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NC_000017.10:g.(?_7120455)_(8151423_?)del AND Li-Fraumeni syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 10, 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:
RCV003111420.2

Allele description

NC_000017.10:g.(?_7120455)_(8151423_?)del

Genes:
  • ATP1B2:ATPase Na+/K+ transporting subunit beta 2 [Gene - OMIM - HGNC]
  • ACAP1:ArfGAP with coiled-coil, ankyrin repeat and PH domains 1 [Gene - OMIM - HGNC]
  • BORCS6:BLOC-1 related complex subunit 6 [Gene - OMIM - HGNC]
  • CD68:CD68 molecule [Gene - OMIM - HGNC]
  • CTC1:CST telomere replication complex component 1 [Gene - OMIM - HGNC]
  • CTDNEP1:CTD nuclear envelope phosphatase 1 [Gene - OMIM - HGNC]
  • FXR2:FMR1 autosomal homolog 2 [Gene - OMIM - HGNC]
  • GPS2:G protein pathway suppressor 2 [Gene - OMIM - HGNC]
  • GABARAP:GABA type A receptor-associated protein [Gene - OMIM - HGNC]
  • NAA38:N-alpha-acetyltransferase 38, NatC auxiliary subunit [Gene - OMIM - HGNC]
  • PHF23:PHD finger protein 23 [Gene - OMIM - HGNC]
  • POLR2A:RNA polymerase II subunit A [Gene - OMIM - HGNC]
  • SPEM2:SPEM family member 2 [Gene - HGNC]
  • SOX15:SRY-box transcription factor 15 [Gene - OMIM - HGNC]
  • SENP3:SUMO specific peptidase 3 [Gene - OMIM - HGNC]
  • TNFSF12:TNF superfamily member 12 [Gene - OMIM - HGNC]
  • TNFSF13:TNF superfamily member 13 [Gene - OMIM - HGNC]
  • TNFSF12-TNFSF13:TNFSF12-TNFSF13 readthrough [Gene - HGNC]
  • WRAP53:WD repeat containing antisense to TP53 [Gene - OMIM - HGNC]
  • YBX2:Y-box binding protein 2 [Gene - OMIM - HGNC]
  • ACADVL:acyl-CoA dehydrogenase very long chain [Gene - OMIM - HGNC]
  • ALOX12B:arachidonate 12-lipoxygenase, 12R type [Gene - OMIM - HGNC]
  • ALOX15B:arachidonate 15-lipoxygenase type B [Gene - OMIM - HGNC]
  • ALOXE3:arachidonate lipoxygenase 3 [Gene - OMIM - HGNC]
  • AURKB:aurora kinase B [Gene - OMIM - HGNC]
  • CNTROB:centrobin, centriole duplication and spindle assembly protein [Gene - OMIM - HGNC]
  • CHRNB1:cholinergic receptor nicotinic beta 1 subunit [Gene - OMIM - HGNC]
  • CHD3:chromodomain helicase DNA binding protein 3 [Gene - OMIM - HGNC]
  • CLDN7:claudin 7 [Gene - OMIM - HGNC]
  • CYB5D1:cytochrome b5 domain containing 1 [Gene - HGNC]
  • DLG4:discs large MAGUK scaffold protein 4 [Gene - OMIM - HGNC]
  • DVL2:dishevelled segment polarity protein 2 [Gene - OMIM - HGNC]
  • DNAH2:dynein axonemal heavy chain 2 [Gene - OMIM - HGNC]
  • ELP5:elongator acetyltransferase complex subunit 5 [Gene - OMIM - HGNC]
  • EFNB3:ephrin B3 [Gene - OMIM - HGNC]
  • EIF4A1:eukaryotic translation initiation factor 4A1 [Gene - OMIM - HGNC]
  • EIF5A:eukaryotic translation initiation factor 5A [Gene - OMIM - HGNC]
  • FGF11:fibroblast growth factor 11 [Gene - OMIM - HGNC]
  • GUCY2D:guanylate cyclase 2D, retinal [Gene - OMIM - HGNC]
  • HES7:hes family bHLH transcription factor 7 [Gene - OMIM - HGNC]
  • KDM6B:lysine demethylase 6B [Gene - OMIM - HGNC]
  • MPDU1:mannose-P-dolichol utilization defect 1 [Gene - OMIM - HGNC]
  • NEURL4:neuralized E3 ubiquitin protein ligase 4 [Gene - OMIM - HGNC]
  • NLGN2:neuroligin 2 [Gene - OMIM - HGNC]
  • PER1:period circadian regulator 1 [Gene - OMIM - HGNC]
  • PLSCR3:phospholipid scramblase 3 [Gene - OMIM - HGNC]
  • KCTD11:potassium channel tetramerization domain containing 11 [Gene - OMIM - HGNC]
  • KCNAB3:potassium voltage-gated channel subfamily A regulatory beta subunit 3 [Gene - OMIM - HGNC]
  • SHBG:sex hormone binding globulin [Gene - OMIM - HGNC]
  • SLC2A4:solute carrier family 2 member 4 [Gene - OMIM - HGNC]
  • SLC35G6:solute carrier family 35 member G6 [Gene - HGNC]
  • SPEM1:spermatid maturation 1 [Gene - OMIM - HGNC]
  • SAT2:spermidine/spermine N1-acetyltransferase family member 2 [Gene - OMIM - HGNC]
  • TRR-TCT2-1:tRNA-Arg (anticodon TCT) 2-1 [Gene - OMIM - HGNC]
  • TRQ-CTG1-5:tRNA-Gln (anticodon CTG) 1-5 [Gene - OMIM - HGNC]
  • TRG-GCC2-6:tRNA-Gly (anticodon GCC) 2-6 [Gene - OMIM - HGNC]
  • TRL-TAG1-1:tRNA-Leu (anticodon TAG) 1-1 [Gene - OMIM - HGNC]
  • TRK-TTT3-5:tRNA-Lys (anticodon TTT) 3-5 [Gene - OMIM - HGNC]
  • TRAPPC1:trafficking protein particle complex subunit 1 [Gene - OMIM - HGNC]
  • TMEM102:transmembrane protein 102 [Gene - OMIM - HGNC]
  • TMEM107:transmembrane protein 107 [Gene - OMIM - HGNC]
  • TMEM256:transmembrane protein 256 [Gene - OMIM - HGNC]
  • TMEM88:transmembrane protein 88 [Gene - OMIM - HGNC]
  • TMEM95:transmembrane protein 95 [Gene - OMIM - HGNC]
  • TP53:tumor protein p53 [Gene - OMIM - HGNC]
  • TNK1:tyrosine kinase non receptor 1 [Gene - OMIM - HGNC]
  • VAMP2:vesicle associated membrane protein 2 [Gene - OMIM - HGNC]
  • ZBTB4:zinc finger and BTB domain containing 4 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17p13.1
Genomic location:
Chr17: 7120455 - 8151423 (on Assembly GRCh37)
Preferred name:
NC_000017.10:g.(?_7120455)_(8151423_?)del
HGVS:
NC_000017.10:g.(?_7120455)_(8151423_?)del

