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NM_000251.3(MSH2):c.1953del (p.Pro652fs) AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 3, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003350724.2

Allele description [Variation Report for NM_000251.3(MSH2):c.1953del (p.Pro652fs)]

NM_000251.3(MSH2):c.1953del (p.Pro652fs)

Gene:
MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_000251.3(MSH2):c.1953del (p.Pro652fs)
HGVS:
  • NC_000002.12:g.47475218del
  • NG_007110.2:g.77095del
  • NM_000251.3:c.1953delMANE SELECT
  • NM_001258281.1:c.1755del
  • NM_001406631.1:c.1953del
  • NM_001406632.1:c.1953del
  • NM_001406633.1:c.1953del
  • NM_001406634.1:c.1953del
  • NM_001406635.1:c.1953del
  • NM_001406636.1:c.1920del
  • NM_001406637.1:c.1953del
  • NM_001406638.1:c.1992del
  • NM_001406639.1:c.1953del
  • NM_001406640.1:c.1953del
  • NM_001406641.1:c.1953del
  • NM_001406642.1:c.1953del
  • NM_001406643.1:c.1953del
  • NM_001406644.1:c.1953del
  • NM_001406645.1:c.1953del
  • NM_001406646.1:c.1953del
  • NM_001406647.1:c.1803del
  • NM_001406648.1:c.1953del
  • NM_001406649.1:c.1803del
  • NM_001406650.1:c.1803del
  • NM_001406651.1:c.1803del
  • NM_001406652.1:c.1803del
  • NM_001406653.1:c.1893del
  • NM_001406654.1:c.1533del
  • NM_001406655.1:c.1953del
  • NM_001406656.1:c.1056del
  • NM_001406657.1:c.*163del
  • NM_001406658.1:c.597del
  • NM_001406659.1:c.597del
  • NM_001406660.1:c.597del
  • NM_001406661.1:c.597del
  • NM_001406662.1:c.597del
  • NM_001406669.1:c.597del
  • NM_001406674.1:c.1953del
  • NP_000242.1:p.Pro652Leufs
  • NP_000242.1:p.Pro652fs
  • NP_001245210.1:p.Pro586fs
  • NP_001393560.1:p.Pro652fs
  • NP_001393561.1:p.Pro652fs
  • NP_001393562.1:p.Pro652fs
  • NP_001393563.1:p.Pro652fs
  • NP_001393564.1:p.Pro652fs
  • NP_001393565.1:p.Pro641fs
  • NP_001393566.1:p.Pro652fs
  • NP_001393567.1:p.Pro665fs
  • NP_001393568.1:p.Pro652fs
  • NP_001393569.1:p.Pro652fs
  • NP_001393570.1:p.Pro652fs
  • NP_001393571.1:p.Pro652fs
  • NP_001393572.1:p.Pro652fs
  • NP_001393573.1:p.Pro652fs
  • NP_001393574.1:p.Pro652fs
  • NP_001393575.1:p.Pro652fs
  • NP_001393576.1:p.Pro602fs
  • NP_001393577.1:p.Pro652fs
  • NP_001393578.1:p.Pro602fs
  • NP_001393579.1:p.Pro602fs
  • NP_001393580.1:p.Pro602fs
  • NP_001393581.1:p.Pro602fs
  • NP_001393582.1:p.Pro632fs
  • NP_001393583.1:p.Pro512fs
  • NP_001393584.1:p.Pro652fs
  • NP_001393585.1:p.Pro353fs
  • NP_001393587.1:p.Pro200fs
  • NP_001393588.1:p.Pro200fs
  • NP_001393589.1:p.Pro200fs
  • NP_001393590.1:p.Pro200fs
  • NP_001393591.1:p.Pro200fs
  • NP_001393598.1:p.Pro200fs
  • NP_001393603.1:p.Pro652fs
  • LRG_218t1:c.1953del
  • LRG_218:g.77095del
  • LRG_218p1:p.Pro652Leufs
  • NC_000002.11:g.47702357del
  • NM_000251.1:c.1953delT
  • NM_000251.2:c.1953delT
  • NR_176230.1:n.1989del
  • NR_176231.1:n.1989del
  • NR_176232.1:n.1989del
  • NR_176233.1:n.1831del
  • NR_176234.1:n.1989del
  • NR_176235.1:n.1989del
  • NR_176236.1:n.1989del
  • NR_176237.1:n.1989del
  • NR_176238.1:n.2122del
  • NR_176239.1:n.1989del
  • NR_176240.1:n.1989del
  • NR_176241.1:n.1989del
  • NR_176242.1:n.1989del
  • NR_176243.1:n.1839del
  • NR_176244.1:n.1989del
  • NR_176245.1:n.1989del
  • NR_176246.1:n.1989del
  • NR_176247.1:n.1989del
  • NR_176248.1:n.1989del
  • NR_176249.1:n.2219del
  • NR_176250.1:n.1729del
Protein change:
P200fs
Molecular consequence:
  • NM_001406657.1:c.*163del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000251.3:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001258281.1:c.1755del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406631.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406632.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406633.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406634.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406635.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406636.1:c.1920del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406637.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406638.1:c.1992del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406639.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406640.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406641.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406642.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406643.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406644.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406645.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406646.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406647.1:c.1803del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406648.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406649.1:c.1803del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406650.1:c.1803del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406651.1:c.1803del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406652.1:c.1803del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406653.1:c.1893del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406654.1:c.1533del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406655.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406656.1:c.1056del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406658.1:c.597del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406659.1:c.597del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406660.1:c.597del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406661.1:c.597del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406662.1:c.597del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406669.1:c.597del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406674.1:c.1953del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_176230.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176231.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176232.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176233.1:n.1831del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176234.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176235.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176236.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176237.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176238.1:n.2122del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176239.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176240.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176241.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176242.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176243.1:n.1839del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176244.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176245.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176246.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176247.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176248.1:n.1989del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176249.1:n.2219del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176250.1:n.1729del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004055851Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Jul 3, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV004055851.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.1953delT pathogenic mutation, located in coding exon 12 of the MSH2 gene, results from a deletion of one nucleotide at nucleotide position 1953, causing a translational frameshift with a predicted alternate stop codon (p.P652Lfs*33). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 1, 2024