NM_001370259.2(MEN1):c.1393_1407del (p.Ala465_Glu469del) AND Multiple endocrine neoplasia, type 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 8, 2016
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:: RCV000467609.8

Allele description [Variation Report for NM_001370259.2(MEN1):c.1393_1407del (p.Ala465_Glu469del)]

NM_001370259.2(MEN1):c.1393_1407del (p.Ala465_Glu469del)

Gene:

MEN1:menin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q13.1

Genomic location:

Preferred name:

NM_001370259.2(MEN1):c.1393_1407del (p.Ala465_Glu469del)

HGVS:

NC_000011.10:g.64804761_64804775del
NG_008929.1:g.11521_11535del
NG_033040.1:g.3468_3482del
NM_000244.4:c.1408_1422del
NM_001370251.2:c.1519_1533del
NM_001370259.2:c.1393_1407delMANE SELECT
NM_001370260.2:c.1393_1407del
NM_001370261.2:c.1393_1407del
NM_001370262.2:c.1288_1302del
NM_001370263.2:c.1288_1302del
NM_130799.3:c.1393_1407del
NM_130800.3:c.1408_1422del
NM_130801.3:c.1408_1422del
NM_130802.3:c.1408_1422del
NM_130803.3:c.1408_1422del
NM_130804.3:c.1408_1422del
NP_000235.3:p.Ala470_Glu474del
NP_001357180.2:p.Ala507_Glu511del
NP_001357188.2:p.Ala465_Glu469del
NP_001357189.2:p.Ala465_Glu469del
NP_001357190.2:p.Ala465_Glu469del
NP_001357191.2:p.Ala430_Glu434del
NP_001357192.2:p.Ala430_Glu434del
NP_570711.2:p.Ala465_Glu469del
NP_570712.2:p.Ala470_Glu474del
NP_570713.2:p.Ala470_Glu474del
NP_570714.2:p.Ala470_Glu474del
NP_570715.2:p.Ala470_Glu474del
NP_570716.2:p.Ala470_Glu474del
LRG_509:g.11521_11535del
NC_000011.9:g.64572232_64572246del
NC_000011.9:g.64572233_64572247del
NM_130799.2:c.1393_1407delGCCGAGGCCGAGGAG

Links:

dbSNP: rs1064792907

NCBI 1000 Genomes Browser:

rs1064792907

Molecular consequence:

NM_000244.4:c.1408_1422del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370251.2:c.1519_1533del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370259.2:c.1393_1407del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370260.2:c.1393_1407del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370261.2:c.1393_1407del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370262.2:c.1288_1302del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370263.2:c.1288_1302del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_130799.3:c.1393_1407del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_130800.3:c.1408_1422del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_130801.3:c.1408_1422del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_130802.3:c.1408_1422del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_130803.3:c.1408_1422del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_130804.3:c.1408_1422del - inframe_deletion - [Sequence Ontology: SO:0001822]

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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Ttll2 tubulin tyrosine ligase-like family, member 2 [Mus musculus]
Ttll2 tubulin tyrosine ligase-like family, member 2 [Mus musculus]
Gene ID:100216474

Gene
100216474[uid] AND (alive[prop]) (1)
Gene
olfactory receptor 906 [Mus musculus]
olfactory receptor 906 [Mus musculus]
gi|116174752|ref|NP_667014.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000541230	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 8, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000541230

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 8, 2016)

germline

clinical testing

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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000541230.5

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

Description

This sequence change deletes 15 nucleotides from exon 10 of the MEN1 mRNA (c.1393_1407delGCCGAGGCCGAGGAG). This leads to the deletion of 5 amino acid residues in the MEN1 protein (p.Ala465_Glu469del) but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a MEN1-related disease. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acids is currently unknown. In summary, this is a novel in-frame deletion with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance.

#	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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