NM_002230.4(JUP):c.469-16del AND not specified

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Sep 26, 2023
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:: RCV000485526.2

Allele description [Variation Report for NM_002230.4(JUP):c.469-16del]

NM_002230.4(JUP):c.469-16del

Gene:

JUP:junction plakoglobin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q21.2

Genomic location:

Preferred name:

NM_002230.4(JUP):c.469-16del

HGVS:

NC_000017.11:g.41769223del
NG_009090.2:g.22490del
NM_001352773.2:c.469-16del
NM_001352774.2:c.469-16del
NM_001352775.2:c.469-16del
NM_001352776.2:c.469-16del
NM_001352777.2:c.469-16del
NM_002230.4:c.469-16delMANE SELECT
NM_021991.2:c.469-16delT
NM_021991.4:c.469-16del
LRG_401t1:c.469-16del
LRG_401t2:c.469-16del
LRG_401:g.22490del
NC_000017.10:g.39925475del
NM_002230.2:c.469-16delT

Links:

dbSNP: rs782421393

NCBI 1000 Genomes Browser:

rs782421393

Molecular consequence:

NM_001352773.2:c.469-16del - intron variant - [Sequence Ontology: SO:0001627]
NM_001352774.2:c.469-16del - intron variant - [Sequence Ontology: SO:0001627]
NM_001352775.2:c.469-16del - intron variant - [Sequence Ontology: SO:0001627]
NM_001352776.2:c.469-16del - intron variant - [Sequence Ontology: SO:0001627]
NM_001352777.2:c.469-16del - intron variant - [Sequence Ontology: SO:0001627]
NM_002230.4:c.469-16del - intron variant - [Sequence Ontology: SO:0001627]
NM_021991.4:c.469-16del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000568961	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely benign (Apr 25, 2017)	germline	clinical testing	Citation Link,
SCV004100179	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Sep 26, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000568961

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely benign
(Apr 25, 2017)

germline

clinical testing

Citation Link,

SCV004100179

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(Sep 26, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000568961.4

#	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 likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004100179.1

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

Description

Variant summary: JUP c.469-16delT alters a non-conserved nucleotide located at a position not widely known to affect splicing. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 2.1e-05 in 237266 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.469-16delT in individuals affected with Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

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

Last Updated: Sep 29, 2024

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