VCV000664768.2 - ClinVar

NM_001370259.2(MEN1):c.623_1050-143del

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001370259.2(MEN1):c.623_1050-143del

Variation ID: 664768 Accession: VCV000664768.2

Type and length

Deletion, 2,010 bp

Location

Cytogenetic: 11q13.1 11: 64805913-64807922 (GRCh38) [ NCBI UCSC ] 11: 64573385-64575394 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Aug 14, 2019	Aug 14, 2019	Oct 15, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NM_001370259.2:c.623_1050-143del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice acceptor splice donor
NM_000244.4:c.638_1065-143del		splice acceptor splice donor
NM_001370251.2:c.620_1147del528	NP_001357180.2:p.Gly208_Trp383del	splice acceptor splice donor inframe deletion
NM_001370260.2:c.623_1050-143del		splice acceptor splice donor
NM_001370261.2:c.623_1050-143del		splice acceptor splice donor
NM_001370262.2:c.549+74_945-143del		splice acceptor splice donor
NM_001370263.2:c.549+74_945-143del		splice acceptor splice donor
NM_130799.3:c.623_1050-143del		splice acceptor splice donor
NM_130800.3:c.638_1065-143del		splice acceptor splice donor
NM_130801.3:c.638_1065-143del		splice acceptor splice donor
NM_130802.3:c.638_1065-143del		splice acceptor splice donor
NM_130803.3:c.638_1065-143del		splice acceptor splice donor
NM_130804.3:c.638_1065-143del		splice acceptor splice donor
NC_000011.10:g.64805916_64807925del
NC_000011.9:g.64573388_64575397del
NG_008929.1:g.8373_10382del
NG_033040.1:g.320_2329del
LRG_509:g.8373_10382del
LRG_509t2:c.623_1050-143del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
MEN1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2579	2600

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Multiple endocrine neoplasia, type 1	Pathogenic (1)	criteria provided, single submitter	Oct 15, 2018	RCV000822934.3

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Oct 15, 2018)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Multiple endocrine neoplasia, type 1 Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000963760.1 First in ClinVar: Aug 14, 2019 Last updated: Aug 14, 2019	Publications: PubMed (3) PubMed: 19953642‚ 9463336‚ 15635078 Comment: This variant is a deletion of the genomic region encompassing exons 4-7 and part of exon 3 (c.623_1050-143del) of the MEN1 gene. It is expected … (more) This variant is a deletion of the genomic region encompassing exons 4-7 and part of exon 3 (c.623_1050-143del) of the MEN1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with MEN1-related disease. This variant disrupts the p.Ala284 amino acid residue in MEN1. Other variant(s) that disrupt this residue have been observed in affected individuals (PMID: 9463336, 19953642, 15635078), suggesting that it is a clinically significant residue. As a result, variants that disrupt this residue are likely to be causative of disease. Loss-of-function variants in MEN1 are known to be pathogenic (PMID: 12112656, 17853334). For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

This variant is a deletion of the genomic region encompassing exons 4-7 and part of exon 3 (c.623_1050-143del) of the MEN1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with MEN1-related disease. This variant disrupts the p.Ala284 amino acid residue in MEN1. Other variant(s) that disrupt this residue have been observed in affected individuals (PMID: 9463336, 19953642, 15635078), suggesting that it is a clinically significant residue. As a result, variants that disrupt this residue are likely to be causative of disease. Loss-of-function variants in MEN1 are known to be pathogenic (PMID: 12112656, 17853334). For these reasons, this variant has been classified as Pathogenic.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Diagnostic challenges due to phenocopies: lessons from Multiple Endocrine Neoplasia type1 (MEN1).	Turner JJ	Human mutation	2010	PMID: 19953642
A report of a national mutation testing service for the MEN1 gene: clinical presentations and implications for mutation testing.	Cardinal JW	Journal of medical genetics	2005	PMID: 15635078
Characterization of mutations in patients with multiple endocrine neoplasia type 1.	Bassett JH	American journal of human genetics	1998	PMID: 9463336

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_001370259.2(MEN1):c.623_1050-143del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...