ClinVar Genomic variation as it relates to human health

Has not been previously published as pathogenic or benign to our knowledge; Canonical splice site variant in a gene for which loss-of-function is not a known mechanism of disease

This sequence change affects a donor splice site in intron 37 of the LAMA4 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), however the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in LAMA4 cause disease. This variant is present in population databases (rs368035482, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with LAMA4-related conditions. ClinVar contains an entry for this variant (Variation ID: 635222). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

The c.5185+1G>A intronic variant results from a G to A substitution one nucleotide after coding exon 36 of the LAMA4 gene. This nucleotide position is highly conserved in available vertebrate species. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. However, the evidence for this gene-disease relationship is limited; therefore, the clinical significance of this alteration is unclear.

Criteria applied: PVS1_SUP,PM2_SUP

This variant was seen in a patient with dilated cardiomyopathy and left ventricular non compaction. He had genetic testing with the GeneDx laboratory with their comprehensive cardiomyopathy panel. The test included 76 genes associated with various hereditary cardiomyopathies: ABCC9, ACTC1, ACTN2, ANKRD1, BAG3, BRAF, CAV3, CRYAB, CSRP3, DES, DMD, DSC2, DSG2, DSP, DTNA, EMD, FKTN, GATAD1, GLA, HRAS, ILK, JPH2, JUP, KRAS, LAMA4, LAMP2, LDB3, LMNA, MAP2K1, MAP2K2, MTND1, MTND5, MTND6, MTTD, MTTG, MTTH, MTTI, MTTK, MTTL1, MTTL2, MTTM, MTTQ, MTTS1, MTTS2, MYBPC3, MYH7, MYL2, MYL3, MYLK2, MYOZ2, MYPN, NEBL, NEXN, NRAS, PDLIM3, PKP2, PLN, PRKAG2, PTPN11, RAF1, RBM20, RYR2, SCN5A, SGCD, TAZ, TCAP, TMEM43,TMPO, TNNC1, TNNI3, TNNT2, TPM1, TTN, TTR, VCL. This variant was found in combination with a likely pathogenic variant in the TTN gene. IVS37+1G>A (c.5185+1G>A; 6:112435865) in the LAMA4 gene NM_002290.3) Given that the gene-phenotype relationship is weak, the lack of case reports in the literature and its presence in population databases, we consider this variant to be of uncertain significance and we do not feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). LAMA4 variants have been reported in association with DCM, however only minimal evidence is available: only two variants in LAMA4 have been reported as causative of DCM in two patients. These variants are reviewed below. Thyboll and colleagues (2002) and Wang and colleagues (2005) determined that mice null for LAMA4 eventually develop heart failure. LAMA4 interacts with Integrin-linked kinase (ILK ), which has been associated with severe defects in cardiomyocytes leading to dilated cardiomyopathy. Knoll et al (2007) identified LAMA4 as a candidate gene after a zebrafish screen. They sequenced a total of 180 white individuals with DCM for variants in LAMA4 and compared this to 362 white controls and 200 Japanese controls. They found a missense variant (Pro943Leu) and a nonsense variant (Arg1073X). The Pro943Leu variant was observed in another individual with DCM. These patients were both male, 53 and 68 years old, of Dutch and German descent, with ejection fractions of 29 and 31%, respectively. The Arg1073X variant was observed in a 29 year old female with an ejection fraction of 20% who was preparing for heart transplantation. The authors do not specify whether or not these variants were seen in heterozygous or homozygous form. When analyzed in vitro, these variants demonstrated a loss of integrin-binding capacity compared to wildtype. However, the loss of laminin binding with integrin cannot be interpreted as causative of dilated cardiomyopathy. The pathogenicity of these variants was inferred from the functional study and their absence in population databases. We would classify these variants as variants of uncertain significance based on their presence in a single study and their low frequency in population databases. No other LAMA4 variants in patients with cardiovascular disease have been reported in the literature. The variant (IVS37+1G>A) has not been reported in the literature and is not listed in ClinVar. The variant was reported online in 7 of 125,832 (MAF 0.00271%) individuals in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >140,000 unrelated individuals of African, Asian, European, Ashkenazi, Latino descent. Specifically, the variant was observed in 6 of 55,840 individuals of non-Finnish European descent (0.0054% MAF) and 1 of 3176 people of Other descent (MAF: 0.015%). This variant was reported online in 3 of 60,542 individuals in the Exome Aggregation Consortium Dataset (ExAC; http://exac.broadinstitute.org/), which currently includes variant calls on >60,000 unrelated individuals of African, Asian, European and Latino descent (0.002748% MAF). Specifically, the variant was observed in 3 of 33,303 individuals of European (non-Finnish) descent (0.004504% MAF). The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. Note that other variants with strong evidence for pathogenicity have been seen at similar frequencies in datasets like this so this does not necessarily rule out pathogenicity (Pan et al 2012).