chr11-64804201-CGGGACCGGGAACCTAGGGTTTGGGTAGAGGTGAGGCCTGTCCCCTTTGGGCTGGGGGCAGAACATGGGCTCAGAGTTGGGGGACTAAGGGCGGAGCCTGGGTCCCCACAAGCGGTCCGAAGTCCCCAGTAGTTCAGAGGCCTTTGCGCTGCCGCTTGAGGAAAGACAGAGTGTAGTCACTAGGGGTGGACACTTTCTGCTTCTTCATCTGCACTTGCGACTGTGCCGTGAGTTGCAGCTTGATGGCGCTCGAGTTGATCTTGGTGGCCACCAGCAGCTCCTTCATGCCCTTCATCTTCTCACTCTGGAAAGTGAGCACTGGACCCTCCGGCGGTGGTGATGCTGTGGGTGCTGGCACCTGAGCCGTGCTGCCACCTTCAGGGCCTCGGGCTGTGCCAGCGACAGTCCCAGGAGGCTTCCGGGGGGGTCCTGACACTGCACCCTGGCCGGTGCCCAGGCCCTTGTCCAGTGCTGGCTTCTTGGGCGGCGGGGGCTCCTCTGGCTTGGACTCCCGCCGTGGGCCCCGCCGCCGGCCTTCCCGGGCTTCCTCGCCCCACGGCTCCTCGGCCTCGGCCGCCTCGGCCTCTCGGCTCACTATGCGCACCTTCTGCCGCACCT-C

Variant names:

• chr11-64804201-CGGGACCGGGAACCTAGGGTTTGGGTAGAGGTGAGGCCTGTCCCCTTTGGGCTGGGGGCAGAACATGGGCTCAGAGTTGGGGGACTAAGGGCGGAGCCTGGGTCCCCACAAGCGGTCCGAAGTCCCCAGTAGTTCAGAGGCCTTTGCGCTGCCGCTTGAGGAAAGACAGAGTGTAGTCACTAGGGGTGGACACTTTCTGCTTCTTCATCTGCACTTGCGACTGTGCCGTGAGTTGCAGCTTGATGGCGCTCGAGTTGATCTTGGTGGCCACCAGCAGCTCCTTCATGCCCTTCATCTTCTCACTCTGGAAAGTGAGCACTGGACCCTCCGGCGGTGGTGATGCTGTGGGTGCTGGCACCTGAGCCGTGCTGCCACCTTCAGGGCCTCGGGCTGTGCCAGCGACAGTCCCAGGAGGCTTCCGGGGGGGTCCTGACACTGCACCCTGGCCGGTGCCCAGGCCCTTGTCCAGTGCTGGCTTCTTGGGCGGCGGGGGCTCCTCTGGCTTGGACTCCCGCCGTGGGCCCCGCCGCCGGCCTTCCCGGGCTTCCTCGCCCCACGGCTCCTCGGCCTCGGCCGCCTCGGCCTCTCGGCTCACTATGCGCACCTTCTGCCGCACCT-C
• rs1565634591
• NM_001370259.2:c.1351-2_*132del

Variant summary

Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PM1 PM4 PP5_Moderate

The NM_001370259.2(MEN1):​c.1351-2_*132del variant causes a stop lost, conservative inframe deletion, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. V451V) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MEN1 NM_001370259.2 stop_lost, conservative_inframe_deletion, splice_region
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 0.580
• Publications: 0 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 6 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 13 uncertain in NM_001370259.2
• PM4: Stoplost variant in NM_001370259.2
• 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 rank	MANE	Protein	UniProt
MEN1	NM_001370259.2	c.1351-2_*132del		stop_lost, conservative_inframe_deletion, splice_region_variant	Exon 10 of 10	ENST00000450708.7	NP_001357188.2
MEN1	NM_001370259.2	c.1351-2_*132del		splice_acceptor_variant, 3_prime_UTR_variant, intron_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.1351-2_*132del		stop_lost, conservative_inframe_deletion, splice_region_variant	Exon 10 of 10	5	NM_001370259.2	ENSP00000394933.3
MEN1	ENST00000450708.7	c.1351-2_*132del		splice_acceptor_variant, 3_prime_UTR_variant, intron_variant	Exon 10 of 10	5	NM_001370259.2	ENSP00000394933.3

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

Apr 13, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

For these reasons, this variant has been classified as Pathogenic. 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1565634591; hg19: chr11-64571673;