ClinVar Genomic variation as it relates to human health
NM_000251.3(MSH2):c.1889del (p.Gly630fs)
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000251.3(MSH2):c.1889del (p.Gly630fs)
Variation ID: 1782026 Accession: VCV001782026.3
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 2p21 2: 47475153 (GRCh38) [ NCBI UCSC ] 2: 47702292 (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 Nov 29, 2022 May 1, 2024 Aug 4, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000251.3:c.1889del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000242.1:p.Gly630fs frameshift NM_001258281.1:c.1691del NP_001245210.1:p.Gly564fs frameshift NM_001406631.1:c.1889delG NP_001393560.1:p.Gly630Glufs frameshift NM_001406632.1:c.1889delG NP_001393561.1:p.Gly630Glufs frameshift NM_001406633.1:c.1889delG NP_001393562.1:p.Gly630Glufs frameshift NM_001406634.1:c.1889delG NP_001393563.1:p.Gly630Glufs frameshift NM_001406635.1:c.1889delG NP_001393564.1:p.Gly630Glufs frameshift NM_001406636.1:c.1856delG NP_001393565.1:p.Gly619Glufs frameshift NM_001406637.1:c.1889delG NP_001393566.1:p.Gly630Glufs frameshift NM_001406638.1:c.1928delG NP_001393567.1:p.Gly643Glufs frameshift NM_001406639.1:c.1889delG NP_001393568.1:p.Gly630Glufs frameshift NM_001406640.1:c.1889delG NP_001393569.1:p.Gly630Glufs frameshift NM_001406641.1:c.1889delG NP_001393570.1:p.Gly630Glufs frameshift NM_001406642.1:c.1889delG NP_001393571.1:p.Gly630Glufs frameshift NM_001406643.1:c.1889delG NP_001393572.1:p.Gly630Glufs frameshift NM_001406644.1:c.1889delG NP_001393573.1:p.Gly630Glufs frameshift NM_001406645.1:c.1889delG NP_001393574.1:p.Gly630Glufs frameshift NM_001406646.1:c.1889delG NP_001393575.1:p.Gly630Glufs frameshift NM_001406647.1:c.1739delG NP_001393576.1:p.Gly580Glufs frameshift NM_001406648.1:c.1889delG NP_001393577.1:p.Gly630Glufs frameshift NM_001406649.1:c.1739delG NP_001393578.1:p.Gly580Glufs frameshift NM_001406650.1:c.1739delG NP_001393579.1:p.Gly580Glufs frameshift NM_001406651.1:c.1739delG NP_001393580.1:p.Gly580Glufs frameshift NM_001406652.1:c.1739delG NP_001393581.1:p.Gly580Glufs frameshift NM_001406653.1:c.1829delG NP_001393582.1:p.Gly610Glufs frameshift NM_001406654.1:c.1469delG NP_001393583.1:p.Gly490Glufs frameshift NM_001406655.1:c.1889delG NP_001393584.1:p.Gly630Glufs frameshift NM_001406656.1:c.992delG NP_001393585.1:p.Gly331Glufs frameshift NM_001406657.1:c.*99delG NM_001406658.1:c.533delG NP_001393587.1:p.Gly178Glufs frameshift NM_001406659.1:c.533delG NP_001393588.1:p.Gly178Glufs frameshift NM_001406660.1:c.533delG NP_001393589.1:p.Gly178Glufs frameshift NM_001406661.1:c.533delG NP_001393590.1:p.Gly178Glufs frameshift NM_001406662.1:c.533delG NP_001393591.1:p.Gly178Glufs frameshift NM_001406669.1:c.533delG NP_001393598.1:p.Gly178Glufs frameshift NM_001406674.1:c.1889delG NP_001393603.1:p.Gly630Glufs frameshift NR_176230.1:n.1925delG NR_176231.1:n.1925delG NR_176232.1:n.1925delG NR_176233.1:n.1767delG NR_176234.1:n.1925delG NR_176235.1:n.1925delG NR_176236.1:n.1925delG NR_176237.1:n.1925delG NR_176238.1:n.2058delG NR_176239.1:n.1925delG NR_176240.1:n.1925delG NR_176241.1:n.1925delG NR_176242.1:n.1925delG NR_176243.1:n.1775delG NR_176244.1:n.1925delG NR_176245.1:n.1925delG NR_176246.1:n.1925delG NR_176247.1:n.1925delG NR_176248.1:n.1925delG NR_176249.1:n.2155delG NR_176250.1:n.1665delG NC_000002.12:g.47475154del NC_000002.11:g.47702293del NG_007110.2:g.77031del LRG_218:g.77031del LRG_218t1:c.1889del LRG_218p1:p.Gly630Glufs - Protein change
- G630fs, G564fs
- Other names
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- Canonical SPDI
- NC_000002.12:47475152:GG: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
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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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
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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 |
7401 | 7563 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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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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Pathogenic (1) |
criteria provided, single submitter
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Apr 7, 2020 | RCV002407981.2 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 4, 2023 | RCV003454298.1 |
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
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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
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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
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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
(Aug 04, 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: SCV004187958.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
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Pathogenic
(Apr 07, 2020)
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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: SCV002723849.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The c.1889delG pathogenic mutation, located in coding exon 12 of the MSH2 gene, results from a deletion of one nucleotide at nucleotide position 1889, causing … (more)
The c.1889delG pathogenic mutation, located in coding exon 12 of the MSH2 gene, results from a deletion of one nucleotide at nucleotide position 1889, causing a translational frameshift with a predicted alternate stop codon (p.G630Efs*5). 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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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
HelpThere 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 ...
HelpRecord last updated Jun 10, 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.