Submissions for variant NM_000249.4(MLH1):c.469dup (p.Tyr157fs)

dbSNP: rs63751101

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Color Diagnostics, LLC DBA Color Health	RCV000583004	SCV000689890	pathogenic	Hereditary cancer-predisposing syndrome	2022-10-10	criteria provided, single submitter	clinical testing	This variant inserts 1 nucleotide in exon 6 of the MLH1 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, this variant has not been reported in individuals affected with hereditary cancer in the literature. 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 Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000780415	SCV000917642	likely pathogenic	Lynch syndrome	2017-10-10	criteria provided, single submitter	clinical testing	Variant summary: The MLH1 c.469dupT (p.Tyr157LeufsX15) variant results in a premature termination codon, predicted to cause a truncated or absent MLH1 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (e.g. c.1210_1211delCT, p.Leu404fsX12; c.1459C>T, p.Arg487X; c.1489dupC, p.Arg497fsX6). One in silico tool predicts a damaging outcome for this variant. This variant is absent in 277064 control chromosomes. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as likely pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001062982	SCV001227809	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2024-12-02	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Tyr157Leufs*15) in the MLH1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MLH1 are known to be pathogenic (PMID: 15713769, 24362816). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of Lynch Syndrome (internal data). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 491710). 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.
Ambry Genetics	RCV000583004	SCV002637839	pathogenic	Hereditary cancer-predisposing syndrome	2024-10-29	criteria provided, single submitter	clinical testing	The c.469dupT pathogenic mutation, located in coding exon 6 of the MLH1 gene, results from a duplication of T at nucleotide position 469, causing a translational frameshift with a predicted alternate stop codon (p.Y157Lfs*15). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.
Myriad Genetics, Inc.	RCV003451299	SCV004186342	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-14	criteria provided, single submitter	clinical testing	This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
Laboratory for Genotyping Development, RIKEN	RCV003159981	SCV002758277	pathogenic	Gastric cancer	2021-07-01	no assertion criteria provided	research