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NC_000017.11:g.(?_7669599)_(8382320_?)del AND Li-Fraumeni syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 22, 2020
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:
RCV000803922.6

Allele description [Variation Report for NC_000017.11:g.(?_7669599)_(8382320_?)del]

NC_000017.11:g.(?_7669599)_(8382320_?)del

Genes:
  • LOC130060172:ATAC-STARR-seq lymphoblastoid active region 11641 [Gene]
  • LOC130060173:ATAC-STARR-seq lymphoblastoid active region 11643 [Gene]
  • LOC130060179:ATAC-STARR-seq lymphoblastoid active region 11645 [Gene]
  • LOC130060182:ATAC-STARR-seq lymphoblastoid active region 11646 [Gene]
  • LOC130060185:ATAC-STARR-seq lymphoblastoid active region 11647 [Gene]
  • LOC130060186:ATAC-STARR-seq lymphoblastoid active region 11650 [Gene]
  • LOC130060188:ATAC-STARR-seq lymphoblastoid active region 11653 [Gene]
  • LOC130060191:ATAC-STARR-seq lymphoblastoid active region 11654 [Gene]
  • LOC130060192:ATAC-STARR-seq lymphoblastoid active region 11655 [Gene]
  • LOC130060193:ATAC-STARR-seq lymphoblastoid active region 11656 [Gene]
  • LOC130060194:ATAC-STARR-seq lymphoblastoid active region 11657 [Gene]
  • LOC130060196:ATAC-STARR-seq lymphoblastoid active region 11660 [Gene]
  • LOC130060199:ATAC-STARR-seq lymphoblastoid active region 11663 [Gene]
  • LOC130060207:ATAC-STARR-seq lymphoblastoid active region 11665 [Gene]
  • LOC130060211:ATAC-STARR-seq lymphoblastoid active region 11666 [Gene]
  • LOC130060214:ATAC-STARR-seq lymphoblastoid active region 11668 [Gene]
  • LOC130060215:ATAC-STARR-seq lymphoblastoid active region 11669 [Gene]
  • LOC130060217:ATAC-STARR-seq lymphoblastoid active region 11670 [Gene]
  • LOC130060222:ATAC-STARR-seq lymphoblastoid active region 11671 [Gene]
  • LOC130060223:ATAC-STARR-seq lymphoblastoid active region 11672 [Gene]
  • LOC130060224:ATAC-STARR-seq lymphoblastoid active region 11673 [Gene]
  • LOC130060225:ATAC-STARR-seq lymphoblastoid active region 11674 [Gene]
  • LOC130060227:ATAC-STARR-seq lymphoblastoid active region 11679 [Gene]
  • LOC130060230:ATAC-STARR-seq lymphoblastoid active region 11680 [Gene]
  • LOC130060231:ATAC-STARR-seq lymphoblastoid active region 11682 [Gene]
  • LOC130060232:ATAC-STARR-seq lymphoblastoid active region 11683 [Gene]
  • LOC130060233:ATAC-STARR-seq lymphoblastoid active region 11686 [Gene]
  • LOC130060235:ATAC-STARR-seq lymphoblastoid active region 11687 [Gene]
  • LOC130060237:ATAC-STARR-seq lymphoblastoid active region 11690 [Gene]
  • LOC130060239:ATAC-STARR-seq lymphoblastoid active region 11691 [Gene]
  • LOC130060240:ATAC-STARR-seq lymphoblastoid active region 11692 [Gene]
  • LOC130060241:ATAC-STARR-seq lymphoblastoid active region 11693 [Gene]
  • LOC130060243:ATAC-STARR-seq lymphoblastoid active region 11694 [Gene]
  • LOC130060244:ATAC-STARR-seq lymphoblastoid active region 11695 [Gene]
  • LOC130060245:ATAC-STARR-seq lymphoblastoid active region 11696 [Gene]
  • LOC130060246:ATAC-STARR-seq lymphoblastoid active region 11697 [Gene]
  • LOC130060171:ATAC-STARR-seq lymphoblastoid silent region 8136 [Gene]
  • LOC130060174:ATAC-STARR-seq lymphoblastoid silent region 8137 [Gene]
  • LOC130060175:ATAC-STARR-seq lymphoblastoid silent region 8138 [Gene]
  • LOC130060176:ATAC-STARR-seq lymphoblastoid silent region 8139 [Gene]
  • LOC130060177:ATAC-STARR-seq lymphoblastoid silent region 8140 [Gene]
  • LOC130060178:ATAC-STARR-seq lymphoblastoid silent region 8141 [Gene]
  • LOC130060180:ATAC-STARR-seq lymphoblastoid silent region 8142 [Gene]
  • LOC130060181:ATAC-STARR-seq lymphoblastoid silent region 8143 [Gene]
  • LOC130060183:ATAC-STARR-seq lymphoblastoid silent region 8144 [Gene]
  • LOC130060184:ATAC-STARR-seq lymphoblastoid silent region 8145 [Gene]
