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NM_000546.6(TP53):c.993G>A (p.Gln331=) AND not provided

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Feb 22, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000521745.5

Allele description [Variation Report for NM_000546.6(TP53):c.993G>A (p.Gln331=)]

NM_000546.6(TP53):c.993G>A (p.Gln331=)

Gene:
TP53:tumor protein p53 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p13.1
Genomic location:
Preferred name:
NM_000546.6(TP53):c.993G>A (p.Gln331=)
HGVS:
  • NC_000017.11:g.7673535C>T
  • NG_017013.2:g.19016G>A
  • NM_000546.6:c.993G>AMANE SELECT
  • NM_001126112.3:c.993G>A
  • NM_001126113.3:c.993G>A
  • NM_001126114.3:c.993G>A
  • NM_001126115.2:c.597G>A
  • NM_001126116.2:c.597G>A
  • NM_001126117.2:c.597G>A
  • NM_001126118.2:c.876G>A
  • NM_001276695.3:c.876G>A
  • NM_001276696.3:c.876G>A
  • NM_001276697.3:c.516G>A
  • NM_001276698.3:c.516G>A
  • NM_001276699.3:c.516G>A
  • NM_001276760.3:c.876G>A
  • NM_001276761.3:c.876G>A
  • NP_000537.3:p.Gln331=
  • NP_000537.3:p.Gln331=
  • NP_001119584.1:p.Gln331=
  • NP_001119585.1:p.Gln331=
  • NP_001119586.1:p.Gln331=
  • NP_001119587.1:p.Gln199=
  • NP_001119588.1:p.Gln199=
  • NP_001119589.1:p.Gln199=
  • NP_001119590.1:p.Gln292=
  • NP_001263624.1:p.Gln292=
  • NP_001263625.1:p.Gln292=
  • NP_001263626.1:p.Gln172=
  • NP_001263627.1:p.Gln172=
  • NP_001263628.1:p.Gln172=
  • NP_001263689.1:p.Gln292=
  • NP_001263690.1:p.Gln292=
  • LRG_321t1:c.993G>A
  • LRG_321:g.19016G>A
  • LRG_321p1:p.Gln331=
  • NC_000017.10:g.7576853C>T
  • NM_000546.4:c.993G>A
  • NM_000546.5:c.993G>A
Links:
dbSNP: rs11575996
NCBI 1000 Genomes Browser:
rs11575996
Molecular consequence:
  • NM_000546.6:c.993G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126112.3:c.993G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126113.3:c.993G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126114.3:c.993G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126115.2:c.597G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126116.2:c.597G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126117.2:c.597G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126118.2:c.876G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276695.3:c.876G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276696.3:c.876G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276697.3:c.516G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276698.3:c.516G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276699.3:c.516G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276760.3:c.876G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276761.3:c.876G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Functional consequence:
sequence_variant_affecting_splicing [Sequence Ontology: SO:1000071] - Comment(s)

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000617733GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely pathogenic
(Feb 22, 2021) 		germlineclinical testing

Citation Link,

SCV002822971MutSpliceDB: a database of splice sites variants effects on splicing, NIH
no classification provided
not providedsomaticresearch

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedsomaticnot applicablenot providednot providednot providednot providednot providedresearch

Details of each submission

From GeneDx, SCV000617733.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Alters the last nucleotide of the exon and is predicted to destroy the splice donor site and result in aberrant splicing; Published functional studies revealed expression of only the wild-type allele, suggesting that the variant resulted in an unstable transcript that was degraded (Magnusson 2012); Not observed in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 14678961, 30720243, 24665023, 15347601, 17062677, 18798306, 22653678, 29324801, 31081129)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From MutSpliceDB: a database of splice sites variants effects on splicing, NIH, SCV002822971.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided

Description

Intron inclusion between exons 9 & 10, based on review of RNA-seq in TCGA-MP-A4T9-01A tumor which has TP53 NM_000546.6:c.993G>A variant

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1somaticnot applicablenot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 11, 2024