Submissions for variant NM_000057.4(BLM):c.2432A>G (p.Tyr811Cys)

gnomAD frequency: 0.00004  dbSNP: rs145029382

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000477499	SCV000543378	uncertain significance	Bloom syndrome	2024-01-29	criteria provided, single submitter	clinical testing	This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 811 of the BLM protein (p.Tyr811Cys). This variant is present in population databases (rs145029382, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with BLM-related conditions. ClinVar contains an entry for this variant (Variation ID: 405315). 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 expected to disrupt BLM protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects BLM function (PMID: 23129629, 26788541). 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.
Ambry Genetics	RCV002451078	SCV002736675	likely pathogenic	Hereditary cancer-predisposing syndrome	2022-10-25	criteria provided, single submitter	clinical testing	The p.Y811C variant (also known as c.2432A>G), located in coding exon 11 of the BLM gene, results from an A to G substitution at nucleotide position 2432. The tyrosine at codon 811 is replaced by cysteine, an amino acid with highly dissimilar properties. Functional studies performed in yeast showed a lack of activity comparable to known BLM mutations (Mirzaei H et al. Proc. Natl. Acad. Sci. U.S.A. 2012 Nov;109:19357-62; Shastri VM et al. Mol Genet Genomic Med. 2016 Jan;4:106-19). Based on internal structural analysis, this variant disrupts the protein structure more than a nearby known pathogenic variant (Swan MK et al. Acta Crystallogr. D Biol. Crystallogr. 2014 May;70:1465-75). This amino acid position is highly conserved in available vertebrate species. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). In addition, the in silico prediction for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Fulgent Genetics, Fulgent Genetics	RCV000477499	SCV002790255	uncertain significance	Bloom syndrome	2022-01-05	criteria provided, single submitter	clinical testing
GeneDx	RCV003441864	SCV004170080	uncertain significance	not provided	2023-10-18	criteria provided, single submitter	clinical testing	Published functional studies suggest a damaging effect: demonstrates sensitivity to DNA-damaging agents similar to other known pathogenic BLM variants (Mirzaei and Schmidt, 2012; Shastri and Schmidt, 2016); Observed in an individual with colorectal cancer (DeRycke et al., 2017); Not observed at significant frequency in large population cohorts (gnomAD); 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: 32704157, 26788541, 28944238, 24816114, 23129629)
Natera, Inc.	RCV000477499	SCV001461106	uncertain significance	Bloom syndrome	2018-07-23	no assertion criteria provided	clinical testing
Genetic Services Laboratory, University of Chicago	RCV003151059	SCV003839259	uncertain significance	not specified	2022-08-05	no assertion criteria provided	clinical testing	DNA sequence analysis of the BLM gene demonstrated a sequence change, c.2432A>G, in exon 12 that results in an amino acid change, p.Tyr811Cys. This sequence change does not appear to have been previously described in individuals with BLM-related disorders. Experimental studies have shown that this missense change may impact BLM function (PMID: 23129629, 26788541). This sequence change has been described in the gnomAD database in two individuals which corresponds to a population frequency of 0.0015% (dbSNP rs145029382). The p.Tyr811Cys change affects a highly conserved amino acid residue located in a domain of the BLM protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Tyr811Cys substitution. Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Tyr811Cys change remains unknown at this time.