  • LOC130060187:ATAC-STARR-seq lymphoblastoid silent region 8146 [Gene]
  • LOC130060189:ATAC-STARR-seq lymphoblastoid silent region 8147 [Gene]
  • LOC130060190:ATAC-STARR-seq lymphoblastoid silent region 8148 [Gene]
  • LOC130060195:ATAC-STARR-seq lymphoblastoid silent region 8149 [Gene]
  • LOC130060197:ATAC-STARR-seq lymphoblastoid silent region 8150 [Gene]
  • LOC130060198:ATAC-STARR-seq lymphoblastoid silent region 8151 [Gene]
  • LOC130060200:ATAC-STARR-seq lymphoblastoid silent region 8152 [Gene]
  • LOC130060201:ATAC-STARR-seq lymphoblastoid silent region 8153 [Gene]
  • LOC130060202:ATAC-STARR-seq lymphoblastoid silent region 8154 [Gene]
  • LOC130060203:ATAC-STARR-seq lymphoblastoid silent region 8155 [Gene]
  • LOC130060204:ATAC-STARR-seq lymphoblastoid silent region 8156 [Gene]
  • LOC130060205:ATAC-STARR-seq lymphoblastoid silent region 8157 [Gene]
  • LOC130060206:ATAC-STARR-seq lymphoblastoid silent region 8159 [Gene]
  • LOC130060208:ATAC-STARR-seq lymphoblastoid silent region 8160 [Gene]
  • LOC130060209:ATAC-STARR-seq lymphoblastoid silent region 8161 [Gene]
  • LOC130060210:ATAC-STARR-seq lymphoblastoid silent region 8162 [Gene]
  • LOC130060212:ATAC-STARR-seq lymphoblastoid silent region 8163 [Gene]
  • LOC130060213:ATAC-STARR-seq lymphoblastoid silent region 8164 [Gene]
  • LOC130060216:ATAC-STARR-seq lymphoblastoid silent region 8165 [Gene]
  • LOC130060218:ATAC-STARR-seq lymphoblastoid silent region 8166 [Gene]
  • LOC130060219:ATAC-STARR-seq lymphoblastoid silent region 8167 [Gene]
  • LOC130060220:ATAC-STARR-seq lymphoblastoid silent region 8168 [Gene]
  • LOC130060221:ATAC-STARR-seq lymphoblastoid silent region 8169 [Gene]
  • LOC130060226:ATAC-STARR-seq lymphoblastoid silent region 8170 [Gene]
  • LOC130060228:ATAC-STARR-seq lymphoblastoid silent region 8171 [Gene]
  • LOC130060229:ATAC-STARR-seq lymphoblastoid silent region 8172 [Gene]
  • LOC130060234:ATAC-STARR-seq lymphoblastoid silent region 8176 [Gene]
  • LOC130060236:ATAC-STARR-seq lymphoblastoid silent region 8177 [Gene]
  • LOC130060238:ATAC-STARR-seq lymphoblastoid silent region 8178 [Gene]
  • LOC130060242:ATAC-STARR-seq lymphoblastoid silent region 8179 [Gene]
  • BORCS6:BLOC-1 related complex subunit 6 [Gene - OMIM - HGNC]
  • LOC126862483:BRD4-independent group 4 enhancer GRCh37_chr17:7589699-7590898 [Gene]
  • LOC126862484:CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:7797066-7798265 [Gene]
  • LOC126862485:CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:8020998-8022197 [Gene]
  • LOC116276454:CRISPRi-validated cis-regulatory element chr17.641 [Gene]
  • CTC1:CST telomere replication complex component 1 [Gene - OMIM - HGNC]
  • KRBA2:KRAB-A domain containing 2 [Gene - OMIM - HGNC]
  • LOC129390832:MPRA-validated peak2715 silencer [Gene]
  • NAA38:N-alpha-acetyltransferase 38, NatC auxiliary subunit [Gene - OMIM - HGNC]
  • RANGRF:RAN guanine nucleotide release factor [Gene - OMIM - HGNC]
  • ARHGEF15:Rho guanine nucleotide exchange factor 15 [Gene - OMIM - HGNC]
  • LOC121587574:Sharpr-MPRA regulatory region 3930 [Gene]
  • LOC112533665:Sharpr-MPRA regulatory region 4002 [Gene]
  • LOC121587575:Sharpr-MPRA regulatory region 8148 [Gene]
  • WRAP53:WD repeat containing antisense to TP53 [Gene - OMIM - HGNC]
  • ALOX12B:arachidonate 12-lipoxygenase, 12R type [Gene - OMIM - HGNC]
  • ALOX15B:arachidonate 15-lipoxygenase type B [Gene - OMIM - HGNC]
  • ALOXE3:arachidonate epidermal lipoxygenase 3 [Gene - OMIM - HGNC]
  • AURKB:aurora kinase B [Gene - OMIM - HGNC]
  • CNTROB:centrobin, centriole duplication and spindle assembly protein [Gene - OMIM - HGNC]
  • CHD3:chromodomain helicase DNA binding protein 3 [Gene - OMIM - HGNC]
  • CYB5D1:cytochrome b5 domain containing 1 [Gene - HGNC]
  • DNAH2:dynein axonemal heavy chain 2 [Gene - OMIM - HGNC]
