NM_001370259.2(MEN1):c.783+1G>A AND Multiple endocrine neoplasia, type 1

Clinical significance:Pathogenic (Last evaluated: Aug 5, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000697334.3

Allele description [Variation Report for NM_001370259.2(MEN1):c.783+1G>A]

NM_001370259.2(MEN1):c.783+1G>A

Gene:
MEN1:menin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q13.1
Genomic location:
Preferred name:
NM_001370259.2(MEN1):c.783+1G>A
HGVS:
  • NC_000011.10:g.64807551C>T
  • NG_008929.1:g.8744G>A
  • NG_033040.1:g.691G>A
  • NM_000244.3:c.798+1G>A
  • NM_001370251.1:c.783+1G>A
  • NM_001370259.2:c.783+1G>AMANE SELECT
  • NM_001370260.1:c.783+1G>A
  • NM_001370261.1:c.783+1G>A
  • NM_001370262.1:c.678+1G>A
  • NM_001370263.1:c.678+1G>A
  • NM_130799.2:c.783+1G>A
  • NM_130800.2:c.798+1G>A
  • NM_130801.2:c.798+1G>A
  • NM_130802.2:c.798+1G>A
  • NM_130803.2:c.798+1G>A
  • NM_130804.2:c.798+1G>A
  • LRG_509t1:c.798+1G>A
  • LRG_509t2:c.783+1G>A
  • LRG_509:g.8744G>A
  • NC_000011.9:g.64575023C>T
Links:
dbSNP: rs794728652
NCBI 1000 Genomes Browser:
rs794728652
Molecular consequence:
  • NM_000244.3:c.798+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370251.1:c.783+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370259.2:c.783+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370260.1:c.783+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370261.1:c.783+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370262.1:c.678+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370263.1:c.678+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130799.2:c.783+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130800.2:c.798+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130801.2:c.798+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130802.2:c.798+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130803.2:c.798+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130804.2:c.798+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000825936Invitaecriteria provided, single submitter
Pathogenic
(Aug 5, 2019)
germlineclinical testing

PubMed (8)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

MEN1 gene mutation analysis in Italian patients with multiple endocrine neoplasia type 1.

Morelli A, Falchetti A, Martineti V, Becherini L, Mark M, Friedman E, Brandi ML.

Eur J Endocrinol. 2000 Feb;142(2):131-7.

PubMed [citation]
PMID:
10664520

Mutation analysis in two Chinese families with multiple endocrine neoplasia type 1.

Wen Z, Liao Q, Hu Y, Zhao Y.

Arq Bras Endocrinol Metabol. 2012 Apr;56(3):184-9.

PubMed [citation]
PMID:
22666734
See all PubMed Citations (8)

Details of each submission

From Invitae, SCV000825936.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (8)

Description

This sequence change affects a donor splice site in intron 4 of the MEN1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been reported in individuals affected with multiple endocrine neoplasia type 1 (PMID: 10664520, 22666734). This variant is also referred to as c.893+1G>A or IVS4+1 T>A in the literature. ClinVar contains an entry for this variant (Variation ID: 428081). Other variants affecting this nucleotide (c.783+1G>C and c.783+1G>T, also known as c.893+1G>C and c.893+1G>T in the literature) have been determined to be pathogenic (PMID: 9888389, 9683585). This suggests that this nucleotide is important for normal RNA splicing, and that other variants at this position may also be pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in MEN1 are known to be pathogenic (PMID: 12112656, 17853334). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 10, 2021

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