NM_001370259.2(MEN1):c.307del (p.Leu103fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 15, 2021
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:: RCV000491671.5

Allele description [Variation Report for NM_001370259.2(MEN1):c.307del (p.Leu103fs)]

NM_001370259.2(MEN1):c.307del (p.Leu103fs)

Gene:

MEN1:menin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q13.1

Genomic location:

Preferred name:

NM_001370259.2(MEN1):c.307del (p.Leu103fs)

HGVS:

NC_000011.10:g.64809804del
NC_000011.9:g.64577275del
NG_008929.1:g.6492del
NM_000244.4:c.307del
NM_001370251.2:c.307del
NM_001370259.2:c.307delMANE SELECT
NM_001370260.2:c.307del
NM_001370261.2:c.307del
NM_001370262.2:c.307del
NM_001370263.2:c.307del
NM_130799.3:c.307del
NM_130800.3:c.307del
NM_130801.3:c.307del
NM_130802.3:c.307del
NM_130803.3:c.307del
NM_130804.3:c.307del
NP_000235.3:p.Leu103fs
NP_001357180.2:p.Leu103fs
NP_001357188.2:p.Leu103fs
NP_001357189.2:p.Leu103fs
NP_001357190.2:p.Leu103fs
NP_001357191.2:p.Leu103fs
NP_001357192.2:p.Leu103fs
NP_570711.1:p.Leu103fs
NP_570711.2:p.Leu103fs
NP_570712.2:p.Leu103fs
NP_570713.2:p.Leu103fs
NP_570714.2:p.Leu103fs
NP_570715.2:p.Leu103fs
NP_570716.2:p.Leu103fs
LRG_509t2:c.307del
LRG_509:g.6492del
LRG_509p2:p.Leu103fs
NC_000011.9:g.64577275del
NC_000011.9:g.64577275delG
NC_000011.9:g.64577276del
NM_130799.2:c.307del
NM_130799.2:c.307delC
NM_130804.2:c.307delC
p.L103CfsX16
p.Leu103CysfsX16

Protein change:

L103fs

Links:

OMIM: 613733.0003; dbSNP: rs794728639

NCBI 1000 Genomes Browser:

rs794728639

Molecular consequence:

NM_000244.4:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370251.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370259.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370260.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370261.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370262.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370263.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130799.3:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130800.3:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130801.3:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130802.3:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130803.3:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130804.3:c.307del - 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
SCV000579622	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Oct 15, 2021)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 10090472, 15522929, 15714081, 29927501, 30865533, 34515662, 9103196 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000579622

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Oct 15, 2021)

germline

clinical testing

PubMed (7)
[See all records that cite these PMIDs]

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

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

Gonadotroph tumor associated with multiple endocrine neoplasia type 1.

Benito M, Asa SL, Livolsi VA, West VA, Snyder PJ.

J Clin Endocrinol Metab. 2005 Jan;90(1):570-4. Epub 2004 Nov 2.

PubMed [citation]

PMID:: 15522929

See all PubMed Citations (7)

Details of each submission

From Ambry Genetics, SCV000579622.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

The c.307delC pathogenic mutation, located in coding exon 1 of the MEN1 gene, results from a deletion of one nucleotide at nucleotide position 307, causing a translational frameshift with a predicted alternate stop codon (p.L103Cfs*16). This mutation has been reported in multiple individuals/families with a clinical diagnosis of MEN1 syndrome (Chandrasekharappa SC et al. Science. 1997 Apr;276:404-7; Benito M et al. J. Clin. Endocrinol. Metab. 2005 Jan;90:570-4; Klein RD et al. Genet. Med. 2005 Feb;7:131-8; Mutch MG et al. Hum. Mutat. 1999;13:175-85; Makri A et al. Clin Endocrinol (Oxf), 2018 10;89:437-443; Tirosh A et al. Endocr Pract, 2019 Jun;25:580-588; Mandl A et al. Endocr Relat Cancer, 2021 Oct;28:L15-L19). Of note, this mutation is also designated as 416delC in published literature. In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. 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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