ClinVar Genomic variation as it relates to human health
NM_000546.6(TP53):c.993+1del
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_000546.6(TP53):c.993+1del
Variation ID: 428898 Accession: VCV000428898.6
- Type and length
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Deletion, 1 bp
- Location
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Cytogenetic: 17p13.1 17: 7673534 (GRCh38) [ NCBI UCSC ] 17: 7576852 (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 Jul 1, 2017 Feb 14, 2024 Aug 28, 2019 - HGVS
- ... more HGVS ... less HGVS
- Protein change
- Other names
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- Canonical SPDI
- NC_000017.11:7673533:CC:C
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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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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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TP53 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
3196 | 3291 |
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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Pathogenic (1) |
criteria provided, single submitter
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Apr 25, 2014 | RCV000492434.1 | |
Pathogenic (3) |
reviewed by expert panel
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Aug 28, 2019 | RCV000991147.3 |
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
(Aug 28, 2019)
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reviewed by expert panel
Method: curation
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Li-Fraumeni syndrome
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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ClinGen TP53 Variant Curation Expert Panel, ClinGen
Accession: SCV001142556.1
First in ClinVar: Jan 12, 2020 Last updated: Jan 12, 2020 |
Comment:
The c.993+1delG variant is predicted to result in a premature stop codon that leads to a truncated or absent protein (PVS1). This variant is absent … (more)
The c.993+1delG variant is predicted to result in a premature stop codon that leads to a truncated or absent protein (PVS1). This variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). This variant has been reported in a proband meeting classic Li-Fraumeni syndrome criteria (PS4_Supporting; PMID: 10980596). This variant was found to co-segregation with disease in multiple affected family members, with 5 meioses observed (PP1_Moderate; PMID: 10980596). In summary, TP53 c.993+1delG meets criteria to be classified as pathogenic for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: PVS1, PM2_Supporting, PS4_Supporting, PP1_Moderate. (less)
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Pathogenic
(May 05, 2020)
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criteria provided, single submitter
Method: clinical testing
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Li-Fraumeni syndrome
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001370554.1
First in ClinVar: Jul 16, 2020 Last updated: Jul 16, 2020 |
Comment:
Variant summary: TP53 c.993+1delG is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to … (more)
Variant summary: TP53 c.993+1delG is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: four predict the variant abolishes a 5' splicing donor site. These predictions were confirmed by a publication that demonstrated exon 9 skipping in a patient derived immortalized cell line, and the lack of the variant-transcript in mRNA isolated from patient derived leukocytes (Verselis_2000). The variant was absent in 251342 control chromosomes (gnomAD). c.993+1delG has been reported in the literature in a large family, in multiple family members affected with various tumors belonging to the Li-Fraumeni Syndrome tumor spectrum (Verselis_2000); this family met the classic Li-Fraumeni syndrome criteria, and the variant co-segregated with the disease in multiple family members. These data indicate that the variant is likely to be associated with disease. One submitter (i.e. ClinGen TP53 Variant Curation Expert Panel) has provided clinical-significance assessments for this variant in ClinVar after 2014, and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Apr 25, 2014)
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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: SCV000581155.4
First in ClinVar: Jul 01, 2017 Last updated: Jul 01, 2017 |
Comment:
​The c.993+1delG intronic pathogenic mutation results from a deletion of the first nucleotide after coding exon 8 of the TP53 gene. This mutation tracked with … (more)
​The c.993+1delG intronic pathogenic mutation results from a deletion of the first nucleotide after coding exon 8 of the TP53 gene. This mutation tracked with disease in a large family with multiple members diagnosed with a wide spectrum of Li-Fraumeni related cancers. RT-PCR analyses showed that this alteration, referred to as IVS9+1delG, led to exon 9 skipping (Verselis SJ et al. Oncogene. 2000 Aug 31;19(37):4230-5). In addition to the clinical data presented in the literature, since alterations that disrupt the canonical splice donor site are typically deleterious in nature, this alteration is interpreted as a disease-causing mutation (ACMG Recommendations for Standards for Interpretation and Reporting of Sequence Variations. Revision 2007. Genet Med. 2008;10:294). (less)
Number of individuals with the variant: 1
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Likely pathogenic
(Feb 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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Li-Fraumeni syndrome
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV004296690.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
Comment:
This sequence change affects a splice site in intron 9 of the TP53 gene. It is expected to disrupt RNA splicing. Variants that disrupt the … (more)
This sequence change affects a splice site in intron 9 of the TP53 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 TP53 are known to be pathogenic (PMID: 20522432). This variant is not present in population databases (gnomAD no frequency). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Studies have shown that disruption of this splice site is associated with altered splicing resulting in unknown protein product impact (PMID: 10980596). ClinVar contains an entry for this variant (Variation ID: 428898). This variant is also known as IVS9+1delG. Disruption of this splice site has been observed in individual(s) with clinical features of Li-Fraumeni syndrome (PMID: 10980596, 31970404). It has also been observed to segregate with disease in related individuals. (less)
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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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Germline cancer predisposition variants and pediatric glioma: a population-based study in California. | Muskens IS | Neuro-oncology | 2020 | PMID: 31970404 |
TP53 germline mutation testing in 180 families suspected of Li-Fraumeni syndrome: mutation detection rate and relative frequency of cancers in different familial phenotypes. | Ruijs MW | Journal of medical genetics | 2010 | PMID: 20522432 |
Splicing in action: assessing disease causing sequence changes. | Baralle D | Journal of medical genetics | 2005 | PMID: 16199547 |
Novel p53 splice site mutations in three families with Li-Fraumeni syndrome. | Verselis SJ | Oncogene | 2000 | PMID: 10980596 |
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/a608c703-2232-4c79-86dd-00844776434d | - | - | - | - |
Text-mined citations for rs1131691033 ...
HelpRecord last updated Feb 14, 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.