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NC_000009.11:g.(?_71627953)_(72006720_?)del AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 7, 2023
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:
RCV004582096.2

Allele description [Variation Report for NC_000009.11:g.(?_71627953)_(72006720_?)del]

NC_000009.11:g.(?_71627953)_(72006720_?)del

Genes:
BANCR:BRAF-activated non-protein coding RNA [Gene - OMIM - HGNC]
ENTREP1:endosomal transmembrane epsin interactor 1 [Gene - OMIM - HGNC]
FXN:frataxin [Gene - OMIM - HGNC]
PRKACG:protein kinase cAMP-activated catalytic subunit gamma [Gene - OMIM - HGNC]
TJP2:tight junction protein 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q21.11
Genomic location:
Chr9: 71627953 - 72006720 (on Assembly GRCh37)
Preferred name:
NC_000009.11:g.(?_71627953)_(72006720_?)del
HGVS:
NC_000009.11:g.(?_71627953)_(72006720_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005062697Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 7, 2023) 		unknownclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Mutations in TJP2 cause progressive cholestatic liver disease.

Sambrotta M, Strautnieks S, Papouli E, Rushton P, Clark BE, Parry DA, Logan CV, Newbury LJ, Kamath BM, Ling S, Grammatikopoulos T, Wagner BE, Magee JC, Sokol RJ, Mieli-Vergani G; University of Washington Center for Mendelian Genomics, Smith JD, Johnson CA, McClean P, Simpson MA, Knisely AS, Bull LN, et al.

Nat Genet. 2014 Apr;46(4):326-8. doi: 10.1038/ng.2918. Epub 2014 Mar 9.

PubMed [citation]
PMID:
24614073
PMCID:
PMC4061468

Hepatocellular carcinoma associated with tight-junction protein 2 deficiency.

Zhou S, Hertel PM, Finegold MJ, Wang L, Kerkar N, Wang J, Wong LJ, Plon SE, Sambrotta M, Foskett P, Niu Z, Thompson RJ, Knisely AS.

Hepatology. 2015 Dec;62(6):1914-6. doi: 10.1002/hep.27872. Epub 2015 Jun 19. No abstract available.

PubMed [citation]
PMID:
25921221
PMCID:
PMC4626433
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005062697.1

#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 TJP2 gene has been identified. Loss-of-function variants in TJP2 are known to be pathogenic (PMID: 24614073, 25921221, 28039895). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with TJP2-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024