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NM_002230.4(JUP):c.-42_-27del AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 16, 2018
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:
RCV000599350.1

Allele description [Variation Report for NM_002230.4(JUP):c.-42_-27del]

NM_002230.4(JUP):c.-42_-27del

Genes:
LOC130060847:ATAC-STARR-seq lymphoblastoid silent region 8499 [Gene]
JUP:junction plakoglobin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17q21.2
Genomic location:
Preferred name:
NM_002230.4(JUP):c.-42_-27del
HGVS:
  • NC_000017.11:g.41786615_41786630del
  • NG_009090.2:g.5092_5107del
  • NM_001352773.2:c.-64_-49del
  • NM_001352774.2:c.-39_-24del
  • NM_001352775.2:c.-61_-46del
  • NM_001352776.2:c.-151_-136del
  • NM_002230.4:c.-42_-27delMANE SELECT
  • NM_021991.4:c.-42_-27del
  • LRG_401t2:c.-42_-27del16
  • LRG_401:g.5092_5107del
  • NC_000017.10:g.39942867_39942882del
  • NM_002230.2:c.-42_-27del16
Links:
dbSNP: rs1284180333
NCBI 1000 Genomes Browser:
rs1284180333
Molecular consequence:
  • NM_001352773.2:c.-64_-49del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001352774.2:c.-39_-24del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001352775.2:c.-61_-46del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001352776.2:c.-151_-136del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_002230.4:c.-42_-27del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_021991.4:c.-42_-27del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000710395GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jan 16, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000710395.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

A variant of uncertain significance has been identified in the JUP gene. The c.-42_-27del16 variant has not been published as pathogenic or been reported as benign to our knowledge. This variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). The c.-42_-27del16 variant is located in the 5' untranslated region of the JUP gene and in silico splicing algorithms are inconsistent in their predictions as to whether this variant creates a new splice donor site or results in abnormal gene splicing. Furthermore, no regulatory variants in the JUP gene have been reported in the Human Gene Mutation Database in association with disease (Stenson et al., 2014). In the absence of functional studies, the consequence of the c.-42_-27del16 variant cannot be precisely determined.

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

Last Updated: Oct 14, 2023