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NM_000546.6(TP53):c.943T>A (p.Ser315Thr)

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Interpretation:
Likely benign​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
5 (Most recent: Jun 18, 2021)
Last evaluated:
Sep 4, 2020
Accession:
VCV000185212.10
Variation ID:
185212
Description:
single nucleotide variant
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NM_000546.6(TP53):c.943T>A (p.Ser315Thr)

Allele ID
185339
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17p13.1
Genomic location
17: 7673585 (GRCh38) GRCh38 UCSC
17: 7576903 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.7576903A>T
NC_000017.11:g.7673585A>T
LRG_321:g.18966T>A
... more HGVS
Protein change
S183T, S276T, S315T, S156T
Other names
-
Canonical SPDI
NC_000017.11:7673584:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA000506
dbSNP: rs762620193
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 reviewed by expert panel Sep 4, 2020 RCV000793553.4
Uncertain significance 1 criteria provided, single submitter Aug 31, 2020 RCV001255575.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jan 17, 2020 RCV000164586.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TP53 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2215 2278

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Sep 04, 2020)
reviewed by expert panel
Method: curation
Li-Fraumeni syndrome
(Autosomal dominant inheritance)
Allele origin: germline
ClinGen TP53 Variant Curation Expert Panel,ClinGen
FDA Recognized Database
Accession: SCV001737918.1
Submitted: (Jun 18, 2021)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
This variant has a BayesDel score < 0.16 and Align GVGD (Zebrafish) is Class C0 or Class C15 (BP4). Additionally, transactivation assays show retained function … (more)
Likely benign
(Jan 17, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000215245.5
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
In silico models in agreement (benign);Other data supporting benign classification
Uncertain significance
(Apr 10, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000908779.2
Submitted: (May 19, 2020)
Evidence details
Uncertain significance
(Aug 31, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001432066.1
Submitted: (Sep 09, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: TP53 c.943T>A (p.Ser315Thr) results in a conservative amino acid change in the encoded protein sequence. Three of four in-silico tools predict a benign … (more)
Uncertain significance
(Oct 07, 2020)
criteria provided, single submitter
Method: clinical testing
Li-Fraumeni syndrome
Allele origin: germline
Invitae
Accession: SCV000932911.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces serine with threonine at codon 315 of the TP53 protein (p.Ser315Thr). The serine residue is moderately conserved and there is a … (more)

Functional evidence

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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 this variant

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Title Author Journal Year Link
Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis. Kato S Proceedings of the National Academy of Sciences of the United States of America 2003 PMID: 12826609
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/5193a588-32d8-40ff-a27b-172881bdd1f0 - - - -

Text-mined citations for rs762620193...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 04, 2021