ClinVar Miner

Submissions for variant NM_003849.4(SUCLG1):c.825+1G>A

gnomAD frequency: 0.00002  dbSNP: rs750388794
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000779336 SCV000915928 uncertain significance Mitochondrial DNA depletion syndrome 9 2018-08-31 criteria provided, single submitter clinical testing The SUCLG1 c.825+1G>A variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. A literature search was performed for the gene and cDNA change. No publications were found based on this search. The variant is reported at a frequency of 0.000039 in the European (non-Finnish) population of the Genome Aggregation Database. Based on the potential impact of splice donor variants and the lack of clarifying evidence, the c.825+1G>A variant is classified as a variant of unknown significance but suspicious for pathogenicity for SUCLG1-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Labcorp Genetics (formerly Invitae), Labcorp RCV000779336 SCV003251372 likely pathogenic Mitochondrial DNA depletion syndrome 9 2022-03-20 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 632364). This variant has not been reported in the literature in individuals affected with SUCLG1-related conditions. This variant is present in population databases (rs750388794, gnomAD 0.004%). This sequence change affects a donor splice site in intron 7 of the SUCLG1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SUCLG1 are known to be pathogenic (PMID: 20693550).

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