rs398124437

Variant names:

• chr11-64807010-C-G
• rs398124437
• NM_001370259.2:c.912+1G>C

Your query was ambiguous. Multiple possible variants found:

• chr11-64807010-C-G
• chr11-64807010-C-T

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_001370259.2(MEN1):​c.912+1G>C variant causes a splice donor, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MEN1 NM_001370259.2 splice_donor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 6.41
• Publications: 6 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: Pathogenic. The variant received 18 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-64807010-C-G is Pathogenic according to our data. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-64807010-C-G is described in CliVar as Pathogenic. Clinvar id is 428012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEN1	NM_001370259.2	c.912+1G>C		splice_donor_variant, intron_variant	Intron 6 of 9	ENST00000450708.7	NP_001357188.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEN1	ENST00000450708.7	c.912+1G>C		splice_donor_variant, intron_variant	Intron 6 of 9	5	NM_001370259.2	ENSP00000394933.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Multiple endocrine neoplasia, type 1 Pathogenic:1

Nov 15, 2022

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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 428012). This variant is also known as IVS6+1G>C. Disruption of this splice site has been observed in individuals with clinical features of multiple endocrine neoplasia type 1 (PMID: 10090472, 15714081, 18753104). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 6 of the MEN1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in MEN1 are known to be pathogenic (PMID: 12112656, 17853334). -

Hereditary cancer-predisposing syndrome Pathogenic:1

Feb 26, 2013

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.62	D
BayesDel_noAF	Pathogenic	0.32
CADD	Pathogenic	32
DANN	Uncertain	1.0
Eigen	Pathogenic	0.99
Eigen_PC	Pathogenic	0.80
FATHMM_MKL	Pathogenic	0.99	D
PhyloP100		6.4
GERP RS		4.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.91
SpliceAI score (max)		0.93		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.93		Position offset: 1

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

Other links and lift over

dbSNP: rs398124437; hg19: chr11-64574482;