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NM_001370259.2(MEN1):c.1672_1679del (p.Met558fs) AND Multiple endocrine neoplasia, type 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 27, 2019
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:
RCV001065726.7

Allele description [Variation Report for NM_001370259.2(MEN1):c.1672_1679del (p.Met558fs)]

NM_001370259.2(MEN1):c.1672_1679del (p.Met558fs)

Gene:
MEN1:menin 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11q13.1
Genomic location:
Preferred name:
NM_001370259.2(MEN1):c.1672_1679del (p.Met558fs)
HGVS:
  • NC_000011.10:g.64804489_64804496del
  • NG_008929.1:g.11800_11807del
  • NG_033040.1:g.3747_3754del
  • NM_000244.4:c.1687_1694del
  • NM_001370251.2:c.1798_1805del
  • NM_001370259.2:c.1672_1679delMANE SELECT
  • NM_001370260.2:c.1672_1679del
  • NM_001370261.2:c.1672_1679del
  • NM_001370262.2:c.1567_1574del
  • NM_001370263.2:c.1567_1574del
  • NM_130799.3:c.1672_1679del
  • NM_130800.3:c.1687_1694del
  • NM_130801.3:c.1687_1694del
  • NM_130802.3:c.1687_1694del
  • NM_130803.3:c.1687_1694del
  • NM_130804.3:c.1687_1694del
  • NP_000235.3:p.Met563fs
  • NP_001357180.2:p.Met600fs
  • NP_001357188.2:p.Met558fs
  • NP_001357189.2:p.Met558fs
  • NP_001357190.2:p.Met558fs
  • NP_001357191.2:p.Met523fs
  • NP_001357192.2:p.Met523fs
  • NP_570711.1:p.Met558fs
  • NP_570711.2:p.Met558fs
  • NP_570712.2:p.Met563fs
  • NP_570713.2:p.Met563fs
  • NP_570714.2:p.Met563fs
  • NP_570715.2:p.Met563fs
  • NP_570716.2:p.Met563fs
  • LRG_509t2:c.1672_1679del
  • LRG_509:g.11800_11807del
  • LRG_509p2:p.Met558fs
  • NC_000011.9:g.64571960_64571967del
  • NC_000011.9:g.64571961_64571968del
  • NM_130799.2:c.1672_1679del
Protein change:
M523fs
Links:
dbSNP: rs1941501683
NCBI 1000 Genomes Browser:
rs1941501683
Molecular consequence:
  • NM_000244.4:c.1687_1694del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370251.2:c.1798_1805del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370259.2:c.1672_1679del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370260.2:c.1672_1679del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370261.2:c.1672_1679del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370262.2:c.1567_1574del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370263.2:c.1567_1574del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130799.3:c.1672_1679del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130800.3:c.1687_1694del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130801.3:c.1687_1694del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130802.3:c.1687_1694del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130803.3:c.1687_1694del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_130804.3:c.1687_1694del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Multiple endocrine neoplasia, type 1 (MEN1)
Synonyms:
MEA I; MEN I; Endocrine adenomatosis multiple; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007540; MeSH: D018761; MedGen: C0025267; Orphanet: 652; OMIM: 131100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001230699Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Mar 27, 2019) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001230699.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the C-terminus of the MEN1 protein. Other variant(s) that disrupt this region (p.Lys559Glufs*38) have been determined to be pathogenic (PMID: 10090472, Invitae). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. This variant has been observed in an individual affected with clinical features of multiple endocrine neoplasia type 1 (Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change results in a premature translational stop signal in the MEN1 gene (p.Met558Hisfs*36). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 53 amino acids of the MEN1 protein.

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

Last Updated: Feb 28, 2024