ClinVar Genomic variation as it relates to human health

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

The MYLK c.5477C>T; p.Ala1826Val variant (rs147187907) is reported in the literature in an individual with a suspected heritable thoracic aortic disorder, but without clear association with disease (Overwater 2018). This variant is reported in ClinVar (Variation ID: 252775), and is found in the general population with an overall allele frequency of 0.028% (78/282626 alleles) in the Genome Aggregation Database. The alanine at codon 1826 is moderately conserved, and computational analyses (SIFT: tolerated, PolyPhen-2: probably damaging) predict conflicting effects of this variant on protein structure/function. Given the lack of clinical and functional data, the significance of the p.Ala1826Val variant is uncertain at this time. References: Overwater E et al. Results of next-generation sequencing gene panel diagnostics including copy-number variation analysis in 810 patients suspected of heritable thoracic aortic disorders. Hum Mutat. 2018 Sep;39(9):1173-1192.

The p.A1826V variant (also known as c.5477C>T), located in coding exon 30 of the MYLK gene, results from a C to T substitution at nucleotide position 5477. The alanine at codon 1826 is replaced by valine, an amino acid with similar properties. This variant co-occurred with a COL3A1 variant in a pediatric individual with borderline aortic root aneurysm and family history of aortic aneurysm (Overwater E. Hum Mutat. 2018 09;39(9):1173-1192). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

Identified in conjunction with a COL3A1 variant in an infant with a borderline aortic aneurysm; this proband's father, who had a thoracic aortic aneurysm (TAA), was found to be heterozygous for both variants (PMID: 29907982); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29961567, 29907982)

Variant summary: MYLK c.5477C>T (p.Ala1826Val) results in a non-conservative amino acid change located in the Immunoglobulin-like domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00029 in 251230 control chromosomes, predominantly at a frequency of 0.00049 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 200 fold of the estimated maximal expected allele frequency for a pathogenic variant in MYLK causing Aortopathy phenotype (2.5e-06). However, this data must be interpreted with caution as the sequencing techology utalized does not distinguish between this gene and highly homologous pseudogenes. c.5477C>T has been reported in the literature in individuals with suspected Hereditary Thoracic Aortic Disease (Overwater_2018). This report does not provide an unequivocal conclusion about association of the variant with Aortopathy. One publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect (Kwartler_2018). The following publications have been ascertained in the context of this evaluation (PMID: 29907982, 29961567). ClinVar contains an entry for this variant (Variation ID: 252775). Based on the evidence outlined above, the variant was classified as uncertain significance.

The MYLK p.Ala1706Val variant was not identified in the literature nor was it identified in Cosmic. The variant was identified in dbSNP (ID: rs147187907), LOVD 3.0 (classified as a VUS) and in ClinVar (classified as a VUS by Invitae, GeneDx, Illumina, Ambry Genetics, EGL Genetic Diagnostics and the Division of Genomic Diagnostics at The Children's Hospital of Philadelphia). The variant was also identified in control databases in 78 of 282626 chromosomes at a frequency of 0.000276 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 59 of 128966 chromosomes (freq: 0.000458), South Asian in 10 of 30614 chromosomes (freq: 0.000327), African in 4 of 24968 chromosomes (freq: 0.00016), Other in 1 of 7212 chromosomes (freq: 0.000139), Latino in 3 of 35436 chromosomes (freq: 0.000085) and European (Finnish) in 1 of 25122 chromosomes (freq: 0.00004), but was not observed in the Ashkenazi Jewish or East Asian populations. The p.Ala1706 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

The MYLK c.5477C>T variant is predicted to result in the amino acid substitution p.Ala1826Val. This variant was reported as uncertain significance in an individual suspected of thoracic aortic disorder and in an individual with vascular type Ehlers-Danlos syndrome (Patient #69 in Table S1, Overwater et al. 2018. PubMed ID: 29907982; Table S10, Vandersteen et al. 2024. PubMed ID: 37813462). Functional studies suggested that this variant does not impact normal protein function (Figure 1B, Kwartler et al. 2018. PubMed ID: 29961567). This variant is reported in 0.046% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.