ClinVar Miner

Submissions for variant NM_000249.3(MLH1):c.80G>A (p.Arg27Gln) (rs138705565)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000573727 SCV000662012 uncertain significance Hereditary cancer-predisposing syndrome 2018-04-13 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Conflicting evidence,Insufficient evidence
Color RCV000573727 SCV000689923 uncertain significance Hereditary cancer-predisposing syndrome 2018-07-23 criteria provided, single submitter clinical testing
Counsyl RCV000662868 SCV000785757 uncertain significance Lynch syndrome II 2017-11-20 criteria provided, single submitter clinical testing
GeneDx RCV000215376 SCV000279261 uncertain significance not specified 2017-05-18 criteria provided, single submitter clinical testing This variant is denoted MLH1 c.80G>A at the cDNA level, p.Arg27Gln (R27Q) at the protein level, and results in the change of an Arginine to a Glutamine (CGG>CAG). This variant was observed in at least one individual with early onset breast cancer (Maxwell 2014). MLH1 Arg27Gln was not observed at a significant allele frequency in the NHLBI Exome Sequencing Project. Since Arginine and Glutamine differ in some properties, this is considered a semi-conservative amino acid substitution. MLH1 Arg27Gln occurs at a position that is conserved across species and is located within the ATPase and MLH1 domain (Pang 1997, Hardt 2011). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on currently available information, it is unclear whether MLH1 Arg27Gln is pathogenic or benign. We consider it to be a variant of uncertain significance.
Integrated Genetics/Laboratory Corporation of America RCV000587717 SCV000696182 uncertain significance not provided 2017-08-09 criteria provided, single submitter clinical testing Variant summary: The MLH1 c.80G>A (p.Arg27Gln) variant involves the alteration of a conserved nucleotide, resulting in a missense change in the histidine kinase-like ATPase, C-terminal domain (InterPro). 3/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in the large control database ExAC at a frequency of 0.0000165 (2/121156 control chromosomes), which does not exceed the estimated maximal expected allele frequency of a pathogenic MLH1 variant (0.0007105). The variant has been reported in a patient with early onset breast cancer without strong evidence for or against pathogenicity (Maxwell_Genet Med_2014). In addition, multiple clinical diagnostic laboratories have classified this variant as one of uncertain significance. Taken together, this variant is classified as a VUS.
Invitae RCV000197307 SCV000254372 uncertain significance Hereditary nonpolyposis colon cancer 2018-09-20 criteria provided, single submitter clinical testing This sequence change replaces arginine with glutamine at codon 27 of the MLH1 protein (p.Arg27Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs138705565, ExAC 0.003%). This variant has been reported in an individual affected with breast cancer (PMID: 25503501). ClinVar contains an entry for this variant (Variation ID: 216337). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000587717 SCV000889404 uncertain significance not provided 2018-04-30 criteria provided, single submitter clinical testing

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