VCV002574069.1 - ClinVar

NM_001370259.2(MEN1):c.116T>A (p.Leu39Ter)

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

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001370259.2(MEN1):c.116T>A (p.Leu39Ter)

Variation ID: 2574069 Accession: VCV002574069.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 11q13.1 11: 64809994 (GRCh38) [ NCBI UCSC ] 11: 64577466 (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	Feb 4, 2024	Feb 4, 2024	Jul 21, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001370259.2:c.116T>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001357188.2:p.Leu39Ter	nonsense
NM_000244.4:c.116T>A	NP_000235.3:p.Leu39Ter	nonsense
NM_001370251.2:c.116T>A	NP_001357180.2:p.Leu39Ter	nonsense
NM_001370260.2:c.116T>A	NP_001357189.2:p.Leu39Ter	nonsense
NM_001370261.2:c.116T>A	NP_001357190.2:p.Leu39Ter	nonsense
NM_001370262.2:c.116T>A	NP_001357191.2:p.Leu39Ter	nonsense
NM_001370263.2:c.116T>A	NP_001357192.2:p.Leu39Ter	nonsense
NM_001407142.1:c.116T>A	NP_001394071.1:p.Leu39Ter	nonsense
NM_001407143.1:c.116T>A	NP_001394072.1:p.Leu39Ter	nonsense
NM_001407144.1:c.116T>A	NP_001394073.1:p.Leu39Ter	nonsense
NM_001407145.1:c.116T>A	NP_001394074.1:p.Leu39Ter	nonsense
NM_001407146.1:c.116T>A	NP_001394075.1:p.Leu39Ter	nonsense
NM_001407147.1:c.116T>A	NP_001394076.1:p.Leu39Ter	nonsense
NM_001407148.1:c.116T>A	NP_001394077.1:p.Leu39Ter	nonsense
NM_001407149.1:c.116T>A	NP_001394078.1:p.Leu39Ter	nonsense
NM_001407150.1:c.116T>A	NP_001394079.1:p.Leu39Ter	nonsense
NM_001407151.1:c.116T>A	NP_001394080.1:p.Leu39Ter	nonsense
NM_001407152.1:c.116T>A	NP_001394081.1:p.Leu39Ter	nonsense
NM_130799.3:c.116T>A	NP_570711.2:p.Leu39Ter	nonsense
NM_130800.3:c.116T>A	NP_570712.2:p.Leu39Ter	nonsense
NM_130801.3:c.116T>A	NP_570713.2:p.Leu39Ter	nonsense
NM_130802.3:c.116T>A	NP_570714.2:p.Leu39Ter	nonsense
NM_130803.3:c.116T>A	NP_570715.2:p.Leu39Ter	nonsense
NM_130804.3:c.116T>A	NP_570716.2:p.Leu39Ter	nonsense
NR_176284.1:n.165T>A		non-coding transcript variant
NR_176285.1:n.177T>A		non-coding transcript variant
NR_176286.1:n.165T>A		non-coding transcript variant
NR_176287.1:n.423T>A		non-coding transcript variant
NC_000011.10:g.64809994A>T
NC_000011.9:g.64577466A>T
NG_008929.1:g.6301T>A
LRG_509:g.6301T>A
LRG_509t1:c.116T>A	LRG_509p1:p.Leu39Ter
LRG_509t2:c.116T>A	LRG_509p2:p.Leu39Ter

... more HGVS ... less HGVS

Protein change

L39*

Other names

Canonical SPDI

NC_000011.10:64809993:A:T

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	2581	2602

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)	no assertion criteria provided	Jul 21, 2023	RCV003485895.1

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 (Jul 21, 2023)	no assertion criteria provided Method: research	Multiple endocrine neoplasia, type 1 Affected status: yes Allele origin: germline	deCODE genetics, Amgen Accession: SCV004022144.1 First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024	Comment: The variant NM_001370259.2:c.116T>A (chr11:64809994) in MEN1 was detected in 2 heterozygotes out of 58K WGS Icelanders (MAF= 0,002%). Following imputation in a set of 166K … (more) The variant NM_001370259.2:c.116T>A (chr11:64809994) in MEN1 was detected in 2 heterozygotes out of 58K WGS Icelanders (MAF= 0,002%). Following imputation in a set of 166K Icelanders (3 imputed heterozygotes) we observed an association with hyperparathyroidism using 390 cases and 265373 controls (OR= 85.12, P= 5.60e-03) and neoplasm of the parathyroid gland using 271 cases and 265492 controls (OR= 83.91, P= 6.07e-03). This variant has not been reported in ClinVar previously. Based on ACMG criteria (PVS1, PS4) this variant classifies as pathogenic. (less) Number of individuals with the variant: 3 Ethnicity/Population group: Icelandic

Comment:

The variant NM_001370259.2:c.116T>A (chr11:64809994) in MEN1 was detected in 2 heterozygotes out of 58K WGS Icelanders (MAF= 0,002%). Following imputation in a set of 166K Icelanders (3 imputed heterozygotes) we observed an association with hyperparathyroidism using 390 cases and 265373 controls (OR= 85.12, P= 5.60e-03) and neoplasm of the parathyroid gland using 271 cases and 265492 controls (OR= 83.91, P= 6.07e-03). This variant has not been reported in ClinVar previously. Based on ACMG criteria (PVS1, PS4) this variant classifies 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

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Feb 14, 2024

ClinVar Genomic variation as it relates to human health

NM_001370259.2(MEN1):c.116T>A (p.Leu39Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...