ClinVar Genomic variation as it relates to human health
NM_001370259.2(MEN1):c.1429del (p.Glu477fs)
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.
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001370259.2(MEN1):c.1429del (p.Glu477fs)
Variation ID: 1772445 Accession: VCV001772445.1
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 11q13.1 11: 64804738 (GRCh38) [ NCBI UCSC ] 11: 64572210 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Nov 29, 2022 Nov 29, 2022 Jul 30, 2021 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001370259.2:c.1429del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357188.2:p.Glu477fs frameshift NM_000244.4:c.1444del NP_000235.3:p.Glu482fs frameshift NM_001370251.2:c.1555del NP_001357180.2:p.Glu519fs frameshift NM_001370260.2:c.1429del NP_001357189.2:p.Glu477fs frameshift NM_001370261.2:c.1429del NP_001357190.2:p.Glu477fs frameshift NM_001370262.2:c.1324del NP_001357191.2:p.Glu442fs frameshift NM_001370263.2:c.1324del NP_001357192.2:p.Glu442fs frameshift NM_001407142.1:c.1553delG NP_001394071.1:p.Glu519Lysfs frameshift NM_001407143.1:c.1553delG NP_001394072.1:p.Glu519Lysfs frameshift NM_001407144.1:c.1553delG NP_001394073.1:p.Glu519Lysfs frameshift NM_001407145.1:c.1442delG NP_001394074.1:p.Glu482Lysfs frameshift NM_001407146.1:c.1427delG NP_001394075.1:p.Glu477Lysfs frameshift NM_001407147.1:c.1427delG NP_001394076.1:p.Glu477Lysfs frameshift NM_001407148.1:c.1322delG NP_001394077.1:p.Glu442Lysfs frameshift NM_001407149.1:c.1322delG NP_001394078.1:p.Glu442Lysfs frameshift NM_001407150.1:c.1568delG NP_001394079.1:p.Glu524Lysfs frameshift NM_001407151.1:c.1448delG NP_001394080.1:p.Glu484Lysfs frameshift NM_001407152.1:c.1262delG NP_001394081.1:p.Glu422Lysfs frameshift NM_130799.2:c.1429delG frameshift NM_130799.3:c.1429del NP_570711.2:p.Glu477fs frameshift NM_130800.3:c.1444del NP_570712.2:p.Glu482fs frameshift NM_130801.3:c.1444del NP_570713.2:p.Glu482fs frameshift NM_130802.3:c.1444del NP_570714.2:p.Glu482fs frameshift NM_130803.3:c.1444del NP_570715.2:p.Glu482fs frameshift NM_130804.3:c.1444del NP_570716.2:p.Glu482fs frameshift NR_176284.1:n.1625delG NR_176285.1:n.1637delG NR_176286.1:n.1640delG NR_176287.1:n.1898delG NC_000011.10:g.64804740del NC_000011.9:g.64572212del NG_008929.1:g.11557del NG_033040.2:g.3476del LRG_509:g.11557del LRG_509t1:c.1442del LRG_509p1:p.Glu482Lysfs LRG_509t2:c.1427del LRG_509p2:p.Glu477Lysfs - Protein change
- E442fs, E519fs, E477fs, E482fs
- Other names
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- Canonical SPDI
- NC_000011.10:64804737:CCC:CC
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe 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.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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. |
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MEN1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
2443 | 2460 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (1) |
criteria provided, single submitter
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Jul 30, 2021 | RCV002392007.1 |
Submissions - Germline
Classification
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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
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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
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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
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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. |
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Pathogenic
(Jul 30, 2021)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002701031.1
First in ClinVar: Nov 29, 2022 Last updated: Nov 29, 2022 |
Comment:
The c.1429delG variant, located in coding exon 9 of the MEN1 gene, results from a deletion of one nucleotide at nucleotide position 1429, causing a … (more)
The c.1429delG variant, located in coding exon 9 of the MEN1 gene, results from a deletion of one nucleotide at nucleotide position 1429, causing a translational frameshift with a predicted alternate stop codon (p.E477Kfs*82). This alteration occurs at the 3' terminus of theMEN1 gene, is not expected to trigger nonsense-mediated mRNA decay, and only impacts the last 134 amino acids of the protein. However, premature stop codons are typically deleterious in nature and a significant portion of the protein is affected (Ambry internal data). This alteration, referred to as "nt 1539delG (fs81aaX)," has been seen in a Portuguese family whose phenotype is consistent with multiple endocrine neoplasia type 1 (MEN1) (Cavaco BM et al. Clin Endocrinol (Oxf), 2002 Apr;56:465-73). In addition to the clinical data presented in the literature, this variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). As such, this alteration is interpreted as a disease-causing mutation. (less)
Number of individuals with the variant: 1
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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. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Mutational analysis of Portuguese families with multiple endocrine neoplasia type 1 reveals large germline deletions. | Cavaco BM | Clinical endocrinology | 2002 | PMID: 11966739 |
Text-mined citations for this variant ...
HelpRecord last updated Dec 25, 2023
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.