ClinVar Genomic variation as it relates to human health

The p.Thr123Met variant in ANKRD1 has been reported in 1 individual with HCM (Ar imura 2009). In vitro functional studies provide some evidence that this variant may impact protein function (Arimura 2009, Crocini 2013). However, these types of sometimes do not accurately represent biological function. The p.Thr123Met va riant has also been identified in 20/66418 European chromosomes by the Exome Agg regation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs145387010). T hreonine (Thr) at position 123 is not conserved in evolution and 2 mammals (oran gutan and cow) carry a methionine (Met) at this position, raising the possibilit y that this change may be tolerated. In summary, the available data is conflicti ng and the clinical significance of the p.Thr123Met variant is uncertain.

The p.T123M variant (also known as c.368C>T), located in coding exon 4 of the ANKRD1 gene, results from a C to T substitution at nucleotide position 368. The threonine at codon 123 is replaced by methionine, an amino acid with similar properties. This alteration has been reported in one subject with hypertrophic cardiomyopathy (HCM) and may have an impact on protein function (Arimura T et al. J. Am. Coll. Cardiol., 2009 Jul;54:334-42; Crocini C et al. Basic Res. Cardiol., 2013 May;108:349). This alteration has also been seen in exome cohorts, but cardiovascular history was not provided (Andreasen C et al. Eur J Hum Genet. 2013;21(9):918-28; Ng D et al. Circ Cardiovasc Genet. 2013;6(4):337-46).This amino acid position is poorly conserved in available vertebrate species, and methionine is the reference amino acid in other vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

The ANKRD1 c.368C>T; p.Thr123Met variant (rs145387010) is reported in the literature in at least one individual affected with hypertrophic cardiomyopathy (Arimura 2009). This variant is reported as uncertain significance by multiple laboratories in ClinVar (Variation ID: 191577), and is found in the non-Finnish European population with an allele frequency of 0.053% (68/128218 alleles, including a single homozygote) in the Genome Aggregation Database. Functional analyses demonstrate slightly altered protein interactions and functional effects (Arimura 2009, Crocini 2013). The threonine at codon 123 is weakly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is tolerated. Due to limited information, the clinical significance of the p.Thr123Met variant is uncertain at this time. References: Arimura T et al. Cardiac ankyrin repeat protein gene (ANKRD1) mutations in hypertrophic cardiomyopathy. J Am Coll Cardiol. 2009 Jul 21;54(4):334-42. Crocini et al. Impact of ANKRD1 mutations associated with hypertrophic cardiomyopathy on contraction parameters of engineered heart tissue. Basic Res Cardiol. 2013 May;108(3):349.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

This variant is associated with the following publications: (PMID: 31737537, 30659708, 28672880, 27143260, 28518168, 23861362, 19608031, 23572067, 23299917)

Variant summary: ANKRD1 c.368C>T (p.Thr123Met) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00029 in 248014 control chromosomes, predominantly at a frequency of 0.00053 within the Non-Finnish European subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 21 fold of the estimated maximal expected allele frequency for a pathogenic variant in ANKRD1 causing Cardiomyopathy phenotype (2.5e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. c.368C>T has been reported in the literature in at least one individual affected with Cardiomyopathy (e.g., Arimura_2009), however without strong evidence for causality. This report therefore does not provide unequivocal conclusions about association of the variant with Cardiomyopathy. At least two publications report experimental evidence evaluating an impact on protein function, suggesting that the variant may represent a gain-of-contractile-function mutation as it led to increased binding to I-band components and mislocalization to the nucleus, although the variant did incorporate correctly into the sarcomere (Arimura_2009, Crocini_2013). These findings do not allow convincing conclusions about the variant effect. The following publications have been ascertained in the context of this evaluation (PMID: 19608031, 23572067, 28518168). Ten ClinVar submitters (evaluation after 2014) have reported the variant with conflicting assessments (VUS, n = 9, likely benign, n = 1) citing overlapping evidence used in the context of this evaluation. Based on the evidence outlined above, the variant was classified as likely benign.

This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 123 of the ANKRD1 protein (p.Thr123Met). This variant is present in population databases (rs145387010, gnomAD 0.05%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 19608031, 31737537). ClinVar contains an entry for this variant (Variation ID: 191577). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ANKRD1 protein function with a negative predictive value of 80%. 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.

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).