ClinVar Miner

Submissions for variant NM_000112.4(SLC26A2):c.1203_1204insTTTTTTTTTTTTTTTTTTTNNNNNNNNNNGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCATTTTCT (p.Glu402delinsPhePhePhePhePhePheXaaXaaXaaXaaThrGlyPheHisLeuValSerGlnAspGlyLeuAspLeuLeuThrSerTer)

dbSNP: rs2113698410
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001879344 SCV002144201 pathogenic Achondrogenesis, type IB; Atelosteogenesis type II; Multiple epiphyseal dysplasia type 4; Diastrophic dysplasia 2021-05-24 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Retrotransposon insertions including LINE1 (L1), Alu, and SVA (SINE-VNTR-Alu) have been reported to disrupt protein function (PMID: 19763152, 20307669, 22406018). However the effect of this particular variant is unknown. This variant disrupts the C-terminus of the SLC26A2 protein. Other variant(s) that disrupt this region (p.Lys575Serfs*10) have been determined to be pathogenic (PMID: 7923357, 8528239, 8571951). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with SLC26A2-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change inserts a large fragment of DNA, likely a transposable element, in exon 3 of the SLC26A2 gene (c.1203_1204ins), causing a frameshift at codon 402 (p.Glu402fs). The exact size and sequence of the insertion cannot be determined by the current assay. However, the insertion is expected to result in an absent or disrupted protein product.

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