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NM_001370259.2(MEN1):c.654+1G>A AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 12, 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:
RCV002510773.1

Allele description [Variation Report for NM_001370259.2(MEN1):c.654+1G>A]

NM_001370259.2(MEN1):c.654+1G>A

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.654+1G>A
HGVS:
  • NC_000011.10:g.64807890C>T
  • NG_008929.1:g.8405G>A
  • NG_033040.1:g.352G>A
  • NG_033040.2:g.324G>A
  • NM_000244.4:c.669+1G>A
  • NM_001370251.2:c.654+1G>A
  • NM_001370259.2:c.654+1G>AMANE SELECT
  • NM_001370260.2:c.654+1G>A
  • NM_001370261.2:c.654+1G>A
  • NM_001370262.2:c.549+106G>A
  • NM_001370263.2:c.549+106G>A
  • NM_001407142.1:c.654+1G>A
  • NM_001407143.1:c.654+1G>A
  • NM_001407144.1:c.654+1G>A
  • NM_001407145.1:c.669+1G>A
  • NM_001407146.1:c.654+1G>A
  • NM_001407147.1:c.654+1G>A
  • NM_001407148.1:c.549+106G>A
  • NM_001407149.1:c.549+106G>A
  • NM_001407150.1:c.669+1G>A
  • NM_001407151.1:c.549+106G>A
  • NM_001407152.1:c.654+1G>A
  • NM_130799.3:c.654+1G>A
  • NM_130800.3:c.669+1G>A
  • NM_130801.3:c.669+1G>A
  • NM_130802.3:c.669+1G>A
  • NM_130803.3:c.669+1G>A
  • NM_130804.3:c.669+1G>A
  • LRG_509t2:c.654+1G>A
  • LRG_509:g.8405G>A
  • NC_000011.9:g.64575362C>T
  • NM_130799.2:c.654+1G>A
Note:
ClinGen staff contributed the HGVS expression for this variant.
Nucleotide change:
IVS3DS, G-A, +1
Links:
OMIM: 613733.0035; dbSNP: rs794728622
NCBI 1000 Genomes Browser:
rs794728622
Molecular consequence:
  • NM_001370262.2:c.549+106G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001370263.2:c.549+106G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001407148.1:c.549+106G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001407149.1:c.549+106G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001407151.1:c.549+106G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000244.4:c.669+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370251.2:c.654+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370259.2:c.654+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370260.2:c.654+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370261.2:c.654+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407142.1:c.654+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407143.1:c.654+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407144.1:c.654+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407145.1:c.669+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407146.1:c.654+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407147.1:c.654+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407150.1:c.669+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407152.1:c.654+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130799.3:c.654+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130800.3:c.669+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130801.3:c.669+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130802.3:c.669+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130803.3:c.669+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_130804.3:c.669+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV002820519GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Jan 12, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV002820519.1

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

Description

Canonical splice site variant expected to result in aberrant splicing; Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate in-frame loss of 35 amino acids disrupting TGF-B signaling and leading to reduced activation of p15 and p21 as well as increased cell proliferation (Canaff et al., 2012); This variant is associated with the following publications: (PMID: 22275377, 25733923, 30339208, 28870973)

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

Last Updated: Sep 29, 2024