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NM_001370259.2(MEN1):c.1380_1383del (p.Glu461fs) AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 12, 2022
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:
RCV002381146.2

Allele description [Variation Report for NM_001370259.2(MEN1):c.1380_1383del (p.Glu461fs)]

NM_001370259.2(MEN1):c.1380_1383del (p.Glu461fs)

Gene:
MEN1:menin 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11q13.1
Genomic location:
Preferred name:
NM_001370259.2(MEN1):c.1380_1383del (p.Glu461fs)
HGVS:
  • NC_000011.10:g.64804785_64804788del
  • NG_008929.1:g.11508_11511del
  • NG_033040.2:g.3427_3430del
  • NM_000244.4:c.1395_1398del
  • NM_001370251.2:c.1506_1509del
  • NM_001370259.2:c.1380_1383delMANE SELECT
  • NM_001370260.2:c.1380_1383del
  • NM_001370261.2:c.1380_1383del
  • NM_001370262.2:c.1275_1278del
  • NM_001370263.2:c.1275_1278del
  • NM_001407142.1:c.1505_1508delGAGA
  • NM_001407143.1:c.1505_1508delGAGA
  • NM_001407144.1:c.1505_1508delGAGA
  • NM_001407145.1:c.1394_1397delGAGA
  • NM_001407146.1:c.1379_1382delGAGA
  • NM_001407147.1:c.1379_1382delGAGA
  • NM_001407148.1:c.1274_1277delGAGA
  • NM_001407149.1:c.1274_1277delGAGA
  • NM_001407150.1:c.1520_1523delGAGA
  • NM_001407151.1:c.1400_1403delGAGA
  • NM_001407152.1:c.1214_1217delGAGA
  • NM_130799.3:c.1380_1383del
  • NM_130800.3:c.1395_1398del
  • NM_130801.3:c.1395_1398del
  • NM_130802.3:c.1395_1398del
  • NM_130803.3:c.1395_1398del
  • NM_130804.3:c.1395_1398del
  • NP_000235.2:p.Glu466Profs
  • NP_000235.3:p.Glu466fs
  • NP_001357180.2:p.Glu503fs
  • NP_001357188.2:p.Glu461fs
  • NP_001357189.2:p.Glu461fs
  • NP_001357190.2:p.Glu461fs
  • NP_001357191.2:p.Glu426fs
  • NP_001357192.2:p.Glu426fs
  • NP_001394071.1:p.Glu503Profs
  • NP_001394072.1:p.Glu503Profs
  • NP_001394073.1:p.Glu503Profs
  • NP_001394074.1:p.Glu466Profs
  • NP_001394075.1:p.Glu461Profs
  • NP_001394076.1:p.Glu461Profs
  • NP_001394077.1:p.Glu426Profs
  • NP_001394078.1:p.Glu426Profs
  • NP_001394079.1:p.Glu508Profs
  • NP_001394080.1:p.Glu468Profs
  • NP_001394081.1:p.Glu406Profs
  • NP_570711.1:p.Glu461Profs
  • NP_570711.2:p.Glu461fs
  • NP_570712.2:p.Glu466fs
  • NP_570713.2:p.Glu466fs
  • NP_570714.2:p.Glu466fs
  • NP_570715.2:p.Glu466fs
  • NP_570716.2:p.Glu466fs
  • LRG_509t1:c.1394_1397del
  • LRG_509t2:c.1379_1382del
  • LRG_509:g.11508_11511del
  • LRG_509p1:p.Glu466Profs
  • LRG_509p2:p.Glu461Profs
  • NC_000011.9:g.64572257_64572260del
  • NG_033040.1:g.3455_3458del
  • NM_000244.3:c.1394_1397delGAGA
  • NM_130799.2:c.1379_1382delGAGA
  • NM_130799.2:c.1380_1383delAGAG
  • NR_176284.1:n.1577_1580delGAGA
  • NR_176285.1:n.1589_1592delGAGA
  • NR_176286.1:n.1592_1595delGAGA
  • NR_176287.1:n.1850_1853delGAGA
Protein change:
E426fs
Molecular consequence:
  • NM_000244.4:c.1395_1398del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370251.2:c.1506_1509del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370259.2:c.1380_1383del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370260.2:c.1380_1383del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370261.2:c.1380_1383del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370262.2:c.1275_1278del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370263.2:c.1275_1278del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407142.1:c.1505_1508delGAGA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407143.1:c.1505_1508delGAGA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407144.1:c.1505_1508delGAGA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407145.1:c.1394_1397delGAGA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407146.1:c.1379_1382delGAGA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407147.1:c.1379_1382delGAGA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407148.1:c.1274_1277delGAGA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407149.1:c.1274_1277delGAGA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407150.1:c.1520_1523delGAGA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407151.1:c.1400_1403delGAGA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407152.1:c.1214_1217delGAGA - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130799.3:c.1380_1383del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130800.3:c.1395_1398del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130801.3:c.1395_1398del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130802.3:c.1395_1398del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130803.3:c.1395_1398del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130804.3:c.1395_1398del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV002696729Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Oct 12, 2022) 		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, SCV002696729.2

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

Description

The c.1380_1383delAGAG pathogenic mutation, located in coding exon 9 of the MEN1 gene, results from a deletion of 4 nucleotides at nucleotide positions 1380 to 1383, causing a translational frameshift with a predicted alternate stop codon (p.E461Pfs*97). This alteration occurs at the 3' terminus of theMEN1 gene, is not expected to trigger nonsense-mediated mRNA decay, and impacts the last 150 amino acids of the protein. However, premature stop codons are typically deleterious in nature and the impacted region is critical for protein function and a significant portion of the protein is affected (Ambry internal data). This alteration has been observed in at least one individual with features consistent with MEN1-related disease (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, 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