NM_001370259.2(MEN1):c.29T>A (p.Leu10Gln) AND Multiple endocrine neoplasia, type 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 8, 2023
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:: RCV004016001.2

Allele description [Variation Report for NM_001370259.2(MEN1):c.29T>A (p.Leu10Gln)]

NM_001370259.2(MEN1):c.29T>A (p.Leu10Gln)

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.29T>A (p.Leu10Gln)

HGVS:

NC_000011.10:g.64810081A>T
NG_008929.1:g.6214T>A
NM_000244.4:c.29T>A
NM_001370251.2:c.29T>A
NM_001370259.2:c.29T>AMANE SELECT
NM_001370260.2:c.29T>A
NM_001370261.2:c.29T>A
NM_001370262.2:c.29T>A
NM_001370263.2:c.29T>A
NM_001407142.1:c.29T>A
NM_001407143.1:c.29T>A
NM_001407144.1:c.29T>A
NM_001407145.1:c.29T>A
NM_001407146.1:c.29T>A
NM_001407147.1:c.29T>A
NM_001407148.1:c.29T>A
NM_001407149.1:c.29T>A
NM_001407150.1:c.29T>A
NM_001407151.1:c.29T>A
NM_001407152.1:c.29T>A
NM_130799.3:c.29T>A
NM_130800.3:c.29T>A
NM_130801.3:c.29T>A
NM_130802.3:c.29T>A
NM_130803.3:c.29T>A
NM_130804.3:c.29T>A
NP_000235.2:p.Leu10Gln
NP_000235.3:p.Leu10Gln
NP_001357180.2:p.Leu10Gln
NP_001357188.2:p.Leu10Gln
NP_001357189.2:p.Leu10Gln
NP_001357190.2:p.Leu10Gln
NP_001357191.2:p.Leu10Gln
NP_001357192.2:p.Leu10Gln
NP_001394071.1:p.Leu10Gln
NP_001394072.1:p.Leu10Gln
NP_001394073.1:p.Leu10Gln
NP_001394074.1:p.Leu10Gln
NP_001394075.1:p.Leu10Gln
NP_001394076.1:p.Leu10Gln
NP_001394077.1:p.Leu10Gln
NP_001394078.1:p.Leu10Gln
NP_001394079.1:p.Leu10Gln
NP_001394080.1:p.Leu10Gln
NP_001394081.1:p.Leu10Gln
NP_570711.1:p.Leu10Gln
NP_570711.2:p.Leu10Gln
NP_570712.2:p.Leu10Gln
NP_570713.2:p.Leu10Gln
NP_570714.2:p.Leu10Gln
NP_570715.2:p.Leu10Gln
NP_570716.2:p.Leu10Gln
LRG_509t1:c.29T>A
LRG_509t2:c.29T>A
LRG_509:g.6214T>A
LRG_509p1:p.Leu10Gln
LRG_509p2:p.Leu10Gln
NC_000011.9:g.64577553A>T
NM_000244.3:c.29T>A
NM_130799.2:c.29T>A
NR_176284.1:n.78T>A
NR_176285.1:n.90T>A
NR_176286.1:n.78T>A
NR_176287.1:n.336T>A

Protein change:

L10Q

Molecular consequence:

NM_000244.4:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370251.2:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370259.2:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370260.2:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370261.2:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370262.2:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370263.2:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407142.1:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407143.1:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407144.1:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407145.1:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407146.1:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407147.1:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407148.1:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407149.1:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407150.1:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407151.1:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407152.1:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130799.3:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130800.3:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130801.3:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130802.3:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130803.3:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130804.3:c.29T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_176284.1:n.78T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176285.1:n.90T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176286.1:n.78T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176287.1:n.336T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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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POTE ankyrin domain family member E isoform X3 [Homo sapiens]
POTE ankyrin domain family member E isoform X3 [Homo sapiens]
gi|2462573440|ref|XP_054198118.1|

Protein
Chain A, Proteasome subunit alpha type-2
Chain A, Proteasome subunit alpha type-2
gi|378792443|pdb|3UNH|A

Protein
Chain E, Proteasome subunit alpha type-1
Chain E, Proteasome subunit alpha type-1
gi|378792447|pdb|3UNH|E

Protein
Chain V, Proteasome subunit beta type-10
Chain V, Proteasome subunit beta type-10
gi|378792464|pdb|3UNH|V

Protein
Homologene neighbors for GEO Profiles (Select 131617135) (0)
GEO Profiles

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004829004	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Jun 8, 2023)	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

SCV004829004

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Jun 8, 2023)

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	1	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From All of Us Research Program, National Institutes of Health, SCV004829004.1

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

Description

This missense variant replaces leucine with glutamine at codon 10 of the MEN1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with MEN1-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is 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	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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