ClinVar Miner

Submissions for variant NM_000249.4(MLH1):c.1731+5_1731+6delinsCC

dbSNP: rs2125958437
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV001525706 SCV001735886 likely pathogenic Hereditary cancer-predisposing syndrome 2020-11-02 criteria provided, single submitter clinical testing This variant alters two conserved nucleotides at the +5 and +6 positions in the intron 15 splice donor site of the MLH1 gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. Three other non-canonical splice site variants, c.1731+3A>T, c.1731+4A>G and c.1731+5G>A, are predicted to have a lesser impact in splicing compared to this variant and they have been shown to cause the out-of-frame skipping of exon 15 in carrier RNA samples (PMID: 18769833, 19224586, 19685281, 20305446, 24278394). These other variants also have been observed in individuals affected with Lynch syndrome and whose tumor samples showed microsatellite instability and loss of MLH1 by immunohistochemistry (PMID: 18769833, 19685281, 20305446, 24278394; InSiGHT database), and c.1731+3A>T is reported to segregate with disease in one family (PMID: 18769833; InSiGHT database). These three splice site variants and c.1731G>A that have been shown to impact splicing at the intron 15 splice donor site have been reported as disease-causing in ClinVar (variation ID: 89853, 89854, 89857, 483547). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MLH1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic.
Myriad Genetics, Inc. RCV003451794 SCV004187102 likely pathogenic Colorectal cancer, hereditary nonpolyposis, type 2 2023-07-21 criteria provided, single submitter clinical testing This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad internal data].

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