NM_001370259.2(MEN1):c.1413G>A (p.Trp471Ter) AND Multiple endocrine neoplasia, type 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 5, 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:: RCV001213347.7

Allele description [Variation Report for NM_001370259.2(MEN1):c.1413G>A (p.Trp471Ter)]

NM_001370259.2(MEN1):c.1413G>A (p.Trp471Ter)

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.1413G>A (p.Trp471Ter)

HGVS:

NC_000011.10:g.64804754C>T
NG_008929.1:g.11541G>A
NG_033040.1:g.3488G>A
NM_000244.4:c.1428G>A
NM_001370251.2:c.1539G>A
NM_001370259.2:c.1413G>AMANE SELECT
NM_001370260.2:c.1413G>A
NM_001370261.2:c.1413G>A
NM_001370262.2:c.1308G>A
NM_001370263.2:c.1308G>A
NM_130799.3:c.1413G>A
NM_130800.3:c.1428G>A
NM_130801.3:c.1428G>A
NM_130802.3:c.1428G>A
NM_130803.3:c.1428G>A
NM_130804.3:c.1428G>A
NP_000235.3:p.Trp476Ter
NP_001357180.2:p.Trp513Ter
NP_001357188.2:p.Trp471Ter
NP_001357189.2:p.Trp471Ter
NP_001357190.2:p.Trp471Ter
NP_001357191.2:p.Trp436Ter
NP_001357192.2:p.Trp436Ter
NP_570711.1:p.Trp471Ter
NP_570711.2:p.Trp471Ter
NP_570712.2:p.Trp476Ter
NP_570713.2:p.Trp476Ter
NP_570714.2:p.Trp476Ter
NP_570715.2:p.Trp476Ter
NP_570716.2:p.Trp476Ter
LRG_509t2:c.1413G>A
LRG_509:g.11541G>A
LRG_509p2:p.Trp471Ter
NC_000011.9:g.64572226C>T
NM_130799.2:c.1413G>A

Protein change:

W436*

Links:

dbSNP: rs1941556077

NCBI 1000 Genomes Browser:

rs1941556077

Molecular consequence:

NM_000244.4:c.1428G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001370251.2:c.1539G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001370259.2:c.1413G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001370260.2:c.1413G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001370261.2:c.1413G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001370262.2:c.1308G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001370263.2:c.1308G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_130799.3:c.1413G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_130800.3:c.1428G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_130801.3:c.1428G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_130802.3:c.1428G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_130803.3:c.1428G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_130804.3:c.1428G>A - nonsense - [Sequence Ontology: SO:0001587]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001384973	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 5, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10090472, 10435055, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001384973

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 5, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Germline mutations in the multiple endocrine neoplasia type 1 gene: evidence for frequent splicing defects.

Mutch MG, Dilley WG, Sanjurjo F, DeBenedetti MK, Doherty GM, Wells SA Jr, Goodfellow PJ, Lairmore TC.

Hum Mutat. 1999;13(3):175-85.

PubMed [citation]

PMID:: 10090472

Multiple endocrine neoplasia type 1 (MEN1): clinical heterogeneity in a large family with a nonsense mutation in the MEN1 gene (Trp471Stop).

Valdés N, Pérez de Nanclares G, Alvarez V, Castaño L, Díaz-Cadórniga F, Aller J, Coto E.

Clin Endocrinol (Oxf). 1999 Mar;50(3):309-13.

PubMed [citation]

PMID:: 10435055

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001384973.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Trp471*) in the MEN1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 140 amino acid(s) of the MEN1 protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of MEN1 (PMID: 10090472, 10435055). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 943203). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 1, 2024

ClinVar

Relating variation to medicine