NM_001370259.2(MEN1):c.61C>A (p.Arg21Ser) AND Multiple endocrine neoplasia, type 1

This record was updated by the submitter. Please see the current version.

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Jan 28, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000864930.15

Allele description

NM_001370259.2(MEN1):c.61C>A (p.Arg21Ser)

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.61C>A (p.Arg21Ser)

HGVS:

NC_000011.10:g.64810049G>T
NG_008929.1:g.6246C>A
NM_000244.4:c.61C>A
NM_001370251.2:c.61C>A
NM_001370259.2:c.61C>AMANE SELECT
NM_001370260.2:c.61C>A
NM_001370261.2:c.61C>A
NM_001370262.2:c.61C>A
NM_001370263.2:c.61C>A
NM_130799.3:c.61C>A
NM_130800.3:c.61C>A
NM_130801.3:c.61C>A
NM_130802.3:c.61C>A
NM_130803.3:c.61C>A
NM_130804.3:c.61C>A
NP_000235.3:p.Arg21Ser
NP_001357180.2:p.Arg21Ser
NP_001357188.2:p.Arg21Ser
NP_001357189.2:p.Arg21Ser
NP_001357190.2:p.Arg21Ser
NP_001357191.2:p.Arg21Ser
NP_001357192.2:p.Arg21Ser
NP_570711.1:p.Arg21Ser
NP_570711.2:p.Arg21Ser
NP_570712.2:p.Arg21Ser
NP_570713.2:p.Arg21Ser
NP_570714.2:p.Arg21Ser
NP_570715.2:p.Arg21Ser
NP_570716.2:p.Arg21Ser
LRG_509t2:c.61C>A
LRG_509:g.6246C>A
LRG_509p2:p.Arg21Ser
NC_000011.9:g.64577521G>T
NM_130799.2:c.61C>A

Protein change:

R21S

Links:

dbSNP: rs541476418

NCBI 1000 Genomes Browser:

rs541476418

Molecular consequence:

NM_000244.4:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370251.2:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370259.2:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370260.2:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370261.2:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370262.2:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370263.2:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130799.3:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130800.3:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130801.3:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130802.3:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130803.3:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_130804.3:c.61C>A - missense variant - [Sequence Ontology: SO:0001583]

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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Plantibacter sp. ME-Dv--P-095 NODE_4_length_458290_cov_39.496627, whole genome s...
Plantibacter sp. ME-Dv--P-095 NODE_4_length_458290_cov_39.496627, whole genome shotgun sequence
gi|2519477954|ref|NZ_JARVSB01000000 gnl|WGS:NZ_JARVSB01|NODE_4_length_458290_cov_39.496627

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000373107	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV001005817	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 28, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003808782	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 23, 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

SCV000373107

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Jan 13, 2018)

germline

clinical testing

Citation Link,

SCV001005817

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 28, 2024)

germline

clinical testing

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

SCV003808782

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 23, 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	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

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 Illumina Laboratory Services, Illumina, SCV000373107.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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

From Invitae, SCV001005817.6

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

#	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

From Revvity Omics, Revvity, SCV003808782.2

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

#	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: Jul 23, 2024

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