ClinVar Genomic variation as it relates to human health
NM_000249.4(MLH1):c.191A>G (p.Asn64Ser)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Likely pathogenic(1); Uncertain significance(12); Likely benign(2)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000249.4(MLH1):c.191A>G (p.Asn64Ser)
Variation ID: 89947 Accession: VCV000089947.47
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p22.2 3: 36996693 (GRCh38) [ NCBI UCSC ] 3: 37038184 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jun 15, 2017 Apr 20, 2024 Jan 29, 2024 - HGVS
- ... more HGVS ... less HGVS
- Protein change
- N64S
- Other names
- p.N64S:AAT>AGT
- Canonical SPDI
- NC_000003.12:36996692:A:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
Trans-Omics for Precision Medicine (TOPMed) 0.00003
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00004
Exome Aggregation Consortium (ExAC) 0.00005
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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MLH1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
5564 | 5619 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Uncertain significance (1) |
criteria provided, single submitter
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Jan 29, 2024 | RCV000075426.12 | |
Uncertain significance (2) |
criteria provided, multiple submitters, no conflicts
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Jan 17, 2024 | RCV000217492.13 | |
Uncertain significance (1) |
criteria provided, single submitter
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Jun 29, 2017 | RCV000490571.4 | |
Conflicting interpretations of pathogenicity (4) |
criteria provided, conflicting classifications
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Feb 6, 2023 | RCV000513562.24 | |
Uncertain significance (1) |
criteria provided, single submitter
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Mar 15, 2016 | RCV000584818.3 | |
Uncertain significance (2) |
criteria provided, multiple submitters, no conflicts
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Nov 30, 2023 | RCV000708912.4 | |
Uncertain significance (1) |
criteria provided, single submitter
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Jan 1, 2019 | RCV001262297.4 | |
Conflicting interpretations of pathogenicity (3) |
criteria provided, conflicting classifications
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Sep 29, 2023 | RCV002288569.5 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Uncertain significance
(Jan 01, 2019)
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criteria provided, single submitter
Method: clinical testing
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Muir-Torré syndrome
Affected status: yes
Allele origin:
unknown
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Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001440111.1
First in ClinVar: Oct 31, 2020 Last updated: Oct 31, 2020 |
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Uncertain significance
(Aug 08, 2022)
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criteria provided, single submitter
Method: clinical testing
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Colorectal cancer, hereditary nonpolyposis, type 2
Affected status: yes
Allele origin:
germline
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MGZ Medical Genetics Center
Accession: SCV002581763.1
First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022 |
Number of individuals with the variant: 3
Sex: female
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Uncertain significance
(Jul 02, 2018)
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criteria provided, single submitter
Method: clinical testing
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Lynch syndrome
Affected status: unknown
Allele origin:
unknown
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Mendelics
Accession: SCV000837994.2
First in ClinVar: Oct 10, 2018 Last updated: Dec 11, 2022 |
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Uncertain significance
(Jun 29, 2017)
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criteria provided, single submitter
Method: clinical testing
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Lynch syndrome 1
Affected status: unknown
Allele origin:
unknown
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Counsyl
Accession: SCV000611601.2
First in ClinVar: Jun 15, 2017 Last updated: Dec 24, 2022 |
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Uncertain significance
(May 08, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000276267.10
First in ClinVar: May 29, 2016 Last updated: Jul 08, 2023 |
Comment:
The p.N64S variant (also known as c.191A>G), located in coding exon 2 of the MLH1 gene, results from an A to G substitution at nucleotide … (more)
