ClinVar Miner

Submissions for variant NM_012200.4(B3GAT3):c.673C>T (p.Arg225Ter)

gnomAD frequency: 0.00003  dbSNP: rs377340567
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000760862 SCV000890758 likely pathogenic not provided 2020-01-03 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease This variant is associated with the following publications: (PMID: 31988067)
Labcorp Genetics (formerly Invitae), Labcorp RCV003768289 SCV004686072 pathogenic Larsen-like syndrome, B3GAT3 type 2023-06-20 criteria provided, single submitter clinical testing Experimental studies have shown that this premature translational stop signal affects B3GAT3 function (PMID: 31988067). This sequence change creates a premature translational stop signal (p.Arg225*) in the B3GAT3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in B3GAT3 are known to be pathogenic (PMID: 25893793, 27871226). This variant is present in population databases (rs377340567, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with clinical features consistent with autosomal recessive multiple joint dislocations, short stature and craniofacial dysmorphism (PMID: 31988067). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 620480). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV001260983 SCV001438357 pathogenic MULTIPLE JOINT DISLOCATIONS, SHORT STATURE, AND CRANIOFACIAL DYSMORPHISM WITHOUT CONGENITAL HEART DEFECTS 2020-10-19 no assertion criteria provided literature only

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