Coding sequence variation introducing premature termination codon
ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.181C>T (p.Gln61Ter)
Germline
Top reviewed classifications are shown here.
Submission summary:
Reviewed by expert panel
Pathogenic
Sep 2013 by
International …
for
Lynch Syndrome
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000251.3(MSH2):c.181C>T (p.Gln61Ter)
Variation ID: 90794 Accession: VCV000090794.24
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2p21 2: 47403372 (GRCh38) [ NCBI UCSC ] 2: 47630511 (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 Mar 24, 2015 May 1, 2024 Sep 5, 2013 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000251.3:c.181C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Gln61Ter nonsense NM_001258281.1:c.-18C>T 5 prime UTR NC_000002.12:g.47403372C>T NC_000002.11:g.47630511C>T NG_007110.2:g.5249C>T LRG_218:g.5249C>T LRG_218t1:c.181C>T LRG_218p1:p.Gln61Ter - Protein change
- Q61*
- Other names
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- Canonical SPDI
- NC_000002.12:47403371:C:T
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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.
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The Genome Aggregation Database (gnomAD), exomes 0.00000
- Links
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 | ||
|---|---|---|---|---|---|---|
| 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. |
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| MSH2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
7402 | 7564 | |
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. |
|---|---|---|---|---|
| Pathogenic (2) |
reviewed by expert panel
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Sep 5, 2013 | RCV000076295.5 | |
| Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Mar 18, 2022 | RCV000219541.6 | |
| Pathogenic (5) |
criteria provided, multiple submitters, no conflicts
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Aug 24, 2023 | RCV000202086.9 | |
| Pathogenic (1) |
criteria provided, single submitter
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Aug 7, 2023 | RCV000524363.8 | |
| Pathogenic (1) |
criteria provided, single submitter
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Jul 26, 2023 | RCV003452858.1 |
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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Pathogenic
(Sep 05, 2013)
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reviewed by expert panel
Method: research
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Lynch Syndrome
Affected status: unknown
Allele origin:
germline
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International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
Accession: SCV000107316.3
First in ClinVar: Dec 19, 2013 Last updated: Dec 24, 2022
Comment:
Classified with v1.9 guidelines: https://docs.google.com/file/d/0B3JL6rP6JzhoN2EydHRVMEI1UGs
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Comment:
Coding sequence variation introducing premature termination codon
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Pathogenic
(Aug 24, 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: SCV004220961.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
The MSH2 c.181C>T (p.Gln61*) variant causes the premature termination of MSH2 protein synthesis. This variant has been reported in the published literature in affected individuals … (more)
The MSH2 c.181C>T (p.Gln61*) variant causes the premature termination of MSH2 protein synthesis. This variant has been reported in the published literature in affected individuals with colorectal cancer (PMID: 20587412 (2010)), Lynch Syndrome (PMIDs: 21642682 (2011) and 27064304 (2016)), as well as in an individual with both colorectal and bladder cancer (PMID: 29345684 (2018)). The frequency of this variant in the general population, 0.000057 (1/17498 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. (less)
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Pathogenic
(Aug 01, 2018)
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criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000567927.3
First in ClinVar: Nov 20, 2015 Last updated: Nov 20, 2015 |
Comment:
This pathogenic variant is denoted MSH2 c.181C>T at the cDNA level and p.Gln61Ter (Q61X) at the protein level. The substitution creates a nonsense variant, which … (more)
This pathogenic variant is denoted MSH2 c.181C>T at the cDNA level and p.Gln61Ter (Q61X) at the protein level. The substitution creates a nonsense variant, which changes a Glutamine to a premature stop codon (CAG>TAG), and is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. This variant has been reported in multiple individuals and families with Lynch syndrome (Sarroca 2003, Sjursen 2010, Bonadona 2011). We consider MSH2 Gln61Ter to be pathogenic. (less)
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Pathogenic
(Dec 13, 2021)
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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: SCV000537675.2
First in ClinVar: May 29, 2016 Last updated: Feb 14, 2024 |
Comment:
This variant changes 1 nucleotide in exon 1 of the MSH2 gene, creating a premature translation stop signal. This variant is expected to result in … (more)
This variant changes 1 nucleotide in exon 1 of the MSH2 gene, creating a premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with or suspected of having Lynch syndrome (PMID: 12660027, 20587412, 21642682). This variant has been identified in 1/232530 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. (less)
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Pathogenic
(Aug 07, 2023)
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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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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000548182.8
First in ClinVar: Mar 24, 2015 Last updated: Feb 28, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Gln61*) in the MSH2 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Gln61*) in the MSH2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH2 are known to be pathogenic (PMID: 15849733, 24362816). This variant is present in population databases (rs63750951, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with Lynch syndrome (PMID: 12660027, 21642682). ClinVar contains an entry for this variant (Variation ID: 90794). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Jul 26, 2023)
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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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Myriad Genetics, Inc.