The p.N64S variant (also known as c.191A>G), located in coding exon 2 of the MLH1 gene, results from an A to G substitution at nucleotide position 191. The asparagine at codon 64 is replaced by serine, an amino acid with highly similar properties. This alteration has been identified in several colorectal cancer cohorts that are suspicious for Lynch syndrome and, in at least one case, the tumor retained expression of MLH1 and MSH2 on immunohistochemical staining (Wijnen J et al. Am. J. Hum. Genet. 1997 Aug;61:329-35; Spaepen M et al. Fam. Cancer 2006;5:179-89; Hardt K et al. Fam. Cancer 2011 Jun;10:273-84; Stojcev Z et al. Acta Biochim Pol, 2013 Jun;60:195-8). One report shows that this alteration segregates with 5 of 6 siblings affected with colorectal cancer (Spaepen M et al. Fam. Cancer 2006;5:179-89). In another report, this alteration was found to co-occur with MLH1 c.986A>C, a functionally validated splicing mutation, in a patient with three gastrointestinal primary tumors diagnosed at 47. The MLH1 p.N64S alteration was inherited from the proband's mother who was unaffected at age 71, and while the paternal family history met Amsterdam criteria, suggesting the father likely carried the MLH1 c.986A>C pathogenic mutation, the inheritance of this alteration was not confirmed (Hardt K et al. Fam. Cancer 2011 Jun;10:273-84). Numerous functional studies show reduced but not abolished function including yeast mutator assays, expression assays, in vitro mismatch repair assays and heterodimerization assays (Ellison AR et al. Nucleic Acids Res. 2004 Oct;32:5321-38; Plotz G et al. Nucleic Acids Res. 2006 Nov;34:6574-86; Takahashi M et al. Cancer Res. 2007 May;67:4595-604; Wanat JJ et al. Hum. Mol. Genet. 2007 Feb;16:445-52; Hardt K et al. Fam. Cancer 2011 Jun;10:273-84). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (less)
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Uncertain significance
(Nov 03, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: not provided
Allele origin:
germline
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Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Accession: SCV002009370.3
First in ClinVar: Nov 06, 2021 Last updated: Jul 16, 2023 |
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Likely benign
(Mar 15, 2023)
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criteria provided, single submitter
Method: clinical testing
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Colorectal cancer, hereditary nonpolyposis, type 2
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004018166.1
First in ClinVar: Jul 29, 2023 Last updated: Jul 29, 2023 |
Comment:
This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic … (more)
This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752]. (less)
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Uncertain significance
(Sep 29, 2023)
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criteria provided, single submitter
Method: clinical testing
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Colorectal cancer, hereditary nonpolyposis, type 2
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004195090.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Uncertain significance
(Feb 06, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000889392.4
First in ClinVar: Mar 13, 2019 Last updated: Jan 06, 2024 |
Comment:
The frequency of this variant in the general population, 0.00007 (9/129152 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the … (more)
The frequency of this variant in the general population, 0.00007 (9/129152 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals/families with colorectal cancer (PMIDs: 21404117 (2011), 16736289 (2006), and 9311737 (1997)), endometrial cancer (PMID: 26552419 (2015)), breast cancer (PMID: 33471991 (2021); LOVD3 Shared (https://databases.lovd.nl/shared/)), and also in one case of pancreatic cancer (PMID: 28767289 (2017)). In addition, this variant has been reported in healthy control individuals (PMID: 33471991 (2021); LOVD3 Shared (https://databases.lovd.nl/shared/)). Functional studies have observed the variant having intermediate levels of MLH1 expression, mismatch repair activity, and PMS2 interaction (PMIDs: 30504929 (2018), 26552419 (2015), 22843852 (2012), 21404117 (2011), 17510385 (2007), 17210669 (2007), 17135187 (2006), and 15475387 (2004)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. (less)
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Uncertain significance
(Jan 29, 2024)
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criteria provided, single submitter
Method: clinical testing
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Hereditary nonpolyposis colorectal neoplasms
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000218899.13
First in ClinVar: Mar 29, 2015 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 64 of the MLH1 protein (p.Asn64Ser). … (more)
This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 64 of the MLH1 protein (p.Asn64Ser). This variant is present in population databases (rs63750952, gnomAD 0.006%). This missense change has been observed in individual(s) with colorectal, endometrial, pancreatic, ovarian cancer and/or Lynch syndrome (PMID: 9311737, 16736289, 21404117, 26552419, 28514183, 28767289, 28888541, 31332305). ClinVar contains an entry for this variant (Variation ID: 89947). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt MLH1 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects MLH1 function (PMID: 17135187, 17510385, 21404117, 30504929). 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. (less)
