ClinVar Genomic variation as it relates to human health
NM_000268.4(NF2):c.1593del (p.Ser532fs)
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_000268.4(NF2):c.1593del (p.Ser532fs)
Variation ID: 3071708 Accession: VCV003071708.1
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 22q12.2 22: 29681457 (GRCh38) [ NCBI UCSC ] 22: 30077446 (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 Apr 20, 2024 Apr 20, 2024 Jun 20, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000268.4:c.1593del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000259.1:p.Ser532fs frameshift NM_001407053.1:c.1479del NP_001393982.1:p.Ser494fs frameshift NM_001407054.1:c.1470del NP_001393983.1:p.Ser491fs frameshift NM_001407055.1:c.1467del NP_001393984.1:p.Ser490fs frameshift NM_001407056.1:c.1479del NP_001393985.1:p.Ser494fs frameshift NM_001407057.1:c.1458del NP_001393986.1:p.Ser487fs frameshift NM_001407058.1:c.1470del NP_001393987.1:p.Ser491fs frameshift NM_001407059.1:c.1458del NP_001393988.1:p.Ser487fs frameshift NM_001407060.1:c.1574+3134del intron variant NM_001407062.1:c.1335del NP_001393991.1:p.Ser446fs frameshift NM_001407063.1:c.1344del NP_001393992.1:p.Ser449fs frameshift NM_001407064.1:c.1325+3134del intron variant NM_001407065.1:c.1059del NP_001393994.1:p.Ser354fs frameshift NM_001407066.1:c.1593del NP_001393995.1:p.Ser532fs frameshift NM_001407067.1:c.1362del NP_001393996.1:p.Ser455fs frameshift NM_016418.5:c.1593del NP_057502.2:p.Ser532fs frameshift NM_181825.3:c.1593del NP_861546.1:p.Ser532fs frameshift NM_181828.3:c.1467del NP_861966.1:p.Ser490fs frameshift NM_181829.3:c.1470del NP_861967.1:p.Ser491fs frameshift NM_181830.3:c.1344del NP_861968.1:p.Ser449fs frameshift NM_181831.3:c.1344del NP_861969.1:p.Ser449fs frameshift NM_181832.3:c.1593del NP_861970.1:p.Ser532fs frameshift NM_181833.3:c.448-13295del intron variant NR_156186.2:n.2075delG NC_000022.11:g.29681457del NC_000022.10:g.30077446del NG_009057.1:g.82902del LRG_511:g.82902del LRG_511t1:c.1593del LRG_511p1:p.Ser532Alafs LRG_511t2:c.1593del LRG_511p2:p.Ser532fs - Protein change
- S354fs, S446fs, S449fs, S455fs, S487fs, S490fs, S491fs, S494fs, S532fs
- Other names
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- Canonical SPDI
- NC_000022.11:29681456:G:
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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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NF2 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
2021 | 2067 |
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
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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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Likely pathogenic (1) |
criteria provided, single submitter
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Jun 20, 2023 | RCV004016202.2 |
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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Likely Pathogenic
(Jun 20, 2023)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 2
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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All of Us Research Program, National Institutes of Health
Accession: SCV004830340.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
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Comment:
This variant is predicted to result in loss of protein function through nonsense-mediated or protein truncation. Loss of function is an established mechanism of disease. … (more)
This variant is predicted to result in loss of protein function through nonsense-mediated or protein truncation. Loss of function is an established mechanism of disease. This variant is absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). It has been identified as a somatic mutation in schwannoma samples (PMID: 11809806, 23354516, 32373528). (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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Comprehensive Genomic Profiling of Rare Tumors: Routes to Targeted Therapies. | Wang S | Frontiers in oncology | 2020 | PMID: 32373528 |
Microarray analysis of gene expression in vestibular schwannomas reveals SPP1/MET signaling pathway and androgen receptor deregulation. | Torres-Martin M | International journal of oncology | 2013 | PMID: 23354516 |
The neurofibromatosis type 2 gene product, merlin, reverses the F-actin cytoskeletal defects in primary human Schwannoma cells. | Bashour AM | Molecular and cellular biology | 2002 | PMID: 11809806 |
Text-mined citations for this variant ...
HelpRecord last updated May 08, 2024
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.