ClinVar Genomic variation as it relates to human health

Variant summary: ATM c.3576G>A (p.Lys1192Lys) alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5 splicing donor site. Two predict the variant weakens a 5' donor site. An experimental study, Demuth_2011, supports these predictions by finding that this variant is associated with an in-frame exclusion of exon 26 from the mRNA. The variant allele was found at a frequency of 1.6e-05 in 246056 control chromosomes (gnomAD). The variant, c.3576G>A, has been reported in the literature in multiple individuals affected with Ataxia-Telangiectasia (Chessa_2009, Demuth_2011). These data indicate that the variant is very likely to be associated with disease. Five ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

PS3_MOD, PM3_VSTR

This sequence change affects codon 1192 of the ATM mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the ATM protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs587776551, gnomAD 0.004%). This variant has been observed in individuals with ataxia-telangiectasia and early-onset breast and thyroid cancer (PMID: 8845835, 9887333, 17124347, 19691550, 22071889, 27599564). This variant is also known as 3403del174. ClinVar contains an entry for this variant (Variation ID: 3035). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects ATM function (PMID: 22071889). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 24, but is expected to preserve the integrity of the reading-frame (PMID: 9887333; Invitae). For these reasons, this variant has been classified as Pathogenic.

This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 9887333]. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 8698354].

Located at the last nucleotide of exon 24 (also known as exon 26 in the literature) and demonstrated to result in abnormal splicing leading to skipping of exon 24 and/or exon 24-25 (Sandoval et al., 1999; Teraoka et a., 1999; Demuth et al., 2011; Jacquemin et al., 2012); Published functional studies demonstrate a damaging effect: reduced or absent protein expression and kinase activity (Sandoval et al., 1999; Teraoka et al., 1999; Demuth et al., 2011; Jacquemin et al., 2012); Not observed at significant frequency in large population cohorts (gnomAD); Observed in individuals with breast cancer and other cancers (Prodosmo et al., 2016; Huang et al., 2018; Akcay et al., 2020; Asadollahi et al., 2020; Pastorino et al., 2020); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 21965147, 10873394, 16941484, 17124347, 9463314, 21665257, 16189143, 11382771, 22927201, 27664052, 17910737, 22071889, 12552559, 10330348, 9450906, 9792409, 9443866, 22213089, 11606401, 15503472, 19691550, 8845835, 30819809, 30620386, 9887333, 29625052, 31741144, 32658311, 32325837, 32748564, 26896183, 33624863, 27599564)

This variant alters the conserved c.G at the last nucleotide position of exon 24 of the ATM gene. Splice site prediction tools suggest that this variant may impact RNA splicing. Functional RNA studies have shown that this variant causes an in-frame skipping of exon 24 (hence, known as 3403del174 and p.Ser1135_Lys1192del58 in the literature) or out-of-frame skipping of exons 24 and 25 (PMID: 9887333, 21965147). This variant has been shown to significantly affect protein stability and/or kinase activity (PMID: 9887333, 21965147, 22071889). This variant has been reported in multiple individuals and families affected with ataxia-telangiectasia and is recurrent in Turkish and Italian populations (PMID: 9792409, 9887333, 16941484, 17124347, 19691550, 22071889, 30819809, 31741144, 34107524, 35257272). This variant has also been reported in two individuals affected with breast cancer (PMID: 27599564, 29665859). This variant has been identified in 4/251126 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.

The c.3576G>A pathogenic mutation (also known as p.K1192K) is located in coding exon 23 of the ATM gene. This pathogenic mutation results from a G to A substitution at nucleotide position 3576. This nucleotide substitution does not change the lysine at codon 1192. However, this change occurs in the last base pair of coding exon 23 which makes it likely to have some effect on normal mRNA splicing. This alteration has been reported frequently in individuals with a clinical diagnosis of ataxia telangiectasia, and has been observed in the homozygous state in individuals with severe disease (Chessa L et al. Ann. Hum. Genet. 2009 Sep;73(Pt 5):532-9; Cavalieri S et al. Ann. Hum. Genet. 2008 Jan;72(Pt 1):10-8; Sandoval N et al. Hum. Mol. Genet. 1999 Jan;8:69-79). This alteration has been demonstrated to cause abnormal splicing, resulting in skipping of exon 23 (referred to as exon 26 in the literature) (Demuth I et al. Neurogenetics. 2011 Nov;12:273-82; Sandoval N et al. Hum. Mol. Genet. 1999 Jan;8:69-79). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Furthermore, several studies have shown that this alteration results in decreased/absent ATM protein expression and very low ATM kinase activity (Gilad S et al. Am. J. Hum. Genet. 1998 Mar;62:551-61; Demuth I et al. Neurogenetics. 2011 Nov;12:273-82; Sandoval N et al. Hum. Mol. Genet. 1999 Jan;8:69-79). This nucleotide position is highly conserved in available vertebrate species. Based on the available evidence, c.3576G>A is classified as a pathogenic mutation.