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Likely pathogenic
(Jan 01, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV000609098.19
First in ClinVar: Oct 30, 2017 Last updated: Apr 15, 2024 |
Number of individuals with the variant: 1
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Uncertain Significance
(Nov 30, 2023)
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criteria provided, single submitter
Method: clinical testing
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Lynch syndrome
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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All of Us Research Program, National Institutes of Health
Accession: SCV004835246.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024 |
Comment:
This missense variant replaces asparagine with serine at codon 64 of the MLH1 protein. Computational prediction suggests that this variant may have deleterious impact on … (more)
This missense variant replaces asparagine with serine at codon 64 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). Functional studies have shown that this variant results in a partial loss of mismatch repair function and moderately reduced protein stability and binding ability to PMS2 protein (PMID: 17135187, 17510385, 21404117, 30504929, 36054288). This variant has been reported in individuals from Lynch syndrome families (PMID: 9311737, 16736289, 21404117). In one of these families, two affected siblings were carriers of this variant but their affected sister with microsatellite instability-high tumor did not carry this variant (PMID: 16736289). Three unaffected siblings from this family did not carry this variant. In another family, this variant co-occurred in trans with a different pathogenic variant in the MLH1 gene (PMID: 21404117, 31332305). This variant has also been reported in individuals affected with endometrial cancer (PMID: 26552419) or pancreatic cancer (PMID: 28767289). In a large breast cancer case-control study, this variant was observed in 6/60466 cases and 5/53461 unaffected controls (PMID: 33471991) This variant has been identified in 10/282844 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. (less)
Number of individuals with the variant: 9
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Uncertain significance
(Mar 15, 2016)
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criteria provided, single submitter
Method: clinical testing
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Aqueductal stenosis
Choreoathetosis Global developmental delay
Affected status: yes
Allele origin:
germline
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Center for Personalized Medicine, Children's Hospital Los Angeles
Accession: SCV000692543.1
First in ClinVar: Feb 25, 2018 Last updated: Feb 25, 2018 |
Sex: female
Ethnicity/Population group: Caucasian,Non-Hispanic,unspecified
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Likely benign
(Oct 21, 2020)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000211108.13
First in ClinVar: Feb 24, 2015 Last updated: Oct 30, 2017 |
Comment:
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies are inconclusive: reduced MMR activity, no impact … (more)
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies are inconclusive: reduced MMR activity, no impact on nuclear localization, and conflicting results regarding mutator effect, PMS2 binding, MLH1 protein expression (Ellison 2004, Plotz 2006, Takahashi 2007, Wanat 2007, Hardt 2011, Bolz 2012, Drost 2018); Observed in individuals with MLH1-related cancers including segregation with disease in one family, as well as in individuals with melanoma (Wijnen 1997, Spaepen 2006, Hardt 2011, Shindo 2017, Yehia 2018); This variant is associated with the following publications: (PMID: 17135187, 21404117, 23741719, 29684080, 17510385, 17210669, 25525159, 9311737, 22843852, 15475387, 26552419, 16736289, 24362816, 28767289, 30504929, 31697235, 31332305, 32719484, 30755392) (less)
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Uncertain significance
(Jan 17, 2024)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Color Diagnostics, LLC DBA Color Health
Accession: SCV000684783.5
First in ClinVar: Feb 19, 2018 Last updated: Feb 14, 2024 |
Comment:
This missense variant replaces asparagine with serine at codon 64 of the MLH1 protein. Computational prediction suggests that this variant may have deleterious impact on … (more)
