NM_001370259.2(MEN1):c.307del (p.Leu103fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Mar 15, 2022
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:: RCV000182435.12

Allele description [Variation Report for NM_001370259.2(MEN1):c.307del (p.Leu103fs)]

NM_001370259.2(MEN1):c.307del (p.Leu103fs)

Gene:

MEN1:menin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q13.1

Genomic location:

Preferred name:

NM_001370259.2(MEN1):c.307del (p.Leu103fs)

HGVS:

NC_000011.10:g.64809804del
NC_000011.9:g.64577275del
NG_008929.1:g.6492del
NM_000244.4:c.307del
NM_001370251.2:c.307del
NM_001370259.2:c.307delMANE SELECT
NM_001370260.2:c.307del
NM_001370261.2:c.307del
NM_001370262.2:c.307del
NM_001370263.2:c.307del
NM_130799.3:c.307del
NM_130800.3:c.307del
NM_130801.3:c.307del
NM_130802.3:c.307del
NM_130803.3:c.307del
NM_130804.3:c.307del
NP_000235.3:p.Leu103fs
NP_001357180.2:p.Leu103fs
NP_001357188.2:p.Leu103fs
NP_001357189.2:p.Leu103fs
NP_001357190.2:p.Leu103fs
NP_001357191.2:p.Leu103fs
NP_001357192.2:p.Leu103fs
NP_570711.1:p.Leu103fs
NP_570711.2:p.Leu103fs
NP_570712.2:p.Leu103fs
NP_570713.2:p.Leu103fs
NP_570714.2:p.Leu103fs
NP_570715.2:p.Leu103fs
NP_570716.2:p.Leu103fs
LRG_509t2:c.307del
LRG_509:g.6492del
LRG_509p2:p.Leu103fs
NC_000011.9:g.64577275del
NC_000011.9:g.64577275delG
NC_000011.9:g.64577276del
NM_130799.2:c.307del
NM_130799.2:c.307delC
NM_130804.2:c.307delC
p.L103CfsX16
p.Leu103CysfsX16

Protein change:

L103fs

Links:

OMIM: 613733.0003; dbSNP: rs794728639

NCBI 1000 Genomes Browser:

rs794728639

Molecular consequence:

NM_000244.4:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370251.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370259.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370260.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370261.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370262.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370263.2:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130799.3:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130800.3:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130801.3:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130802.3:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130803.3:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130804.3:c.307del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000234780	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 15, 2022)	germline	clinical testing	Citation Link,
SCV000341446	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Apr 28, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000234780

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 15, 2022)

germline

clinical testing

Citation Link,

SCV000341446

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Apr 28, 2016)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000234780.12

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 15281352, 15126560, 9103196, 9215689, 15522929, 10090472, 9709921, 9671267, 11579199, 9832038, 10617276, 9681840, 12112656, 17853334, 15082967, 17879353, 9437237, 17766710, 29927501, 31447099)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Eurofins Ntd Llc (ga), SCV000341446.4

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

#	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		1	not provided	not provided	not provided

Last Updated: May 1, 2024

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