NM_000546.6(TP53):c.785del (p.Gly262fs) AND Li-Fraumeni syndrome 1

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Feb 20, 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:: RCV002288928.3

Allele description [Variation Report for NM_000546.6(TP53):c.785del (p.Gly262fs)]

NM_000546.6(TP53):c.785del (p.Gly262fs)

Gene:

TP53:tumor protein p53 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.785del (p.Gly262fs)

HGVS:

NC_000017.11:g.7673836del
NG_017013.2:g.18716del
NM_000546.6:c.785delMANE SELECT
NM_001126112.3:c.785del
NM_001126113.3:c.785del
NM_001126114.3:c.785del
NM_001126115.2:c.389del
NM_001126116.2:c.389del
NM_001126117.2:c.389del
NM_001126118.2:c.668del
NM_001276695.3:c.668del
NM_001276696.3:c.668del
NM_001276697.3:c.308del
NM_001276698.3:c.308del
NM_001276699.3:c.308del
NM_001276760.3:c.668del
NM_001276761.3:c.668del
NP_000537.3:p.Gly262fs
NP_001119584.1:p.Gly262fs
NP_001119585.1:p.Gly262fs
NP_001119586.1:p.Gly262fs
NP_001119587.1:p.Gly130fs
NP_001119588.1:p.Gly130fs
NP_001119589.1:p.Gly130fs
NP_001119590.1:p.Gly223fs
NP_001263624.1:p.Gly223fs
NP_001263625.1:p.Gly223fs
NP_001263626.1:p.Gly103fs
NP_001263627.1:p.Gly103fs
NP_001263628.1:p.Gly103fs
NP_001263689.1:p.Gly223fs
NP_001263690.1:p.Gly223fs
LRG_321:g.18716del
NC_000017.10:g.7577153del
NC_000017.10:g.7577154del
NM_000546.4:c.785delG

Protein change:

G103fs

Links:

dbSNP: rs879253905

NCBI 1000 Genomes Browser:

rs879253905

Molecular consequence:

NM_000546.6:c.785del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126112.3:c.785del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126113.3:c.785del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126114.3:c.785del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126115.2:c.389del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126116.2:c.389del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126117.2:c.389del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126118.2:c.668del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276695.3:c.668del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276696.3:c.668del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276697.3:c.308del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276698.3:c.308del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276699.3:c.308del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276760.3:c.668del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276761.3:c.668del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

Recent activity

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SDR family NAD(P)-dependent oxidoreductase [Hydrogenovibrio kuenenii]
SDR family NAD(P)-dependent oxidoreductase [Hydrogenovibrio kuenenii]
gi|640286357|ref|WP_024851727.1|

Protein
uncharacterized protein LOC108167848 isoform X1 [Mus musculus]
uncharacterized protein LOC108167848 isoform X1 [Mus musculus]
gi|1907079570|ref|XP_036012115.1|

Protein
PREDICTED: Oncorhynchus keta ALG9 alpha-1,2-mannosyltransferase (alg9), transcri...
PREDICTED: Oncorhynchus keta ALG9 alpha-1,2-mannosyltransferase (alg9), transcript variant X1, mRNA
gi|2401176639|ref|XM_052529169.1|

Nucleotide
Caprichthys gymnura cytochrome b (Cytb) gene, partial cds; mitochondrial
Caprichthys gymnura cytochrome b (Cytb) gene, partial cds; mitochondrial
gi|408542563|gb|JQ861152.1|

Nucleotide
Brasilonema bromeliae SPC951 NODE_1218_length_24868_cov_4.962439, whole genome s...
Brasilonema bromeliae SPC951 NODE_1218_length_24868_cov_4.962439, whole genome shotgun sequence
gi|1836798741|ref|NZ_QMEB01000067.1 |WGS:NZ_QMEB01|NODE_1218_length_24868_cov_4.962439

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002583122	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 18, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004932813	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Feb 20, 2024)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002583122

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 18, 2022)

germline

clinical testing

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

SCV004932813

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Pathogenic
(Feb 20, 2024)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	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

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 Genome-Nilou Lab, SCV002583122.1

#	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 Myriad Genetics, Inc., SCV004932813.1

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

Description

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.

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

Last Updated: Sep 29, 2024

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