ClinVar Miner

Submissions for variant NM_152490.5(B3GALNT2):c.458A>T (p.Tyr153Phe)

dbSNP: rs757111780
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000552352 SCV000653544 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 2024-03-11 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 153 of the B3GALNT2 protein (p.Tyr153Phe). This variant is present in population databases (rs757111780, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with B3GALNT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 473887). 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 B3GALNT2 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.
Ambry Genetics RCV002530227 SCV003746825 uncertain significance Inborn genetic diseases 2022-09-22 criteria provided, single submitter clinical testing The c.458A>T (p.Y153F) alteration is located in exon 4 (coding exon 4) of the B3GALNT2 gene. This alteration results from a A to T substitution at nucleotide position 458, causing the tyrosine (Y) at amino acid position 153 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV004760591 SCV005369391 uncertain significance not provided 2023-07-24 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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