11-64804201-CGGGACCGGGAACCTAGGGTTTGGGTAGAGGTGAGGCCTGTCCCCTTTGGGCTGGGGGCAGAACATGGGCTCAGAGTTGGGGGACTAAGGGCGGAGCCTGGGTCCCCACAAGCGGTCCGAAGTCCCCAGTAGTTCAGAGGCCTTTGCGCTGCCGCTTGAGGAAAGACAGAGTGTAGTCACTAGGGGTGGACACTTTCTGCTTCTTCATCTGCACTTGCGACTGTGCCGTGAGTTGCAGCTTGATGGCGCTCGAGTTGATCTTGGTGGCCACCAGCAGCTCCTTCATGCCCTTCATCTTCTCACTCTGGAAAGTGAGCACTGGACCCTCCGGCGGTGGTGATGCTGTGGGTGCTGGCACCTGAGCCGTGCTGCCACCTTCAGGGCCTCGGGCTGTGCCAGCGACAGTCCCAGGAGGCTTCCGGGGGGGTCCTGACACTGCACCCTGGCCGGTGCCCAGGCCCTTGTCCAGTGCTGGCTTCTTGGGCGGCGGGGGCTCCTCTGGCTTGGACTCCCGCCGTGGGCCCCGCCGCCGGCCTTCCCGGGCTTCCTCGCCCCACGGCTCCTCGGCCTCGGCCGCCTCGGCCTCTCGGCTCACTATGCGCACCTTCTGCCGCACCT-C

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_001370259.2(MEN1):c.1351-2_*132del variant causes a splice acceptor, coding sequence, 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MEN1 NM_001370259.2 splice_acceptor, coding_sequence, 3_prime_UTR
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 0.580

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 12 ACMG points.

• PVS1: Splicing variant, LoF is a know mechanism of disease,
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-64804201-CGGGACCGGGAACCTAGGGTTTGGGTAGAGGTGAGGCCTGTCCCCTTTGGGCTGGGGGCAGAACATGGGCTCAGAGTTGGGGGACTAAGGGCGGAGCCTGGGTCCCCACAAGCGGTCCGAAGTCCCCAGTAGTTCAGAGGCCTTTGCGCTGCCGCTTGAGGAAAGACAGAGTGTAGTCACTAGGGGTGGACACTTTCTGCTTCTTCATCTGCACTTGCGACTGTGCCGTGAGTTGCAGCTTGATGGCGCTCGAGTTGATCTTGGTGGCCACCAGCAGCTCCTTCATGCCCTTCATCTTCTCACTCTGGAAAGTGAGCACTGGACCCTCCGGCGGTGGTGATGCTGTGGGTGCTGGCACCTGAGCCGTGCTGCCACCTTCAGGGCCTCGGGCTGTGCCAGCGACAGTCCCAGGAGGCTTCCGGGGGGGTCCTGACACTGCACCCTGGCCGGTGCCCAGGCCCTTGTCCAGTGCTGGCTTCTTGGGCGGCGGGGGCTCCTCTGGCTTGGACTCCCGCCGTGGGCCCCGCCGCCGGCCTTCCCGGGCTTCCTCGCCCCACGGCTCCTCGGCCTCGGCCGCCTCGGCCTCTCGGCTCACTATGCGCACCTTCTGCCGCACCT-C is Pathogenic according to our data. Variant chr11-64804201-CGGGACCGGGAACCTAGGGTTTGGGTAGAGGTGAGGCCTGTCCCCTTTGGGCTGGGGGCAGAACATGGGCTCAGAGTTGGGGGACTAAGGGCGGAGCCTGGGTCCCCACAAGCGGTCCGAAGTCCCCAGTAGTTCAGAGGCCTTTGCGCTGCCGCTTGAGGAAAGACAGAGTGTAGTCACTAGGGGTGGACACTTTCTGCTTCTTCATCTGCACTTGCGACTGTGCCGTGAGTTGCAGCTTGATGGCGCTCGAGTTGATCTTGGTGGCCACCAGCAGCTCCTTCATGCCCTTCATCTTCTCACTCTGGAAAGTGAGCACTGGACCCTCCGGCGGTGGTGATGCTGTGGGTGCTGGCACCTGAGCCGTGCTGCCACCTTCAGGGCCTCGGGCTGTGCCAGCGACAGTCCCAGGAGGCTTCCGGGGGGGTCCTGACACTGCACCCTGGCCGGTGCCCAGGCCCTTGTCCAGTGCTGGCTTCTTGGGCGGCGGGGGCTCCTCTGGCTTGGACTCCCGCCGTGGGCCCCGCCGCCGGCCTTCCCGGGCTTCCTCGCCCCACGGCTCCTCGGCCTCGGCCGCCTCGGCCTCTCGGCTCACTATGCGCACCTTCTGCCGCACCT-C is described in ClinVar as [Pathogenic]. Clinvar id is 580649.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEN1	NM_001370259.2	c.1351-2_*132del		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant	10/10	ENST00000450708.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEN1	ENST00000450708.7	c.1351-2_*132del		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant	10/10	5	NM_001370259.2	P3

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Multiple endocrine neoplasia, type 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Apr 13, 2018

This deletion removes the functionally conserved nuclear localization signal 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). Similar deletions of exon 10 of the MEN1 gene have been reported in an individual affected with multiple endocrine neoplasia type 1 (Invitae) and individuals in the Universal Mutation Database (PMID: 10612827). This variant is a gross deletion of the genomic region encompassing exon 10 of the MEN1 gene. The 5' boundary is located at c.1351-2 and the 3' end of this event is located at c.*132. While this deletion is not anticipated to result in nonsense mediated decay, it is expected to create a truncated protein product. For these reasons, this variant has been classified as Pathogenic. -

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: rs1565634591; hg19: chr11-64571673;