ClinVar Miner

Submissions for variant NM_000249.4(MLH1):c.371G>A (p.Cys124Tyr)

gnomAD frequency: 0.00003  dbSNP: rs730881736
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000160520 SCV000211086 uncertain significance not provided 2023-05-25 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in an individual with renal cancer (Yehia et al., 2018); This variant is associated with the following publications: (PMID: 22753075, 29684080)
Invitae RCV000475201 SCV000543650 uncertain significance Hereditary nonpolyposis colorectal neoplasms 2023-01-16 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with MLH1-related conditions. 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. 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. ClinVar contains an entry for this variant (Variation ID: 182515). This variant is present in population databases (rs730881736, gnomAD 0.002%). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 124 of the MLH1 protein (p.Cys124Tyr).
Ambry Genetics RCV000573907 SCV000673829 uncertain significance Hereditary cancer-predisposing syndrome 2021-06-22 criteria provided, single submitter clinical testing The p.C124Y variant (also known as c.371G>A), located in coding exon 4 of the MLH1 gene, results from a G to A substitution at nucleotide position 371. The cysteine at codon 124 is replaced by tyrosine, an amino acid with highly dissimilar properties. In a study of whole-exome sequencing in patients with features of Cowden syndrome (CS) or Bannayan-Riley-Ruvalcaba syndrome (BRRS) and negative PTEN testing, this alteration was identified in 0/87 patients with CS or BRRS and 1/3476 patients from The Cancer Genome Atlas (TCGA) (Yehia L et al. PLoS Genet, 2018 04;14:e1007352). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Color Diagnostics, LLC DBA Color Health RCV000573907 SCV004359179 uncertain significance Hereditary cancer-predisposing syndrome 2023-10-11 criteria provided, single submitter clinical testing This missense variant replaces cysteine with tyrosine at codon 124 of the MLH1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with kidney cancer (PMID: 29684080). This variant has been identified in 3/282810 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
All of Us Research Program, National Institutes of Health RCV003998464 SCV004835276 uncertain significance Lynch syndrome 2023-12-18 criteria provided, single submitter clinical testing This missense variant replaces cysteine with tyrosine at codon 124 of the MLH1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 3/282810 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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