This missense variant replaces asparagine with serine at codon 64 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). Functional studies have inconclusive results, with several showing this variant results in partial loss of mismatch repair function and moderately reduced protein stability and binding ability to PMS2 protein (PMID: 17135187, 17510385, 21404117, 30504929, 36054288). Another cell-based functional assay also demonstrated the variant resulted in partial protein stability, however, the variant also displayed positive damage response signaling and DNA repair function (PMID: 36054288). This variant has been reported in individuals from Lynch syndrome families (PMID: 9311737, 16736289, 21404117). In one of these families, two affected siblings were carriers of this variant but their affected sister with microsatellite instability-high tumor did not carry this variant (PMID: 16736289). Three unaffected siblings from this family did not carry this variant. In another family, this variant co-occurred in trans with a different pathogenic variant in the MLH1 gene (PMID: 21404117, 31332305). This variant has also been reported in individuals affected with endometrial cancer (PMID: 26552419) or pancreatic cancer (PMID: 28767289). In a large breast cancer case-control study, this variant was observed in 6/60466 cases and 5/53461 unaffected controls (PMID: 33471991) This variant has been identified in 10/282844 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. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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A calibrated cell-based functional assay to aid classification of MLH1 DNA mismatch repair gene variants. | Rath A | Human mutation | 2022 | PMID: 36054288 |
Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women. | Breast Cancer Association Consortium | The New England journal of medicine | 2021 | PMID: 33471991 |
Population genetic screening efficiently identifies carriers of autosomal dominant diseases. | Grzymski JJ | Nature medicine | 2020 | PMID: 32719484 |
Full-length transcript amplification and sequencing as universal method to test mRNA integrity and biallelic expression in mismatch repair genes. | Morak M | European journal of human genetics : EJHG | 2019 | PMID: 31332305 |
A functional assay-based procedure to classify mismatch repair gene variants in Lynch syndrome. | Drost M | Genetics in medicine : official journal of the American College of Medical Genetics | 2019 | PMID: 30504929 |
Frequency of mutations in a large series of clinically ascertained ovarian cancer cases tested on multi-gene panels compared to reference controls. | Lilyquist J | Gynecologic oncology | 2017 | PMID: 28888541 |
Deleterious Germline Mutations in Patients With Apparently Sporadic Pancreatic Adenocarcinoma. | Shindo K | Journal of clinical oncology : official journal of the American Society of Clinical Oncology | 2017 | PMID: 28767289 |
Multigene Panel Testing Provides a New Perspective on Lynch Syndrome. | Espenschied CR | Journal of clinical oncology : official journal of the American Society of Clinical Oncology | 2017 | PMID: 28514183 |
Combined Microsatellite Instability, MLH1 Methylation Analysis, and Immunohistochemistry for Lynch Syndrome Screening in Endometrial Cancers From GOG210: An NRG Oncology and Gynecologic Oncology Group Study. | Goodfellow PJ | Journal of clinical oncology : official journal of the American Society of Clinical Oncology | 2015 | PMID: 26552419 |
Development and validation of a new algorithm for the reclassification of genetic variants identified in the BRCA1 and BRCA2 genes. | Pruss D | Breast cancer research and treatment | 2014 | PMID: 25085752 |
Development of a new, simple and cost-effective diagnostic tool for genetic screening of hereditary colorectal cancer--the DNA microarray assay. | Stojcev Z | Acta biochimica Polonica | 2013 | PMID: 23741719 |
Residues in the N-terminal domain of MutL required for mismatch repair in Bacillus subtilis. | Bolz NJ | Journal of bacteriology | 2012 | PMID: 22843852 |
Missense variants in hMLH1 identified in patients from the German HNPCC consortium and functional studies. | Hardt K | Familial cancer | 2011 | PMID: 21404117 |
Functional analysis of human MLH1 variants using yeast and in vitro mismatch repair assays. | Takahashi M | Cancer research | 2007 | PMID: 17510385 |
The effect of genetic background on the function of Saccharomyces cerevisiae mlh1 alleles that correspond to HNPCC missense mutations. | Wanat JJ | Human molecular genetics | 2007 | PMID: 17210669 |
Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair. | Plotz G | Nucleic acids research | 2006 | PMID: 17135187 |
Germline mutations of the hMLH1 and hMSH2 mismatch repair genes in Belgian hereditary nonpolyposis colon cancer (HNPCC) patients. | Spaepen M | Familial cancer | 2006 | PMID: 16736289 |
Human MutL homolog (MLH1) function in DNA mismatch repair: a prospective screen for missense mutations in the ATPase domain. | Ellison AR | Nucleic acids research | 2004 | PMID: 15475387 |
Mutations within the hMLH1 and hPMS2 subunits of the human MutLalpha mismatch repair factor affect its ATPase activity, but not its ability to interact with hMutSalpha. | Räschle M | The Journal of biological chemistry | 2002 | PMID: 11948175 |
Hereditary nonpolyposis colorectal cancer families not complying with the Amsterdam criteria show extremely low frequency of mismatch-repair-gene mutations. | Wijnen J | American journal of human genetics | 1997 | PMID: 9311737 |
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Text-mined citations for rs63750952 ...
HelpRecord last updated Apr 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.