Accession: SCV004188120.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
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Pathogenic
(Mar 18, 2022)
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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: SCV000274919.8
First in ClinVar: May 29, 2016 Last updated: May 01, 2024 |
Comment:
The p.Q61* pathogenic mutation (also known as c.181C>T), located in coding exon 1 of the MSH2 gene, results from a C to T substitution at … (more)
The p.Q61* pathogenic mutation (also known as c.181C>T), located in coding exon 1 of the MSH2 gene, results from a C to T substitution at nucleotide position 181. This changes the amino acid from a glutamine to a stop codon within coding exon 1. This mutation was first described in an extended family originating from Spain who fulfilled Amsterdam criteria for HNPCC/Lynch syndrome (Sarroca C et al. Cancer Genet Cytogenet. 2003 Apr 1;142(1):13-20). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: research
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not provided
Affected status: unknown
Allele origin:
unknown
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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000257153.1
First in ClinVar: Nov 20, 2015 Last updated: Nov 20, 2015 |
Number of individuals with the variant: 1
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001953610.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001973758.1 First in ClinVar: Oct 08, 2021 Last updated: Oct 08, 2021 |
|
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not provided
(-)
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no classification provided
Method: phenotyping only
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Hereditary nonpolyposis colon cancer
Affected status: unknown
Allele origin:
unknown
|
GenomeConnect, ClinGen
Accession: SCV000784702.1
First in ClinVar: Dec 26, 2017 Last updated: Dec 26, 2017 |
Comment:
GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical … (more)
GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. (less)
Clinical Features:
Prenatal maternal abnormality (present) , Hypermetropia (present) , Abnormality of vision (present) , Hypercholesterolemia (present) , Abnormal EKG (present) , Arrhythmia (present) , Abnormality of … (more)
Prenatal maternal abnormality (present) , Hypermetropia (present) , Abnormality of vision (present) , Hypercholesterolemia (present) , Abnormal EKG (present) , Arrhythmia (present) , Abnormality of the intestine (present) , Abnormality of the liver (present) , Abnormality of esophagus morphology (present) , Abnormality of urine homeostasis (present) , Abnormality of the ureter (present) , Abnormal renal morphology (present) , Abnormal renal physiology (present) , Abnormality of the bladder (present) , Colon cancer (present) , Breast carcinoma (present) (less)
Age: 40-49 years
Sex: female
Ethnicity/Population group: Caucasians MedGen:C0043157
Testing laboratory: Ambry Genetics
Date variant was reported to submitter: 2015-04-05
Testing laboratory interpretation: Pathogenic
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Comment:
Comment:
The MSH2 c.181C>T (p.Gln61*) variant causes the premature termination of MSH2 protein synthesis. This variant has been reported in the published literature in affected individuals with colorectal cancer (PMID: 20587412 (2010)), Lynch Syndrome (PMIDs: 21642682 (2011) and 27064304 (2016)), as well as in an individual with both colorectal and bladder cancer (PMID: 29345684 (2018)). The frequency of this variant in the general population, 0.000057 (1/17498 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic.
Comment:
This pathogenic variant is denoted MSH2 c.181C>T at the cDNA level and p.Gln61Ter (Q61X) at the protein level. The substitution creates a nonsense variant, which changes a Glutamine to a premature stop codon (CAG>TAG), and is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. This variant has been reported in multiple individuals and families with Lynch syndrome (Sarroca 2003, Sjursen 2010, Bonadona 2011). We consider MSH2 Gln61Ter to be pathogenic.
Comment:
This variant changes 1 nucleotide in exon 1 of the MSH2 gene, creating a premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with or suspected of having Lynch syndrome (PMID: 12660027, 20587412, 21642682). This variant has been identified in 1/232530 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.
Comment:
This sequence change creates a premature translational stop signal (p.Gln61*) in the MSH2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH2 are known to be pathogenic (PMID: 15849733, 24362816). This variant is present in population databases (rs63750951, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with Lynch syndrome (PMID: 12660027, 21642682). ClinVar contains an entry for this variant (Variation ID: 90794). For these reasons, this variant has been classified as Pathogenic.
Comment:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
Comment:
The p.Q61* pathogenic mutation (also known as c.181C>T), located in coding exon 1 of the MSH2 gene, results from a C to T substitution at nucleotide position 181. This changes the amino acid from a glutamine to a stop codon within coding exon 1. This mutation was first described in an extended family originating from Spain who fulfilled Amsterdam criteria for HNPCC/Lynch syndrome (Sarroca C et al. Cancer Genet Cytogenet. 2003 Apr 1;142(1):13-20). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.
Comment:
GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
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:
Coding sequence variation introducing premature termination codon
Comment:
The MSH2 c.181C>T (p.Gln61*) variant causes the premature termination of MSH2 protein synthesis. This variant has been reported in the published literature in affected individuals with colorectal cancer (PMID: 20587412 (2010)), Lynch Syndrome (PMIDs: 21642682 (2011) and 27064304 (2016)), as well as in an individual with both colorectal and bladder cancer (PMID: 29345684 (2018)). The frequency of this variant in the general population, 0.000057 (1/17498 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic.
