NM_002230.4(JUP):c.1744C>T (p.Arg582Trp) AND multiple conditions

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jun 22, 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:: RCV001324254.8

Allele description [Variation Report for NM_002230.4(JUP):c.1744C>T (p.Arg582Trp)]

NM_002230.4(JUP):c.1744C>T (p.Arg582Trp)

Gene:

JUP:junction plakoglobin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.2

Genomic location:

Preferred name:

NM_002230.4(JUP):c.1744C>T (p.Arg582Trp)

HGVS:

NC_000017.11:g.41758428G>A
NG_009090.2:g.33285C>T
NM_001352773.2:c.1744C>T
NM_001352774.2:c.1744C>T
NM_001352775.2:c.1744C>T
NM_001352776.2:c.1744C>T
NM_001352777.2:c.1744C>T
NM_002230.4:c.1744C>TMANE SELECT
NM_021991.4:c.1744C>T
NP_001339702.1:p.Arg582Trp
NP_001339703.1:p.Arg582Trp
NP_001339704.1:p.Arg582Trp
NP_001339705.1:p.Arg582Trp
NP_001339706.1:p.Arg582Trp
NP_002221.1:p.Arg582Trp
NP_068831.1:p.Arg582Trp
LRG_401:g.33285C>T
NC_000017.10:g.39914680G>A
NM_002230.2:c.1744C>T
NM_021991.2:c.1744C>T

Protein change:

R582W

Links:

dbSNP: rs782205755

NCBI 1000 Genomes Browser:

rs782205755

Molecular consequence:

NM_001352773.2:c.1744C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352774.2:c.1744C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352775.2:c.1744C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352776.2:c.1744C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001352777.2:c.1744C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002230.4:c.1744C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_021991.4:c.1744C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Naxos disease (NXD)
Synonyms:: KERATOSIS PALMOPLANTARIS WITH ARRHYTHMOGENIC CARDIOMYOPATHY; PALMOPLANTAR KERATODERMA WITH ARRHYTHMOGENIC RIGHT VENTRICULAR CARDIOMYOPATHY AND WOOLLY HAIR; WOOLLY HAIR, PALMOPLANTAR KERATODERMA, AND CARDIAC ABNORMALITIES; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011017; MedGen: C1832600; Orphanet: 34217; OMIM: 601214

Name:: Arrhythmogenic right ventricular dysplasia 12
Synonyms:: ARRHYTHMOGENIC RIGHT VENTRICULAR DYSPLASIA, FAMILIAL, 12; Arrhythmogenic right ventricular cardiomyopathy, type 12
Identifiers:: MONDO: MONDO:0012684; MedGen: C1969081; OMIM: 611528

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001515202	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 22, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002786781	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 26, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001515202

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 22, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002786781

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 26, 2021)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001515202.4

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

Description

An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 930073). This variant has not been reported in the literature in individuals affected with JUP-related conditions. This variant is present in population databases (rs782205755, gnomAD 0.003%). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 582 of the JUP protein (p.Arg582Trp).

#	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

From Fulgent Genetics, Fulgent Genetics, SCV002786781.1

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

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

Last Updated: Sep 29, 2024

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