NM_000546.6(TP53):c.1014C>T (p.Phe338=) AND Li-Fraumeni syndrome 1

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Jul 7, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001127283.8

Allele description [Variation Report for NM_000546.6(TP53):c.1014C>T (p.Phe338=)]

NM_000546.6(TP53):c.1014C>T (p.Phe338=)

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.1014C>T (p.Phe338=)

Other names:

p.F338F:TTC>TTT

HGVS:

NC_000017.11:g.7670695G>A
NG_017013.2:g.21856C>T
NM_000546.6:c.1014C>TMANE SELECT
NM_001126112.3:c.1014C>T
NM_001126113.3:c.*33C>T
NM_001126114.3:c.*121C>T
NM_001126115.2:c.618C>T
NM_001126116.2:c.*121C>T
NM_001126117.2:c.*33C>T
NM_001126118.2:c.897C>T
NM_001276695.3:c.*33C>T
NM_001276696.3:c.*121C>T
NM_001276697.3:c.537C>T
NM_001276698.3:c.*121C>T
NM_001276699.3:c.*33C>T
NM_001276760.3:c.897C>T
NM_001276761.3:c.897C>T
NP_000537.3:p.Phe338=
NP_000537.3:p.Phe338=
NP_001119584.1:p.Phe338=
NP_001119587.1:p.Phe206=
NP_001119590.1:p.Phe299=
NP_001263626.1:p.Phe179=
NP_001263689.1:p.Phe299=
NP_001263690.1:p.Phe299=
LRG_321t1:c.1014C>T
LRG_321t6:c.*121C>T
LRG_321:g.21856C>T
LRG_321p1:p.Phe338=
NC_000017.10:g.7574013G>A
NM_000546.4:c.1014C>T
NM_000546.5:c.1014C>T
NM_001126116.1:c.*121C>T
p.F338F
p.Phe338Phe

Links:

dbSNP: rs150293825

NCBI 1000 Genomes Browser:

rs150293825

Molecular consequence:

NM_001126113.3:c.*33C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001126114.3:c.*121C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001126116.2:c.*121C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001126117.2:c.*33C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276695.3:c.*33C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276696.3:c.*121C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276698.3:c.*121C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276699.3:c.*33C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000546.6:c.1014C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126112.3:c.1014C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126115.2:c.618C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126118.2:c.897C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276697.3:c.537C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276760.3:c.897C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276761.3:c.897C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Li-Fraumeni syndrome 1 (LFS)
Identifiers:: Gene: 553989; MedGen: C1835398; Orphanet: 524; OMIM: 151623

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001286578	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Nov 18, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002582776	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jun 18, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004015639	KCCC/NGS Laboratory, Kuwait Cancer Control Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001286578

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Nov 18, 2019)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV002582776

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jun 18, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004015639

KCCC/NGS Laboratory, Kuwait Cancer Control Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jul 7, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Different mutation profiles associated to P53 accumulation in colorectal cancer.

López I, P Oliveira L, Tucci P, Alvarez-Valín F, A Coudry R, Marín M.

Gene. 2012 May 10;499(1):81-7. doi: 10.1016/j.gene.2012.02.011. Epub 2012 Feb 21.

PubMed [citation]

PMID:: 22373952

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001286578.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV002582776.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004015639.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 17, 2024

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