NM_001370259.2(MEN1):c.1478del (p.Pro493fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 13, 2020
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:: RCV002397070.2

Allele description [Variation Report for NM_001370259.2(MEN1):c.1478del (p.Pro493fs)]

NM_001370259.2(MEN1):c.1478del (p.Pro493fs)

Gene:

MEN1:menin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q13.1

Genomic location:

Preferred name:

NM_001370259.2(MEN1):c.1478del (p.Pro493fs)

HGVS:

NC_000011.10:g.64804693del
NG_008929.1:g.11606del
NG_033040.2:g.3525del
NM_000244.4:c.1493del
NM_001370251.2:c.1604del
NM_001370259.2:c.1478delMANE SELECT
NM_001370260.2:c.1478del
NM_001370261.2:c.1478del
NM_001370262.2:c.1373del
NM_001370263.2:c.1373del
NM_001407142.1:c.1600delC
NM_001407143.1:c.1600delC
NM_001407144.1:c.1600delC
NM_001407145.1:c.1489delC
NM_001407146.1:c.1474delC
NM_001407147.1:c.1474delC
NM_001407148.1:c.1369delC
NM_001407149.1:c.1369delC
NM_001407150.1:c.1615delC
NM_001407151.1:c.1495delC
NM_001407152.1:c.1309delC
NM_130799.3:c.1478del
NM_130800.3:c.1493del
NM_130801.3:c.1493del
NM_130802.3:c.1493del
NM_130803.3:c.1493del
NM_130804.3:c.1493del
NP_000235.2:p.Pro498Argfs
NP_000235.3:p.Pro498fs
NP_001357180.2:p.Pro535fs
NP_001357188.2:p.Pro493fs
NP_001357189.2:p.Pro493fs
NP_001357190.2:p.Pro493fs
NP_001357191.2:p.Pro458fs
NP_001357192.2:p.Pro458fs
NP_001394071.1:p.Pro535Argfs
NP_001394072.1:p.Pro535Argfs
NP_001394073.1:p.Pro535Argfs
NP_001394074.1:p.Pro498Argfs
NP_001394075.1:p.Pro493Argfs
NP_001394076.1:p.Pro493Argfs
NP_001394077.1:p.Pro458Argfs
NP_001394078.1:p.Pro458Argfs
NP_001394079.1:p.Pro540Argfs
NP_001394080.1:p.Pro500Argfs
NP_001394081.1:p.Pro438Argfs
NP_570711.1:p.Pro493Argfs
NP_570711.2:p.Pro493fs
NP_570712.2:p.Pro498fs
NP_570713.2:p.Pro498fs
NP_570714.2:p.Pro498fs
NP_570715.2:p.Pro498fs
NP_570716.2:p.Pro498fs
LRG_509t1:c.1489del
LRG_509t2:c.1474del
LRG_509:g.11606del
LRG_509p1:p.Pro498Argfs
LRG_509p2:p.Pro493Argfs
NC_000011.9:g.64572161del
NC_000011.9:g.64572165del
NG_033040.1:g.3553del
NM_000244.3:c.1489delC
NM_130799.2:c.1474delC
NM_130799.2:c.1478delC
NR_176284.1:n.1672delC
NR_176285.1:n.1684delC
NR_176286.1:n.1687delC
NR_176287.1:n.1945delC

Protein change:

P458fs

Molecular consequence:

NM_000244.4:c.1493del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370251.2:c.1604del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370259.2:c.1478del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370260.2:c.1478del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370261.2:c.1478del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370262.2:c.1373del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370263.2:c.1373del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407142.1:c.1600delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407143.1:c.1600delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407144.1:c.1600delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407145.1:c.1489delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407146.1:c.1474delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407147.1:c.1474delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407148.1:c.1369delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407149.1:c.1369delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407150.1:c.1615delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407151.1:c.1495delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407152.1:c.1309delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130799.3:c.1478del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130800.3:c.1493del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130801.3:c.1493del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130802.3:c.1493del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130803.3:c.1493del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130804.3:c.1493del - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002697075	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Aug 13, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002697075

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Aug 13, 2020)

germline

clinical testing

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

Citation Link

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

Developing effective screening strategies in multiple endocrine neoplasia type 1 (MEN 1) on the basis of clinical and sequencing data of German patients with MEN 1.

Schaaf L, Pickel J, Zinner K, Hering U, Höfler M, Goretzki PE, Spelsberg F, Raue F, von zur Mühlen A, Gerl H, Hensen J, Bartsch DK, Rothmund M, Schneyer U, Dralle H, Engelbach M, Karges W, Stalla GK, Höppner W.

Exp Clin Endocrinol Diabetes. 2007 Sep;115(8):509-17.

PubMed [citation]

PMID:: 17853334

Details of each submission

From Ambry Genetics, SCV002697075.2

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

Description

The c.1478delC pathogenic mutation, located in coding exon 9 of the MEN1 gene, results from a deletion of one nucleotide at nucleotide position 1478, causing a translational frameshift with a predicted alternate stop codon (p.P493Rfs*66). This alteration (designated as "1588delC") was identified in at least one individual from a cohort of German patients meeting MEN1 clinical diagnostic criteria (Schaaf L et al. Exp. Clin. Endocrinol. Diabetes, 2007 Sep;115:509-17). In addition to published clinical data, this alteration is expected to result in loss of function by premature protein truncation. As such, this alteration is interpreted as a disease-causing mutation.

#	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: Sep 29, 2024

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