VCV002709090.2 - ClinVar

NM_000249.4(MLH1):c.2079G>C (p.Glu693Asp)

Germline

Classification

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.

(2)

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.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000249.4(MLH1):c.2079G>C (p.Glu693Asp)

Variation ID: 2709090 Accession: VCV002709090.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 3p22.2 3: 37048993 (GRCh38) [ NCBI UCSC ] 3: 37090484 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	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	Feb 14, 2024	Apr 20, 2024	Jan 12, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_000249.4:c.2079G>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000240.1:p.Glu693Asp	missense
NM_001167617.3:c.1785G>C	NP_001161089.1:p.Glu595Asp	missense
NM_001167618.3:c.1356G>C	NP_001161090.1:p.Glu452Asp	missense
NM_001167619.3:c.1356G>C	NP_001161091.1:p.Glu452Asp	missense
NM_001258271.2:c.1896+1310G>C		intron variant
NM_001258273.2:c.1356G>C	NP_001245202.1:p.Glu452Asp	missense
NM_001258274.3:c.1356G>C	NP_001245203.1:p.Glu452Asp	missense
NM_001354615.2:c.1356G>C	NP_001341544.1:p.Glu452Asp	missense
NM_001354616.2:c.1356G>C	NP_001341545.1:p.Glu452Asp	missense
NM_001354617.2:c.1356G>C	NP_001341546.1:p.Glu452Asp	missense
NM_001354618.2:c.1356G>C	NP_001341547.1:p.Glu452Asp	missense
NM_001354619.2:c.1356G>C	NP_001341548.1:p.Glu452Asp	missense
NM_001354620.2:c.1785G>C	NP_001341549.1:p.Glu595Asp	missense
NM_001354621.2:c.1056G>C	NP_001341550.1:p.Glu352Asp	missense
NM_001354622.2:c.1056G>C	NP_001341551.1:p.Glu352Asp	missense
NM_001354623.2:c.1056G>C	NP_001341552.1:p.Glu352Asp	missense
NM_001354624.2:c.1005G>C	NP_001341553.1:p.Glu335Asp	missense
NM_001354625.2:c.1005G>C	NP_001341554.1:p.Glu335Asp	missense
NM_001354626.2:c.1005G>C	NP_001341555.1:p.Glu335Asp	missense
NM_001354627.2:c.1005G>C	NP_001341556.1:p.Glu335Asp	missense
NM_001354628.2:c.1986G>C	NP_001341557.1:p.Glu662Asp	missense
NM_001354629.2:c.1980G>C	NP_001341558.1:p.Glu660Asp	missense
NM_001354630.2:c.1914G>C	NP_001341559.1:p.Glu638Asp	missense
NC_000003.12:g.37048993G>C
NC_000003.11:g.37090484G>C
NG_007109.2:g.60644G>C
LRG_216:g.60644G>C
LRG_216t1:c.2079G>C	LRG_216p1:p.Glu693Asp

... more HGVS ... less HGVS

Protein change

E352D, E595D, E638D, E693D, E335D, E452D, E660D, E662D

Other names

Canonical SPDI

NC_000003.12:37048992:G:C

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

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
Gene	OMIM	HI score Help 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.
MLH1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	5691	5752

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.
Hereditary nonpolyposis colorectal neoplasms	Uncertain significance (1)	criteria provided, single submitter	Jan 12, 2024	RCV003595063.2
Lynch syndrome	Uncertain significance (1)	criteria provided, single submitter	May 16, 2023	RCV004011355.2

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.
Uncertain significance (Jan 12, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Hereditary nonpolyposis colorectal neoplasms Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004260314.1 First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024	Comment: This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 693 of the MLH1 … (more) This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 693 of the MLH1 protein (p.Glu693Asp). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MLH1-related conditions. 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 not expected to disrupt MLH1 protein function with a negative predictive value of 95%. 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)
Uncertain Significance (May 16, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Lynch syndrome (Autosomal dominant inheritance) Affected status: unknown Allele origin: germline	All of Us Research Program, National Institutes of Health Accession: SCV004843270.1 First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024 Comment: This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more) This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)	Comment: This missense variant replaces glutamic acid with aspartic acid at codon 693 of the MLH1 protein. Computational prediction suggests that this variant may not impact … (more) This missense variant replaces glutamic acid with aspartic acid at codon 693 of the MLH1 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, 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 not been identified 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: 1

Comment:

This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 693 of the MLH1 protein (p.Glu693Asp). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MLH1-related conditions. 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 not expected to disrupt MLH1 protein function with a negative predictive value of 95%. 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.

Comment:

This missense variant replaces glutamic acid with aspartic acid at codon 693 of the MLH1 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, 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 not been identified 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.

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.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NM_000249.4(MLH1):c.2079G>C (p.Glu693Asp)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...