ClinVar Miner

Submissions for variant NM_000338.3(SLC12A1):c.3164+1G>A

gnomAD frequency: 0.00002  dbSNP: rs756057922
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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 RCV001379160 SCV001576909 pathogenic not provided 2024-06-04 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 26 of the SLC12A1 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. Disruption of this splice site has been observed in individual(s) with Bartter syndrome (PMID: 18391953, 19096086, 20219833, 35628451). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 1067800). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV001535850 SCV001752463 pathogenic Bartter disease type 1 2022-03-15 criteria provided, single submitter clinical testing
GeneDx RCV001379160 SCV003925030 pathogenic not provided 2023-05-08 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 19096086, 25525159, 18391953, 20219833)

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