NM_000546.6(TP53):c.666G>T (p.Pro222=) AND Li-Fraumeni syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 31, 2024
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:: RCV001085434.10

Allele description [Variation Report for NM_000546.6(TP53):c.666G>T (p.Pro222=)]

NM_000546.6(TP53):c.666G>T (p.Pro222=)

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.666G>T (p.Pro222=)

HGVS:

NC_000017.11:g.7674865C>A
NG_017013.2:g.17686G>T
NM_000546.6:c.666G>TMANE SELECT
NM_001126112.3:c.666G>T
NM_001126113.3:c.666G>T
NM_001126114.3:c.666G>T
NM_001126115.2:c.270G>T
NM_001126116.2:c.270G>T
NM_001126117.2:c.270G>T
NM_001126118.2:c.549G>T
NM_001276695.3:c.549G>T
NM_001276696.3:c.549G>T
NM_001276697.3:c.189G>T
NM_001276698.3:c.189G>T
NM_001276699.3:c.189G>T
NM_001276760.3:c.549G>T
NM_001276761.3:c.549G>T
NP_000537.3:p.Pro222=
NP_000537.3:p.Pro222=
NP_001119584.1:p.Pro222=
NP_001119585.1:p.Pro222=
NP_001119586.1:p.Pro222=
NP_001119587.1:p.Pro90=
NP_001119588.1:p.Pro90=
NP_001119589.1:p.Pro90=
NP_001119590.1:p.Pro183=
NP_001263624.1:p.Pro183=
NP_001263625.1:p.Pro183=
NP_001263626.1:p.Pro63=
NP_001263627.1:p.Pro63=
NP_001263628.1:p.Pro63=
NP_001263689.1:p.Pro183=
NP_001263690.1:p.Pro183=
LRG_321t1:c.666G>T
LRG_321:g.17686G>T
LRG_321p1:p.Pro222=
NC_000017.10:g.7578183C>A
NM_000546.4:c.666G>T
NM_000546.5:c.666G>T
p.P222P

Links:

dbSNP: rs72661118

NCBI 1000 Genomes Browser:

rs72661118

Molecular consequence:

NM_000546.6:c.666G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126112.3:c.666G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126113.3:c.666G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126114.3:c.666G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126115.2:c.270G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126116.2:c.270G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126117.2:c.270G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126118.2:c.549G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276695.3:c.549G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276696.3:c.549G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276697.3:c.189G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276698.3:c.189G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276699.3:c.189G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276760.3:c.549G>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276761.3:c.549G>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Name:: Li-Fraumeni syndrome (LFS)
Synonyms:: Sarcoma family syndrome of Li and Fraumeni
Identifiers:: MONDO: MONDO:0018875; MedGen: C0085390; OMIM: PS151623

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Cited in PMC for PubMed (Select 26236653) (5)
PMC
"[76981-88-9]"[CompleteSynonym] (1)
PubChem Compound
Med4 mediator complex subunit 4 [Rattus norvegicus]
Med4 mediator complex subunit 4 [Rattus norvegicus]
Gene ID:306030

Gene
Salmonella enterica subsp. enterica serovar Newport strain R9_3240_R1 NODE_65_le...
Salmonella enterica subsp. enterica serovar Newport strain R9_3240_R1 NODE_65_length_2618_cov_0.243351_ID_141, whole genome shotgun sequence
gi|1132773416|gb|MOCX01000074.1||gn :MOCX01|NODE_65_length_2618_cov_0.243351_ID_141

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000253314	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004823773	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Oct 2, 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

SCV000253314

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 31, 2024)

germline

clinical testing

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

SCV004823773

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely Benign
(Oct 2, 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	unknown	8	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

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 Invitae, SCV000253314.11

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From All of Us Research Program, National Institutes of Health, SCV004823773.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	8	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	unknown	108544	not provided	not provided		8	not provided	not provided	not provided

Last Updated: Jun 29, 2024

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