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NM_001370259.2(MEN1):c.989G>C (p.Arg330Pro) AND Multiple endocrine neoplasia, type 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 12, 2017
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:
RCV000527000.6

Allele description [Variation Report for NM_001370259.2(MEN1):c.989G>C (p.Arg330Pro)]

NM_001370259.2(MEN1):c.989G>C (p.Arg330Pro)

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.989G>C (p.Arg330Pro)
HGVS:
  • NC_000011.10:g.64806292C>G
  • NG_008929.1:g.10003G>C
  • NG_033040.1:g.1950G>C
  • NM_000244.4:c.1004G>C
  • NM_001370251.2:c.989G>C
  • NM_001370259.2:c.989G>CMANE SELECT
  • NM_001370260.2:c.989G>C
  • NM_001370261.2:c.989G>C
  • NM_001370262.2:c.884G>C
  • NM_001370263.2:c.884G>C
  • NM_130799.3:c.989G>C
  • NM_130800.3:c.1004G>C
  • NM_130801.3:c.1004G>C
  • NM_130802.3:c.1004G>C
  • NM_130803.3:c.1004G>C
  • NM_130804.3:c.1004G>C
  • NP_000235.3:p.Arg335Pro
  • NP_001357180.2:p.Arg330Pro
  • NP_001357188.2:p.Arg330Pro
  • NP_001357189.2:p.Arg330Pro
  • NP_001357190.2:p.Arg330Pro
  • NP_001357191.2:p.Arg295Pro
  • NP_001357192.2:p.Arg295Pro
  • NP_570711.1:p.Arg330Pro
  • NP_570711.2:p.Arg330Pro
  • NP_570712.2:p.Arg335Pro
  • NP_570713.2:p.Arg335Pro
  • NP_570714.2:p.Arg335Pro
  • NP_570715.2:p.Arg335Pro
  • NP_570716.2:p.Arg335Pro
  • LRG_509t2:c.989G>C
  • LRG_509:g.10003G>C
  • LRG_509p2:p.Arg330Pro
  • NC_000011.9:g.64573764C>G
  • NM_130799.2:c.989G>C
Protein change:
R295P
Links:
dbSNP: rs373135175
NCBI 1000 Genomes Browser:
rs373135175
Molecular consequence:
  • NM_000244.4:c.1004G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370251.2:c.989G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370259.2:c.989G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370260.2:c.989G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370261.2:c.989G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370262.2:c.884G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370263.2:c.884G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130799.3:c.989G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130800.3:c.1004G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130801.3:c.1004G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130802.3:c.1004G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130803.3:c.1004G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130804.3:c.1004G>C - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000628117Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 12, 2017) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000628117.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, this variant has uncertain impact on MEN1 function. The available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with a MEN1-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with proline at codon 330 of the MEN1 protein (p.Arg330Pro). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and proline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024