VCV001793790.2 - ClinVar

NM_000546.6(TP53):c.261_270del (p.Ala88fs)

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.

Pathogenic

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.261_270del (p.Ala88fs)

Variation ID: 1793790 Accession: VCV001793790.2

Type and length

Deletion, 10 bp

Location

Cytogenetic: 17p13.1 17: 7676099-7676108 (GRCh38) [ NCBI UCSC ] 17: 7579417-7579426 (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	Nov 29, 2022	May 1, 2024	Dec 13, 2019

HGVS

Nucleotide	Protein	Molecular consequence
NM_000546.6:c.261_270del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000537.3:p.Ala88fs	frameshift
NM_001126112.3:c.261_270del	NP_001119584.1:p.Ala88fs	frameshift
NM_001126113.3:c.261_270del	NP_001119585.1:p.Ala88fs	frameshift
NM_001126114.3:c.261_270del	NP_001119586.1:p.Ala88fs	frameshift
NM_001126118.2:c.144_153del	NP_001119590.1:p.Ala49fs	frameshift
NM_001276695.3:c.144_153del	NP_001263624.1:p.Ala49fs	frameshift
NM_001276696.3:c.144_153del	NP_001263625.1:p.Ala49fs	frameshift
NM_001276760.3:c.144_153del	NP_001263689.1:p.Ala49fs	frameshift
NM_001276761.3:c.144_153del	NP_001263690.1:p.Ala49fs	frameshift
NM_001407262.1:c.259_268delCCAGCCCCCT	NP_001394191.1:p.Ala88Glyfs	frameshift
NM_001407263.1:c.142_151delCCAGCCCCCT	NP_001394192.1:p.Ala49Glyfs	frameshift
NM_001407264.1:c.259_268delCCAGCCCCCT	NP_001394193.1:p.Ala88Glyfs	frameshift
NM_001407265.1:c.142_151delCCAGCCCCCT	NP_001394194.1:p.Ala49Glyfs	frameshift
NM_001407266.1:c.259_268delCCAGCCCCCT	NP_001394195.1:p.Ala88Glyfs	frameshift
NM_001407267.1:c.142_151delCCAGCCCCCT	NP_001394196.1:p.Ala49Glyfs	frameshift
NM_001407268.1:c.259_268delCCAGCCCCCT	NP_001394197.1:p.Ala88Glyfs	frameshift
NM_001407269.1:c.142_151delCCAGCCCCCT	NP_001394198.1:p.Ala49Glyfs	frameshift
NM_001407270.1:c.259_268delCCAGCCCCCT	NP_001394199.1:p.Ala88Glyfs	frameshift
NM_001407271.1:c.142_151delCCAGCCCCCT	NP_001394200.1:p.Ala49Glyfs	frameshift
NR_176326.1:n.401_410delCCAGCCCCCT
NC_000017.11:g.7676101_7676110del
NC_000017.10:g.7579419_7579428del
NG_017013.2:g.16443_16452del
LRG_321:g.16443_16452del
LRG_321t1:c.259_268del	LRG_321p1:p.Ala88Glyfs
LRG_321t2:c.259_268del	LRG_321:p.Ala88Glyfs
LRG_321t3:c.259_268del	LRG_321p3:p.Ala88Glyfs
LRG_321t4:c.259_268del	LRG_321p4:p.Ala88Glyfs
LRG_321t8:c.142_151del	LRG_321p8:p.Ala49Glyfs

... more HGVS ... less HGVS

Protein change

A88fs, A49fs

Other names

Canonical SPDI

NC_000017.11:7676098:GGAGGGGGCTGG:GG

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.
Hereditary cancer-predisposing syndrome	Pathogenic (1)	criteria provided, single submitter	Dec 13, 2019	RCV002437175.2

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.
Pathogenic (Dec 13, 2019)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Hereditary cancer-predisposing syndrome Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV002745559.2 First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024	Comment: The c.261_270del10 variant, located in coding exon 3 of the TP53 gene, results from a deletion of 10 nucleotides at nucleotide positions 261 to 270, … (more) The c.261_270del10 variant, located in coding exon 3 of the TP53 gene, results from a deletion of 10 nucleotides at nucleotide positions 261 to 270, causing a translational frameshift with a predicted alternate stop codon (p.A88Gfs*32). This mutation has been reported as a germline variant in a 5-year-old female with medulloblastoma (Waszak S et al. Lancet Oncol. 2018 06;19(6):785-798). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (less)

Comment:

The c.261_270del10 variant, located in coding exon 3 of the TP53 gene, results from a deletion of 10 nucleotides at nucleotide positions 261 to 270, causing a translational frameshift with a predicted alternate stop codon (p.A88Gfs*32). This mutation has been reported as a germline variant in a 5-year-old female with medulloblastoma (Waszak S et al. Lancet Oncol. 2018 06;19(6):785-798). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

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 May 01, 2024

ClinVar Genomic variation as it relates to human health

NM_000546.6(TP53):c.261_270del (p.Ala88fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...