R) map to exon 4 of all isoforms. Isoform accession numbers and schematic were retrieved from NCBI Entrez Gene website (Gene ID = 27257). (B) PCRs with primer sets 1 (left) and 2 (right) revealed no band in an affected individual (II-6) corresponding to the canonical isoform. Unaffected carrier parents (I-2 and I-1) only have one band corresponding to the canonical isoform, 250-bp band on the left and 176-bp band on the right, in addition to the 134-bp noncoding RNA transcript (NR_045492.1) product (smaller band on the left) in all samples run with primer set 1.