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NM_001370259.2(MEN1):c.1397A>T (p.Glu466Val) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Apr 4, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001811030.14

Allele description [Variation Report for NM_001370259.2(MEN1):c.1397A>T (p.Glu466Val)]

NM_001370259.2(MEN1):c.1397A>T (p.Glu466Val)

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.1397A>T (p.Glu466Val)
HGVS:
  • NC_000011.10:g.64804770T>A
  • NG_008929.1:g.11525A>T
  • NG_033040.1:g.3472A>T
  • NM_000244.4:c.1412A>T
  • NM_001370251.2:c.1523A>T
  • NM_001370259.2:c.1397A>TMANE SELECT
  • NM_001370260.2:c.1397A>T
  • NM_001370261.2:c.1397A>T
  • NM_001370262.2:c.1292A>T
  • NM_001370263.2:c.1292A>T
  • NM_130799.3:c.1397A>T
  • NM_130800.3:c.1412A>T
  • NM_130801.3:c.1412A>T
  • NM_130802.3:c.1412A>T
  • NM_130803.3:c.1412A>T
  • NM_130804.3:c.1412A>T
  • NP_000235.3:p.Glu471Val
  • NP_001357180.2:p.Glu508Val
  • NP_001357188.2:p.Glu466Val
  • NP_001357189.2:p.Glu466Val
  • NP_001357190.2:p.Glu466Val
  • NP_001357191.2:p.Glu431Val
  • NP_001357192.2:p.Glu431Val
  • NP_570711.1:p.Glu466Val
  • NP_570711.2:p.Glu466Val
  • NP_570712.2:p.Glu471Val
  • NP_570713.2:p.Glu471Val
  • NP_570714.2:p.Glu471Val
  • NP_570715.2:p.Glu471Val
  • NP_570716.2:p.Glu471Val
  • LRG_509t2:c.1397A>T
  • LRG_509:g.11525A>T
  • LRG_509p2:p.Glu466Val
  • NC_000011.9:g.64572242T>A
  • NM_130799.2:c.1397A>T
Protein change:
E431V
Links:
dbSNP: rs1352053477
NCBI 1000 Genomes Browser:
rs1352053477
Molecular consequence:
  • NM_000244.4:c.1412A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370251.2:c.1523A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370259.2:c.1397A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370260.2:c.1397A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370261.2:c.1397A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370262.2:c.1292A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370263.2:c.1292A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130799.3:c.1397A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130800.3:c.1412A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130801.3:c.1412A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130802.3:c.1412A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130803.3:c.1412A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_130804.3:c.1412A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002049294ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)		Uncertain significance
(Jan 21, 2021) 		germlineclinical testing

Citation Link,

SCV003915059GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Uncertain significance
(Apr 4, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002049294.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The MEN1 c.1397A>T; p.Glu466Val variant (rs1352053477), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 457293). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The glutamate at codon 466 is moderately conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.484). Due to limited information, the clinical significance of the p.Glu466Val variant is uncertain at this time.

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

From GeneDx, SCV003915059.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 11274402, 11526476)

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

Last Updated: Nov 10, 2024