Submissions for variant NM_000249.4(MLH1):c.116+5G>C

dbSNP: rs267607710

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000075129	SCV000106120	pathogenic	Lynch syndrome	2013-09-05	reviewed by expert panel	research	Variant causes splicing aberration predicted to produce truncated protein: full inactivation of variant allele. Multifactorial likelihood analysis posterior probability >0.99
GeneDx	RCV000413453	SCV000490614	pathogenic	not provided	2020-12-01	criteria provided, single submitter	clinical testing	Non-canonical splice site variant demonstrated to result in loss-of-function (Casey 2005, Arnold 2009, Naruse 2009); Observed in patients with Lynch-related cancers and tumor studies consistent with pathogenic variants in this gene (Casey 2005, Arnold 2009, Choi 2009, Barrow 2010, Thodi 2010); Not observed in large population cohorts (Lek et al., 2016); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 22949379, 20459533, 19698169, 20937110, 15713769, 19685281, 19267393, 32658311)
Invitae	RCV000694368	SCV000822810	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2023-11-27	criteria provided, single submitter	clinical testing	This sequence change falls in intron 1 of the MLH1 gene. It does not directly change the encoded amino acid sequence of the MLH1 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 15713769, 19267393, 19685281, 20937110, 32658311). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 89658). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a high probability of being pathogenic (PMID: 22949379). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 19685281, 22949379). For these reasons, this variant has been classified as Pathogenic.
Color Diagnostics, LLC DBA Color Health	RCV000776333	SCV000911687	pathogenic	Hereditary cancer-predisposing syndrome	2021-07-23	criteria provided, single submitter	clinical testing	This variant causes a G to C nucleotide substitution at the +5 position of intron 1 of the MLH1 gene. Functional RNA studies have shown that this variant causes retention of 227 basepairs of intron, resulting in a frameshift and premature truncation. This variant has been reported in individuals affected with Lynch syndrome or colorectal cancer (PMID: 15713769, 19267393, 20459533, 20937110). 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.
Ambry Genetics	RCV000776333	SCV002624041	pathogenic	Hereditary cancer-predisposing syndrome	2023-04-06	criteria provided, single submitter	clinical testing	The c.116+5G>C intronic mutation results from a G to C substitution 5 nucleotides after coding exon 1 in the MLH1 gene. This alteration has been reported in multiple Lynch syndrome families and has segregated with disease in multiple affected family members (Casey G et al, JAMA 2005 Feb; 293(7):799-809; Arnold S et al, Hum. Mutat. 2009 May; 30(5):757-70; Thodi G et al, BMC Cancer 2010; 10():544). In addition, multiple functional analyses have demonstrated that this alteration causes aberrant splicing (Casey G et al, JAMA 2005 Feb; 293(7):799-809; Arnold S et al, Hum. Mutat. 2009 May; 30(5):757-70; Naruse H et al, Fam. Cancer 2009; 8(4):509-17). This variant has been identified in a proband who met Amsterdam I criteria for Lynch syndrome and tumor demonstrated high microsatellite instability with loss of MLH1/PMS2 expression by immunohistochemistry (IHC) (Ambry internal data). In addition, this variant has been identified in probands whose Lynch syndrome-associated tumor demonstrated loss of MLH1/PMS2 expression by IHC (Ambry internal data). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Myriad Genetics, Inc.	RCV003451008	SCV004186374	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-12	criteria provided, single submitter	clinical testing	This variant is considered pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 15713769].
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001358274	SCV001553963	likely pathogenic	Carcinoma of colon		no assertion criteria provided	clinical testing	The MLH1 c.116+5G>C variant was identified in 2 of 84 proband chromosomes (frequency: 0.02) from individuals or families with Lynch syndrome (Thodi 2010). The variant was also identified in dbSNP (ID: rs267607710) as "With Pathogenic, other allele", ClinVar (classified as pathogenic by Invitae and InSight; as likely pathogenic by GeneDx), Mismatch Repair Genes Variant Database, and the Insight Hereditary Tumors Database (9x). The variant was not identified in COGR, UMD-LSDB, or Zhejiang University Database. The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The c.116+5G>C variant is located in the 5' splice region but does not affect the invariant +1 and +2 positions. However, positions +3 to +6 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In addition, 3 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. Several functional splicing studies identify the variant lead to loss of MLH1 protein expression and inclusion of 227nt of intron 1 which causes frameshift and aberrations likely to be considered pathogenic (Arnold 2009, Casey 2005, Naruse 2009, Thompson 2013). In addition, the variant segregate with disease in one family with 5/5 affected carries (Arnold 2009). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic.