This variant, c.779_781del, is a complex sequence change that results in the deletion of 2 and insertion of 1 amino acid(s) in the TP53 protein (p.Ser260_Ser261delinsCys). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TP53-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
ClinVar Genomic variation as it relates to human health
NM_000546.6(TP53):c.779_781del (p.Ser260_Ser261delinsCys)
Germline
Classification
Help
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)
Help
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.
Uncertain significance
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000546.6(TP53):c.779_781del (p.Ser260_Ser261delinsCys)
Variation ID: 2769320 Accession: VCV002769320.1
- Type and length
-
Deletion, 3 bp
- Location
-
Cytogenetic: 17p13.1 17: 7674182-7674184 (GRCh38) [ NCBI UCSC ] 17: 7577500-7577502 (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 14, 2024 Feb 14, 2024 Nov 20, 2023 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000546.6:c.779_781del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000537.3:p.Ser260_Ser261delinsCys inframe indel NM_001126112.3:c.779_781del NP_001119584.1:p.Ser260_Ser261delinsCys inframe indel NM_001126113.3:c.779_781del NP_001119585.1:p.Ser260_Ser261delinsCys inframe indel NM_001126114.3:c.779_781del NP_001119586.1:p.Ser260_Ser261delinsCys inframe indel NM_001126115.2:c.383_385del NP_001119587.1:p.Ser128_Ser129delinsCys inframe indel NM_001126116.2:c.383_385del NP_001119588.1:p.Ser128_Ser129delinsCys inframe indel NM_001126117.2:c.383_385del NP_001119589.1:p.Ser128_Ser129delinsCys inframe indel NM_001126118.2:c.662_664del NP_001119590.1:p.Ser221_Ser222delinsCys inframe indel NM_001276695.3:c.662_664del NP_001263624.1:p.Ser221_Ser222delinsCys inframe indel NM_001276696.3:c.662_664del NP_001263625.1:p.Ser221_Ser222delinsCys inframe indel NM_001276697.3:c.302_304del NP_001263626.1:p.Ser101_Ser102delinsCys inframe indel NM_001276698.3:c.302_304del NP_001263627.1:p.Ser101_Ser102delinsCys inframe indel NM_001276699.3:c.302_304del NP_001263628.1:p.Ser101_Ser102delinsCys inframe indel NM_001276760.3:c.662_664del NP_001263689.1:p.Ser221_Ser222delinsCys inframe indel NM_001276761.3:c.662_664del NP_001263690.1:p.Ser221_Ser222delinsCys inframe indel NM_001407262.1:c.779_781del NP_001394191.1:p.Ser260_Ser261delinsCys inframe indel NM_001407263.1:c.662_664del NP_001394192.1:p.Ser221_Ser222delinsCys inframe indel NM_001407264.1:c.779_781del NP_001394193.1:p.Ser260_Ser261delinsCys inframe indel NM_001407265.1:c.662_664del NP_001394194.1:p.Ser221_Ser222delinsCys inframe indel NM_001407266.1:c.779_781del NP_001394195.1:p.Ser260_Ser261delinsCys inframe indel NM_001407267.1:c.662_664del NP_001394196.1:p.Ser221_Ser222delinsCys inframe indel NM_001407268.1:c.779_781del NP_001394197.1:p.Ser260_Ser261delinsCys inframe indel NM_001407269.1:c.662_664del NP_001394198.1:p.Ser221_Ser222delinsCys inframe indel NM_001407270.1:c.779_781del NP_001394199.1:p.Ser260_Ser261delinsCys inframe indel NM_001407271.1:c.662_664del NP_001394200.1:p.Ser221_Ser222delinsCys inframe indel NR_176326.1:n.808_810del non-coding transcript variant NC_000017.11:g.7674182_7674184del NC_000017.10:g.7577500_7577502del NG_017013.2:g.18367_18369del LRG_321:g.18367_18369del LRG_321t1:c.779_781del LRG_321p1:p.Ser260_Ser261delinsCys LRG_321t2:c.779_781del LRG_321:p.Ser260_Ser261delinsCys LRG_321t3:c.779_781del LRG_321p3:p.Ser260_Ser261delinsCys LRG_321t4:c.779_781del LRG_321p4:p.Ser260_Ser261delinsCys LRG_321t5:c.383_385del LRG_321p5:p.Ser128_Ser129delinsCys LRG_321t6:c.383_385del LRG_321p6:p.Ser128_Ser129delinsCys LRG_321t7:c.383_385del LRG_321p7:p.Ser128_Ser129delinsCys LRG_321t8:c.662_664del LRG_321p8:p.Ser221_Ser222delinsCys - Protein change
- -
- Other names
- -
- Canonical SPDI
- NC_000017.11:7674181:TGG:
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
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.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- Links
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 | ||
|---|---|---|---|---|---|---|
| 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. |
|||
| TP53 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
3367 | 3466 | |
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. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
|
Nov 20, 2023 | RCV003510368.2 |
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. |
|
|---|---|---|---|---|---|
|
Uncertain significance
(Nov 20, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Li-Fraumeni syndrome
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004335148.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
Comment:
This variant, c.779_781del, is a complex sequence change that results in the deletion of 2 and insertion of 1 amino acid(s) in the TP53 protein … (more)
This variant, c.779_781del, is a complex sequence change that results in the deletion of 2 and insertion of 1 amino acid(s) in the TP53 protein (p.Ser260_Ser261delinsCys). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TP53-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
|
Comment:
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:
This variant, c.779_781del, is a complex sequence change that results in the deletion of 2 and insertion of 1 amino acid(s) in the TP53 protein (p.Ser260_Ser261delinsCys). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TP53-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Citations for germline classification of this variant
Help| 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 ...
HelpRecord last updated Sep 30, 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.