ClinVar Miner

Submissions for variant NM_138413.4(HOGA1):c.834G>A (p.Ala278=) (rs770050262)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000791689 SCV000930949 pathogenic not provided 2018-12-06 criteria provided, single submitter clinical testing This sequence change affects codon 278 of the HOGA1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the HOGA1 protein. This variant also falls at the last nucleotide of exon 6 of the HOGA1 coding sequence, which is part of the consensus splice site for this exon. This variant is present in population databases (rs770050262, ExAC 0.09%). This variant has been observed in an individual with primary hyperoxaluria type 3 (PMID: 26340091). In this individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 204286). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Experimental studies have shown that this variant disrupts mRNA splicing and leads to skipping of exon 6 (PMID: 26340091). For these reasons, this variant has been classified as Pathogenic.
Clinical Biochemistry Laboratory,Health Services Laboratory RCV000186493 SCV000239855 pathogenic Primary hyperoxaluria, type III 2014-11-27 no assertion criteria provided research Predicted to affect splicing
OMIM RCV000186493 SCV000897730 pathogenic Primary hyperoxaluria, type III 2019-04-09 no assertion criteria provided literature only

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