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NM_001370259.2(MEN1):c.1695G>T (p.Leu565=) AND not provided

Germline classification:
Likely benign (1 submission)
Last evaluated:
May 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:
RCV000756336.10

Allele description [Variation Report for NM_001370259.2(MEN1):c.1695G>T (p.Leu565=)]

NM_001370259.2(MEN1):c.1695G>T (p.Leu565=)

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.1695G>T (p.Leu565=)
HGVS:
  • NC_000011.10:g.64804472C>A
  • NG_008929.1:g.11823G>T
  • NG_033040.1:g.3770G>T
  • NM_000244.4:c.1710G>T
  • NM_001370251.2:c.1821G>T
  • NM_001370259.2:c.1695G>TMANE SELECT
  • NM_001370260.2:c.1695G>T
  • NM_001370261.2:c.1695G>T
  • NM_001370262.2:c.1590G>T
  • NM_001370263.2:c.1590G>T
  • NM_130799.3:c.1695G>T
  • NM_130800.3:c.1710G>T
  • NM_130801.3:c.1710G>T
  • NM_130802.3:c.1710G>T
  • NM_130803.3:c.1710G>T
  • NM_130804.3:c.1710G>T
  • NP_000235.3:p.Leu570=
  • NP_001357180.2:p.Leu607=
  • NP_001357188.2:p.Leu565=
  • NP_001357189.2:p.Leu565=
  • NP_001357190.2:p.Leu565=
  • NP_001357191.2:p.Leu530=
  • NP_001357192.2:p.Leu530=
  • NP_570711.1:p.Leu565=
  • NP_570711.2:p.Leu565=
  • NP_570712.2:p.Leu570=
  • NP_570713.2:p.Leu570=
  • NP_570714.2:p.Leu570=
  • NP_570715.2:p.Leu570=
  • NP_570716.1:p.Leu570=
  • NP_570716.2:p.Leu570=
  • LRG_509t2:c.1695G>T
  • LRG_509:g.11823G>T
  • LRG_509p2:p.Leu565=
  • NC_000011.9:g.64571944C>A
  • NM_130799.2:c.1695G>T
  • NM_130804.2:c.1710G>T
  • p.Leu570Leu
Links:
dbSNP: rs767677287
NCBI 1000 Genomes Browser:
rs767677287
Molecular consequence:
  • NM_000244.4:c.1710G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370251.2:c.1821G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370259.2:c.1695G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370260.2:c.1695G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370261.2:c.1695G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370262.2:c.1590G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370263.2:c.1590G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_130799.3:c.1695G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_130800.3:c.1710G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_130801.3:c.1710G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_130802.3:c.1710G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_130803.3:c.1710G>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_130804.3:c.1710G>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000884113ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)		Likely benign
(May 12, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884113.1

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

Description

The MEN1 c.1695G>T; p.Leu565Leu variant (rs767677287) is reported in ClinVar as a likely benign variant (Variation ID: 241810), and is observed in the general population databases at a frequency of 0.001 percent (3/246216 alleles; Genome Aggregation Database). This is a synonymous change, the nucleotide is not well conserved, and computational algorithms (SpliceSiteFinder-like, MaxEntScan, NNSplice, GeneSplicer, Human Splicing Finder) do not predict this variant to impact splicing. Taken together this variant is considered likely benign. REFERENCES Link to ClinVar database for p.Leu565Leu: https://www.ncbi.nlm.nih.gov/clinvar/variation/241810/

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

Last Updated: May 7, 2024