NM_002230.4(JUP):c.1688G>A (p.Cys563Tyr) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 26, 2022
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:: RCV001912927.6

Allele description [Variation Report for NM_002230.4(JUP):c.1688G>A (p.Cys563Tyr)]

NM_002230.4(JUP):c.1688G>A (p.Cys563Tyr)

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.1688G>A (p.Cys563Tyr)

HGVS:

NC_000017.11:g.41758484C>T
NG_009090.2:g.33229G>A
NM_001352773.2:c.1688G>A
NM_001352774.2:c.1688G>A
NM_001352775.2:c.1688G>A
NM_001352776.2:c.1688G>A
NM_001352777.2:c.1688G>A
NM_002230.4:c.1688G>AMANE SELECT
NM_021991.4:c.1688G>A
NP_001339702.1:p.Cys563Tyr
NP_001339703.1:p.Cys563Tyr
NP_001339704.1:p.Cys563Tyr
NP_001339705.1:p.Cys563Tyr
NP_001339706.1:p.Cys563Tyr
NP_002221.1:p.Cys563Tyr
NP_068831.1:p.Cys563Tyr
LRG_401:g.33229G>A
NC_000017.10:g.39914736C>T

Protein change:

C563Y

Links:

dbSNP: rs142006878

NCBI 1000 Genomes Browser:

rs142006878

Molecular consequence:

NM_001352773.2:c.1688G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352774.2:c.1688G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352775.2:c.1688G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352776.2:c.1688G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001352777.2:c.1688G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002230.4:c.1688G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_021991.4:c.1688G>A - 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

Recent activity

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PREDICTED: Homo sapiens caspase recruitment domain family member 14 (CARD14), tr...
PREDICTED: Homo sapiens caspase recruitment domain family member 14 (CARD14), transcript variant X6, mRNA
gi|2462498938|ref|XM_054333203.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002174637	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 26, 2022)	germline	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

SCV002174637

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 26, 2022)

germline

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

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002174637.3

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1401540). This variant has not been reported in the literature in individuals affected with JUP-related conditions. This variant is present in population databases (rs142006878, gnomAD 0.007%). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 563 of the JUP protein (p.Cys563Tyr).

#	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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