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003794236Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Apr 10, 2021) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

TP53 germline mutation testing in 180 families suspected of Li-Fraumeni syndrome: mutation detection rate and relative frequency of cancers in different familial phenotypes.

Ruijs MW, Verhoef S, Rookus MA, Pruntel R, van der Hout AH, Hogervorst FB, Kluijt I, Sijmons RH, Aalfs CM, Wagner A, Ausems MG, Hoogerbrugge N, van Asperen CJ, Gomez Garcia EB, Meijers-Heijboer H, Ten Kate LP, Menko FH, van 't Veer LJ.

J Med Genet. 2010 Jun;47(6):421-8. doi: 10.1136/jmg.2009.073429.

PubMed [citation]
PMID:
20522432

Drastic effect of germline TP53 missense mutations in Li-Fraumeni patients.

Zerdoumi Y, Aury-Landas J, Bonaïti-Pellié C, Derambure C, Sesboüé R, Renaux-Petel M, Frebourg T, Bougeard G, Flaman JM.

Hum Mutat. 2013 Mar;34(3):453-61. doi: 10.1002/humu.22254. Epub 2013 Feb 11.

PubMed [citation]
PMID:
23172776
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV003794236.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the TP53 gene has been identified. Loss-of-function variants in TP53 are known to be pathogenic (PMID: 20522432). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. Similar deletions encompassing the full coding sequence of the TP53 gene have been reported in the literature in affected individuals (PMID: 20522432, 23172776, 26681312). Additionally, a study evaluating eight probands with deletion events involving the TP53 gene suggests that full-length deletions of the entire TP53 gene have a milder cancer-predisposition phenotype than partial deletions of TP53 (PMID: 21056402). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Jul 29, 2023