NM_001370259.2:c.1739delC

Variant names:

• chr11-64804427-CG-C
• rs864622617
• NM_001370259.2:c.1739delC

Variant summary

Our verdict is Likely pathogenic. The variant received 8 ACMG points: 8P and 0B. PVS1_Strong PM2 PP5_Moderate

The NM_001370259.2(MEN1):​c.1739delC​(p.Thr580ArgfsTer8) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. T580T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MEN1 NM_001370259.2 frameshift
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 8.44
• Publications: 1 publications found

Genes affected

MEN1 (HGNC:7010): (menin 1) This gene encodes menin, a tumor suppressor associated with a syndrome known as multiple endocrine neoplasia type 1. Menin is a scaffold protein that functions in histone modification and epigenetic gene regulation. It is thought to regulate several pathways and processes by altering chromatin structure through the modification of histones. [provided by RefSeq, May 2019]

MEN1 Gene-Disease associations (from GenCC):

• multiple endocrine neoplasia type 1

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen, Orphanet, Ambry Genetics
• familial isolated hyperparathyroidism

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• pituitary gigantism

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary pheochromocytoma-paraganglioma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_pathogenic. The variant received 8 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 4 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-64804427-CG-C is Pathogenic according to our data. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-64804427-CG-C is described in CliVar as Likely_pathogenic. Clinvar id is 220647.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEN1	NM_001370259.2	c.1739delC	p.Thr580ArgfsTer8	frameshift_variant	Exon 10 of 10	ENST00000450708.7	NP_001357188.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEN1	ENST00000450708.7	c.1739delC	p.Thr580ArgfsTer8	frameshift_variant	Exon 10 of 10	5	NM_001370259.2	ENSP00000394933.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Multiple endocrine neoplasia, type 1 Pathogenic:1

Oct 20, 2015

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change deletes 1 nucleotide from exon 10 of the MEN1 mRNA (c.1739delC), causing a frameshift at codon 580. This creates a premature translational stop signal in the last exon of the MEN1 mRNA (p.Thr580Argfs*8). While this is not anticipated to result in nonsense mediated decay, it is expected to result in a truncated MEN1 protein. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature. This frameshift change truncates the functionally conserved NLS2 domain of the MEN1 protein. Experimental studies have shown that disruption of this region abrogates the ability of MEN1 to bind DNA, regulate target gene expression, and inhibit cell proliferation (PMID: 15331604, 16449969). In summary, this is a novel frameshift variant that truncates an important functional domain in MEN1. For these reasons, it has been classified as a Likely Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		8.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs864622617; hg19: chr11-64571899;