Comment:
This pathogenic variant is denoted MSH2 c.181C>T at the cDNA level and p.Gln61Ter (Q61X) at the protein level. The substitution creates a nonsense variant, which changes a Glutamine to a premature stop codon (CAG>TAG), and is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. This variant has been reported in multiple individuals and families with Lynch syndrome (Sarroca 2003, Sjursen 2010, Bonadona 2011). We consider MSH2 Gln61Ter to be pathogenic.
Comment:
This variant changes 1 nucleotide in exon 1 of the MSH2 gene, creating a premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with or suspected of having Lynch syndrome (PMID: 12660027, 20587412, 21642682). This variant has been identified in 1/232530 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.
Comment:
This sequence change creates a premature translational stop signal (p.Gln61*) in the MSH2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH2 are known to be pathogenic (PMID: 15849733, 24362816). This variant is present in population databases (rs63750951, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with Lynch syndrome (PMID: 12660027, 21642682). ClinVar contains an entry for this variant (Variation ID: 90794). For these reasons, this variant has been classified as Pathogenic.
Comment:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
Comment:
The p.Q61* pathogenic mutation (also known as c.181C>T), located in coding exon 1 of the MSH2 gene, results from a C to T substitution at nucleotide position 181. This changes the amino acid from a glutamine to a stop codon within coding exon 1. This mutation was first described in an extended family originating from Spain who fulfilled Amsterdam criteria for HNPCC/Lynch syndrome (Sarroca C et al. Cancer Genet Cytogenet. 2003 Apr 1;142(1):13-20). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.
Comment:
GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| A genomic survey of sarcomas on sun-exposed skin reveals distinctive candidate drivers and potentially targetable mutations. | Miller TI | Human pathology | 2020 | PMID: 32540221 |
| Mismatch repair deficiency in metastatic prostate cancer: Response to PD-1 blockade and standard therapies. | Graham LS | PloS one | 2020 | PMID: 32453797 |
| Prevalence of pathogenic germline cancer risk variants in high-risk urothelial carcinoma. | Nassar AH | Genetics in medicine : official journal of the American College of Medical Genetics | 2020 | PMID: 31844177 |
| Screening for hereditary cancers in patients with endometrial cancer reveals a high frequency of germline mutations in cancer predisposition genes. | Tian W | International journal of cancer | 2019 | PMID: 31054147 |
| Single-center study of Lynch syndrome screening in colorectal polyps. | Zhu F | Hereditary cancer in clinical practice | 2019 | PMID: 30918532 |
| MSH6 and PMS2 germ-line pathogenic variants implicated in Lynch syndrome are associated with breast cancer. | Roberts ME | Genetics in medicine : official journal of the American College of Medical Genetics | 2018 | PMID: 29345684 |
| In Silico Systems Biology Analysis of Variants of Uncertain Significance in Lynch Syndrome Supports the Prioritization of Functional Molecular Validation. | Borras E | Cancer prevention research (Philadelphia, Pa.) | 2017 | PMID: 28765196 |
| 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 |
| Exome sequencing covers >98% of mutations identified on targeted next generation sequencing panels. | LaDuca H | PloS one | 2017 | PMID: 28152038 |
| Lynch syndrome mutation spectrum in New South Wales, Australia, including 55 novel mutations. | Sjursen W | Molecular genetics & genomic medicine | 2016 | PMID: 27064304 |
| Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. | Thompson BA | Nature genetics | 2014 | PMID: 24362816 |
| Mutation spectrum in South American Lynch syndrome families. | Dominguez-Valentin M | Hereditary cancer in clinical practice | 2013 | PMID: 24344984 |
| Insights into protein - DNA interactions, stability and allosteric communications: a computational study of mutSα-DNA recognition complexes. | Negureanu L | Journal of biomolecular structure & dynamics | 2012 | PMID: 22208277 |
| Cancer risks associated with germline mutations in MLH1, MSH2, and MSH6 genes in Lynch syndrome. | Bonadona V | JAMA | 2011 | PMID: 21642682 |
| Current clinical criteria for Lynch syndrome are not sensitive enough to identify MSH6 mutation carriers. | Sjursen W | Journal of medical genetics | 2010 | PMID: 20587412 |
| Spectrum and frequencies of mutations in MSH2 and MLH1 identified in 1,721 German families suspected of hereditary nonpolyposis colorectal cancer. | Mangold E | International journal of cancer | 2005 | PMID: 15849733 |
| Three new mutations in hereditary nonpolyposis colorectal cancer (Lynch syndrome II) in Uruguay. | Sarroca C | Cancer genetics and cytogenetics | 2003 | PMID: 12660027 |
| http://www.insight-database.org/classifications/index.html?gene=MSH2&variant=c.181C%3ET | - | - | - | - |
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Text-mined citations for rs63750951 ...
HelpThese citations are identified by LitVar using
the rs number, so they may include citations for more than one variant
at this location. Please review the LitVar results carefully for your
variant of interest.
Record last updated Sep 29, 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.