  • EFNB3:ephrin B3 [Gene - OMIM - HGNC]
  • GUCY2D:guanylate cyclase 2D, retinal [Gene - OMIM - HGNC]
  • HES7:hes family bHLH transcription factor 7 [Gene - OMIM - HGNC]
  • LINC00324:long intergenic non-protein coding RNA 324 [Gene - HGNC]
  • KDM6B:lysine demethylase 6B [Gene - OMIM - HGNC]
  • MIR4314:microRNA 4314 [Gene - HGNC]
  • MIR4521:microRNA 4521 [Gene - HGNC]
  • MIR6883:microRNA 6883 [Gene - HGNC]
  • LOC106794092:nonconserved acetylation island sequence 72 enhancer [Gene]
  • ODF4:outer dense fiber of sperm tails 4 [Gene - OMIM - HGNC]
  • PER1:period circadian regulator 1 [Gene - OMIM - HGNC]
  • PFAS:phosphoribosylformylglycinamidine synthase [Gene - OMIM - HGNC]
  • KCNAB3:potassium voltage-gated channel subfamily A regulatory beta subunit 3 [Gene - OMIM - HGNC]
  • RPL26:ribosomal protein L26 [Gene - OMIM - HGNC]
  • RNF227:ring finger protein 227 [Gene - HGNC]
  • SCARNA21:small Cajal body-specific RNA 21 [Gene - HGNC]
  • SNORD118:small nucleolar RNA, C/D box 118 [Gene - OMIM - HGNC]
  • SLC25A35:solute carrier family 25 member 35 [Gene - OMIM - HGNC]
  • TRR-TCT2-1:tRNA-Arg (anticodon TCT) 2-1 [Gene - OMIM - HGNC]
  • TRD-GTC2-11:tRNA-Asp (anticodon GTC) 2-11 [Gene - 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]
  • TRG-TCC3-1:tRNA-Gly (anticodon TCC) 3-1 [Gene - HGNC]
  • TRI-AAT4-1:tRNA-Ile (anticodon AAT) 4-1 [Gene - HGNC]
  • TRI-AAT5-5:tRNA-Ile (anticodon AAT) 5-5 [Gene - 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]
  • TRP-CGG1-3:tRNA-Pro (anticodon CGG) 1-3 [Gene - HGNC]
  • TRS-AGA2-6:tRNA-Ser (anticodon AGA) 2-6 [Gene - HGNC]
  • TRS-CGA1-1:tRNA-Ser (anticodon CGA) 1-1 [Gene - HGNC]
  • TRS-GCT4-3:tRNA-Ser (anticodon GCT) 4-3 [Gene - HGNC]
  • TRT-AGT1-1:tRNA-Thr (anticodon AGT) 1-1 [Gene - HGNC]
  • TRT-AGT1-2:tRNA-Thr (anticodon AGT) 1-2 [Gene - HGNC]
  • TRT-AGT5-1:tRNA-Thr (anticodon AGT) 5-1 [Gene - HGNC]
  • TRW-CCA1-1:tRNA-Trp (anticodon CCA) 1-1 [Gene - HGNC]
  • TRW-CCA3-3:tRNA-Trp (anticodon CCA) 3-3 [Gene - HGNC]
  • TRAPPC1:trafficking protein particle complex subunit 1 [Gene - OMIM - HGNC]
  • LOC124904106:translation initiation factor IF-2 [Gene]
  • TMEM107:transmembrane protein 107 [Gene - OMIM - HGNC]
  • TMEM88:transmembrane protein 88 [Gene - OMIM - HGNC]
  • TP53:tumor protein p53 [Gene - OMIM - HGNC]
  • LOC100128288:uncharacterized LOC100128288 [Gene]
  • LOC105371520:uncharacterized LOC105371520 [Gene]
  • VAMP2:vesicle associated membrane protein 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17p13.1
Genomic location:
Preferred name:
NC_000017.11:g.(?_7669599)_(8382320_?)del
HGVS:
  • NC_000017.11:g.(?_7669599)_(8382320_?)del
  • NC_000017.10:g.(?_7572917)_(8285638_?)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
SCV000943810Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 22, 2020) 		germlineclinical testing

PubMed (4)
[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

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

A common molecular mechanism underlies two phenotypically distinct 17p13.1 microdeletion syndromes.

Shlien A, Baskin B, Achatz MI, Stavropoulos DJ, Nichols KE, Hudgins L, Morel CF, Adam MP, Zhukova N, Rotin L, Novokmet A, Druker H, Shago M, Ray PN, Hainaut P, Malkin D.

Am J Hum Genet. 2010 Nov 12;87(5):631-42. doi: 10.1016/j.ajhg.2010.10.007.

PubMed [citation]
PMID:
21056402
PMCID:
PMC2978979
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000943810.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the TP53 gene has been identified. The boundaries of this event are unknown as the deletion extends 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). Loss-of-function variants in TP53 are known to be pathogenic (PMID: 20522432). 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: Nov 10, 2024