rs730882136

chr11-64809903-G-GGGGGC

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_001370259.2(MEN1):c.206_207insGCCCC(p.Asp70ProfsTer51) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. P69P) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 30)
• Consequence: MEN1 NM_001370259.2 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 4.58

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]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-64809903-G-GGGGGC is Pathogenic according to our data. Variant chr11-64809903-G-GGGGGC is described in ClinVar as [Pathogenic]. Clinvar id is 183079.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEN1	NM_001370259.2	c.206_207insGCCCC	p.Asp70ProfsTer51	frameshift_variant	2/10	ENST00000450708.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEN1	ENST00000450708.7	c.206_207insGCCCC	p.Asp70ProfsTer51	frameshift_variant	2/10	5	NM_001370259.2	P3

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 30

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Aug 29, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 20, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 19, 2018	The c.202_206dupGCCCC variant in the MEN1 gene has been reported previously in association with multiple endocrine neoplasia type 1 (for examples, see Giraud et al., 1998; Wautot et al., 2002; Park et al., 2003). The duplication causes a frameshift starting with codon Aspartic Acid 70, changes this amino acid to a Proline residue and creates a premature Stop codon at position 51 of the new reading frame, denoted p.Asp70ProfsX51. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Based on currently available evidence, we consider c.202_206dupGCCCC to be pathogenic. -

Multiple endocrine neoplasia, type 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Dec 07, 2023

This sequence change creates a premature translational stop signal (p.Asp70Profs*51) in the MEN1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MEN1 are known to be pathogenic (PMID: 12112656, 17853334). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individuals with multiple endocrine neoplasia type 1 (PMID: 9437237, 22026581). This variant is also known as 317ins5 and c.206_207insGCCC. ClinVar contains an entry for this variant (Variation ID: 183079). For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 21, 2021

The c.202_206dupGCCCC pathogenic mutation, located in coding exon 1 of the MEN1 gene, results from a duplication of GCCCC at nucleotide position 202, causing a translational frameshift with a predicted alternate stop codon (p.D70Pfs*51). This alteration was identified in a cohort of 79 Spanish patients with a MEN1 phenotype (Belar O et al. Clin Endocrinol (Oxf), 2012 May;76:719-24). This alteration was detected in two unrelated Hungarian individuals meeting MEN1 syndrome phenotype (Kövesdi A et al. Endocrine, 2019 08;65:451-459). Of note, this alteration is also designated as "c.206_207insGCCCC" in published literature. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs730882136; hg19: chr11-64577375;