VCV002086647.2 - ClinVar

NM_000546.6(TP53):c.812_814del (p.Glu271del)

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.

Uncertain significance

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.812_814del (p.Glu271del)

Variation ID: 2086647 Accession: VCV002086647.2

Type and length

Deletion, 3 bp

Location

Cytogenetic: 17p13.1 17: 7673806-7673808 (GRCh38) [ NCBI UCSC ] 17: 7577124-7577126 (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 8, 2023	Feb 20, 2024	Jul 17, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_000546.6:c.812_814del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000537.3:p.Glu271del	inframe deletion
NM_001126112.3:c.812_814del	NP_001119584.1:p.Glu271del	inframe deletion
NM_001126113.3:c.812_814del	NP_001119585.1:p.Glu271del	inframe deletion
NM_001126114.3:c.812_814del	NP_001119586.1:p.Glu271del	inframe deletion
NM_001126115.2:c.416_418del	NP_001119587.1:p.Glu139del	inframe deletion
NM_001126116.2:c.416_418del	NP_001119588.1:p.Glu139del	inframe deletion
NM_001126117.2:c.416_418del	NP_001119589.1:p.Glu139del	inframe deletion
NM_001126118.2:c.695_697del	NP_001119590.1:p.Glu232del	inframe deletion
NM_001276695.3:c.695_697del	NP_001263624.1:p.Glu232del	inframe deletion
NM_001276696.3:c.695_697del	NP_001263625.1:p.Glu232del	inframe deletion
NM_001276697.3:c.335_337del	NP_001263626.1:p.Glu112del	inframe deletion
NM_001276698.3:c.335_337del	NP_001263627.1:p.Glu112del	inframe deletion
NM_001276699.3:c.335_337del	NP_001263628.1:p.Glu112del	inframe deletion
NM_001276760.3:c.695_697del	NP_001263689.1:p.Glu232del	inframe deletion
NM_001276761.3:c.695_697del	NP_001263690.1:p.Glu232del	inframe deletion
NM_001407262.1:c.811_813delGAG	NP_001394191.1:p.Glu271del	inframe indel
NM_001407263.1:c.694_696delGAG	NP_001394192.1:p.Glu232del	inframe indel
NM_001407264.1:c.811_813delGAG	NP_001394193.1:p.Glu271del	inframe indel
NM_001407265.1:c.694_696delGAG	NP_001394194.1:p.Glu232del	inframe indel
NM_001407266.1:c.811_813delGAG	NP_001394195.1:p.Glu271del	inframe indel
NM_001407267.1:c.694_696delGAG	NP_001394196.1:p.Glu232del	inframe indel
NM_001407268.1:c.811_813delGAG	NP_001394197.1:p.Glu271del	inframe indel
NM_001407269.1:c.694_696delGAG	NP_001394198.1:p.Glu232del	inframe indel
NM_001407270.1:c.811_813delGAG	NP_001394199.1:p.Glu271del	inframe indel
NM_001407271.1:c.694_696delGAG	NP_001394200.1:p.Glu232del	inframe indel
NR_176326.1:n.840_842delGAG
NC_000017.11:g.7673807_7673809del
NC_000017.10:g.7577125_7577127del
NG_017013.2:g.18743_18745del
LRG_321:g.18743_18745del
LRG_321t1:c.811_813del	LRG_321p1:p.Glu271del
LRG_321t2:c.811_813del	LRG_321:p.Glu271del
LRG_321t3:c.811_813del	LRG_321p3:p.Glu271del
LRG_321t4:c.811_813del	LRG_321p4:p.Glu271del
LRG_321t5:c.415_417del	LRG_321p5:p.Glu139del
LRG_321t6:c.415_417del	LRG_321p6:p.Glu139del
LRG_321t7:c.415_417del	LRG_321p7:p.Glu139del
LRG_321t8:c.694_696del	LRG_321p8:p.Glu232del

... more HGVS ... less HGVS

Protein change

E112del, E232del, E271del, E139del

Other names

Canonical SPDI

NC_000017.11:7673805:CCTC:C

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.
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.
Li-Fraumeni syndrome	Uncertain significance (1)	criteria provided, single submitter	Jul 17, 2023	RCV003007588.3

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 (Jul 17, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Li-Fraumeni syndrome Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003306934.2 First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024	Comment: This variant, c.812_814del, results in the deletion of 1 amino acid(s) of the TP53 protein (p.Glu271del), but otherwise preserves the integrity of the reading frame. … (more) This variant, c.812_814del, results in the deletion of 1 amino acid(s) of the TP53 protein (p.Glu271del), but otherwise preserves the integrity of the reading frame. 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. ClinVar contains an entry for this variant (Variation ID: 2086647). 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:

This variant, c.812_814del, results in the deletion of 1 amino acid(s) of the TP53 protein (p.Glu271del), but otherwise preserves the integrity of the reading frame. 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. ClinVar contains an entry for this variant (Variation ID: 2086647). 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.

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 Nov 10, 2024

ClinVar Genomic variation as it relates to human health

NM_000546.6(TP53):c.812_814del (p.Glu271del)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...