NM_001370259.2(MEN1):c.655-1G>C AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 25, 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:: RCV001025404.3

Allele description [Variation Report for NM_001370259.2(MEN1):c.655-1G>C]

NM_001370259.2(MEN1):c.655-1G>C

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.655-1G>C

HGVS:

NC_000011.10:g.64807681C>G
NG_008929.1:g.8614G>C
NG_033040.1:g.561G>C
NG_033040.2:g.533G>C
NM_000244.4:c.670-1G>C
NM_001370251.2:c.655-1G>C
NM_001370259.2:c.655-1G>CMANE SELECT
NM_001370260.2:c.655-1G>C
NM_001370261.2:c.655-1G>C
NM_001370262.2:c.550-1G>C
NM_001370263.2:c.550-1G>C
NM_001407142.1:c.655-1G>C
NM_001407143.1:c.655-1G>C
NM_001407144.1:c.655-1G>C
NM_001407145.1:c.670-1G>C
NM_001407146.1:c.655-1G>C
NM_001407147.1:c.655-1G>C
NM_001407148.1:c.550-1G>C
NM_001407149.1:c.550-1G>C
NM_001407150.1:c.670-1G>C
NM_001407151.1:c.550-1G>C
NM_001407152.1:c.655-1G>C
NM_130799.3:c.655-1G>C
NM_130800.3:c.670-1G>C
NM_130801.3:c.670-1G>C
NM_130802.3:c.670-1G>C
NM_130803.3:c.670-1G>C
NM_130804.3:c.670-1G>C
LRG_509t2:c.655-1G>C
LRG_509:g.8614G>C
NC_000011.9:g.64575153C>G
NC_000011.9:g.64575153C>G
NM_130799.2:c.655-1G>C

Links:

dbSNP: rs1592649615

NCBI 1000 Genomes Browser:

rs1592649615

Molecular consequence:

NM_000244.4:c.670-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001370251.2:c.655-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001370259.2:c.655-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001370260.2:c.655-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001370261.2:c.655-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001370262.2:c.550-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001370263.2:c.550-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001407142.1:c.655-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001407143.1:c.655-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001407144.1:c.655-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001407145.1:c.670-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001407146.1:c.655-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001407147.1:c.655-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001407148.1:c.550-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001407149.1:c.550-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001407150.1:c.670-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001407151.1:c.550-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001407152.1:c.655-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_130799.3:c.655-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_130800.3:c.670-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_130801.3:c.670-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_130802.3:c.670-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_130803.3:c.670-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_130804.3:c.670-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

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

Recent activity

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putative methylesterase 12, chloroplastic isoform X1 [Cucurbita maxima]
putative methylesterase 12, chloroplastic isoform X1 [Cucurbita maxima]
gi|1281063055|ref|XP_022973979.1|

Protein
AL884862 XGC-egg Xenopus tropicalis cDNA clone TEgg014f15 3', mRNA sequence
AL884862 XGC-egg Xenopus tropicalis cDNA clone TEgg014f15 3', mRNA sequence
gi|38676126|gnl|dbEST|20706301|emb| 862.2|

Nucleotide
AL847340 XGC-egg Xenopus tropicalis cDNA clone TEgg014i23 5', mRNA sequence
AL847340 XGC-egg Xenopus tropicalis cDNA clone TEgg014i23 5', mRNA sequence
gi|38488248|gnl|dbEST|20523493|emb| 340.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001187585	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Sep 25, 2019)	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

SCV001187585

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Sep 25, 2019)

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

Genetic screening methods for the detection of mutations responsible for multiple endocrine neoplasia type 1.

Balogh K, Patócs A, Majnik J, Rácz K, Hunyady L.

Mol Genet Metab. 2004 Sep-Oct;83(1-2):74-81. Review.

PubMed [citation]

PMID:: 15464422

Details of each submission

From Ambry Genetics, SCV001187585.4

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

Description

The c.655-1G>C intronic pathogenic mutation results from a G to C substitution one nucleotide upstream from coding exon 3 of the MEN1 gene. This alteration has been detected in multiple individuals with multiple endocrine neoplasia type 1 (MEN1) syndrome (Balogh K et al. Mol. Genet. Metab.;83:74-81; Ambry internal data). Of note, this alteration has been reported as 765-1G>C in published literature. In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified 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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