PMC10311070_01
Radiology manifestation in the current proband. (A) Electrocardiographic examination demonstrated right axis deviation, enlargement of bi-ventricles and ventricular escape (arrow). (B) Cardiac magnetic resonance (CMR) demonstrated diffuse hypertrophy of ventricular myocardium, T2-weighting imaging revealed abnormal signal intensity of left ventricular subendocardial myocardium. (C) Transthoracic echocardiography (TTE) demonstrated significant hypertrophy of left ventricle and the interventricular septum.
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The electrocardiogram (ECG) revealed right axis deviation, biventricular hypertrophy, and ventricular escape beats (Figure 1A). Transthoracic echocardiography revealed significant hypertrophy of the left ventricular wall, particularly the interventricular septum (IVS) and left posterior ventricular wall (LVPW) (Figure 1C). The thickness of each part during the diastolic period was as follows: LVPW, 28.3 mm; right ventricular anterior wall (RVAW), 8.3 mm; and IVS, 32.2 mm (Figure 1B, left panel). Furthermore, the T2-weighted image revealed an abnormal signal intensity of the left ventricular subendocardial myocardium indicating myocardial ischemia (Figure 1B, right panel).
The ALPK3 variants in this family. (A) Family pedigree revealed the maternal carrier of c.3907_3922del (p.G1303Lfs*28) and the paternal carrier of c.2200A>T (p.R734*). The current proband exhibited significant hypertrophic cardiomyopathy with compound heterozygous variants of ALPK3. circles represent females, squares represent males, and arrow indicates the proband. Black symbols indicate the clinical presentation of hypertrophic cardiomyopathy, grey symbols indicate carriers. (B) Sanger sequencing validation of the current proband and his parents. (C) The prevalence of ALPK3 variants of c.3907_3922del and c.2200A>T. (D) Summary of current reports on individual ALPK3 variants resulting in hypertrophic cardiomyopathy.
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The variant of c.3907_3922del was maternal inherit, and the variant of c.2200A>T was paternal inherit (Figures 2A,B). According to updated data in gnomAD, ExAC and 1000G, these two variants have not been reported in any populations, that means it is the first report of these variants (Figure 2C). Analysis performed with MutationTaster revealed that variant of c.3907_3922del in ALPK3 was considered pathogenic (probability 1.000) due to nonsense-mediated mRNA decay (NMD), amino acid sequence changed, frameshift, protein features affected and splice site changes, while c.2200A>T was also considered pathogenic because of NMD, acid sequence changed, and protein features affected (probability 1.000). While all the reported variants of ALPK3 had been listed in Figure 2D.
The effects of ALPK3 c.3907_3922delGGCCTCCTGGGGGCCT and c.2200A>T variants on the molecular structure of the protein. (A) AlphaFold protein structure database was used to predict the ALPK3 wild-type protein crystal structure. (B) Three domains of ALPK3 protein were labeled in red, green and orange individually. SWISS-MODEL presented the crystal structures of the variant's three domains, including two immunoglobulin-like (Ig-like) domains and an alpha-type protein kinase domain according to 6c6m.2.A, 3uto.2.A, and 1ia9.1.A model template. Ramachandran plots of three functional domains in wild-type sequences were displayed. (C,D) Truncating variant sites of p.G1303Lfs*28 and p.R734* caused by variants of c.3907_3922delGGCCTCCTGGGGGCCT and c.2200A>T was labelled in yellow.
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AlphaFold and assigned the name AF-Q96L96-F1 (Figure 3A). Although the predicted protein covered the entire length of the amino acid sequence, only three domains demonstrated high confidence (pLDDT >70). These domains were labeled red, green, and orange (Figure 3B). The sites of truncated sequences caused by variants were labeled in yellow (Figures 3C,D). SWISS-MODEL was then employed to present the crystal structures of the variant's three domains, including two immunoglobulin-like (Ig-like) domains and an alpha-type protein kinase domain (Figure 3B).