NM_001370259.2(MEN1):c.758del (p.Ser253fs) AND Multiple endocrine neoplasia, type 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 28, 2022
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:: RCV000800811.6

Allele description [Variation Report for NM_001370259.2(MEN1):c.758del (p.Ser253fs)]

NM_001370259.2(MEN1):c.758del (p.Ser253fs)

Gene:

MEN1:menin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q13.1

Genomic location:

Preferred name:

NM_001370259.2(MEN1):c.758del (p.Ser253fs)

HGVS:

NC_000011.10:g.64807577del
NG_008929.1:g.8718del
NG_033040.1:g.665del
NM_000244.4:c.773del
NM_001370251.2:c.758del
NM_001370259.2:c.758delMANE SELECT
NM_001370260.2:c.758del
NM_001370261.2:c.758del
NM_001370262.2:c.653del
NM_001370263.2:c.653del
NM_130799.3:c.758del
NM_130800.3:c.773del
NM_130801.3:c.773del
NM_130802.3:c.773del
NM_130803.3:c.773del
NM_130804.3:c.773del
NP_000235.3:p.Ser258fs
NP_001357180.2:p.Ser253fs
NP_001357188.2:p.Ser253fs
NP_001357189.2:p.Ser253fs
NP_001357190.2:p.Ser253fs
NP_001357191.2:p.Ser218fs
NP_001357192.2:p.Ser218fs
NP_570711.2:p.Ser253fs
NP_570712.2:p.Ser258fs
NP_570713.2:p.Ser258fs
NP_570714.2:p.Ser258fs
NP_570715.2:p.Ser258fs
NP_570716.2:p.Ser258fs
LRG_509:g.8718del
NC_000011.9:g.64575049del
NM_130799.2:c.758delC

Protein change:

S218fs

Links:

dbSNP: rs1592648765

NCBI 1000 Genomes Browser:

rs1592648765

Molecular consequence:

NM_000244.4:c.773del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370251.2:c.758del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370259.2:c.758del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370260.2:c.758del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370261.2:c.758del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370262.2:c.653del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370263.2:c.653del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130799.3:c.758del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130800.3:c.773del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130801.3:c.773del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130802.3:c.773del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130803.3:c.773del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130804.3:c.773del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Recent activity

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Homo sapiens chromosome 17, clone CTD-2532D12, complete sequence
Homo sapiens chromosome 17, clone CTD-2532D12, complete sequence
gi|28933869|gnl|WIBR|L27636|gb|AC12 9|

Nucleotide
RecName: Full=Putative uncharacterized protein encoded by LINC00469
RecName: Full=Putative uncharacterized protein encoded by LINC00469
gi|74729286|sp|Q8N7U9.1|CQ054_HUMAN

Protein
Homo sapiens vascular cell adhesion molecule 1, mRNA (cDNA clone MGC:87170 IMAGE...
Homo sapiens vascular cell adhesion molecule 1, mRNA (cDNA clone MGC:87170 IMAGE:30339170), complete cds
gi|46249772|gb|BC068490.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000940547	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 28, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 29497973, 12112656, 17853334, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000940547

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 28, 2022)

germline

clinical testing

PubMed (4)
[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

Multiple endocrine neoplasia type 1: analysis of germline MEN1 mutations in the Italian multicenter MEN1 patient database.

Marini F, Giusti F, Fossi C, Cioppi F, Cianferotti L, Masi L, Boaretto F, Zovato S, Cetani F, Colao A, Davì MV, Faggiano A, Fanciulli G, Ferolla P, Ferone D, Loli P, Mantero F, Marcocci C, Opocher G, Beck-Peccoz P, Persani L, Scillitani A, et al.

Endocrine. 2018 Oct;62(1):215-233. doi: 10.1007/s12020-018-1566-8. Epub 2018 Mar 1. Erratum in: Endocrine. 2018 Oct;62(1):234-241. doi: 10.1007/s12020-018-1668-3.

PubMed [citation]

PMID:: 29497973

Germline mutation profile of MEN1 in multiple endocrine neoplasia type 1: search for correlation between phenotype and the functional domains of the MEN1 protein.

Wautot V, Vercherat C, Lespinasse J, Chambe B, Lenoir GM, Zhang CX, Porchet N, Cordier M, Béroud C, Calender A.

Hum Mutat. 2002 Jul;20(1):35-47.

PubMed [citation]

PMID:: 12112656

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV000940547.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

ClinVar contains an entry for this variant (Variation ID: 646514). This variant is also known as 868delC. This premature translational stop signal has been observed in individual(s) with MEN1-related disease (PMID: 29497973; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser253Cysfs*28) in the MEN1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MEN1 are known to be pathogenic (PMID: 12112656, 17853334). 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: Feb 20, 2024

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