NM_004100.5(EYA4):c.1750T>C (p.Cys584Arg) AND Dilated cardiomyopathy 1J

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 9, 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:: RCV003616306.2

Allele description [Variation Report for NM_004100.5(EYA4):c.1750T>C (p.Cys584Arg)]

NM_004100.5(EYA4):c.1750T>C (p.Cys584Arg)

Genes:

EYA4:EYA transcriptional coactivator and phosphatase 4 [Gene - OMIM - HGNC]
TARID:TCF21 antisense RNA inducing promoter demethylation [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q23.2

Genomic location:

Preferred name:

NM_004100.5(EYA4):c.1750T>C (p.Cys584Arg)

HGVS:

NC_000006.12:g.133525165T>C
NG_011596.2:g.288809T>C
NM_001301012.2:c.1677+50T>C
NM_001301013.2:c.1768T>C
NM_001370458.1:c.1770+50T>C
NM_001370459.1:c.1606T>C
NM_004100.5:c.1750T>CMANE SELECT
NM_172103.4:c.1681T>C
NM_172105.4:c.1839+50T>C
NP_001287942.1:p.Cys590Arg
NP_001357388.1:p.Cys536Arg
NP_004091.3:p.Cys584Arg
NP_742101.2:p.Cys561Arg
LRG_418t1:c.1750T>C
LRG_418:g.288809T>C
LRG_418p1:p.Cys584Arg
NC_000006.11:g.133846303T>C

Protein change:

C536R

Molecular consequence:

NM_001301012.2:c.1677+50T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001370458.1:c.1770+50T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_172105.4:c.1839+50T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001301013.2:c.1768T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370459.1:c.1606T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004100.5:c.1750T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_172103.4:c.1681T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Dilated cardiomyopathy 1J (CMD1J)
Synonyms:: CARDIOMYOPATHY, DILATED, WITH SENSORINEURAL HEARING LOSS, AUTOSOMAL DOMINANT
Identifiers:: MONDO: MONDO:0011541; MedGen: C1854368; Orphanet: 217622; OMIM: 605362

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004411884	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 9, 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

SCV004411884

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 9, 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, SCV004411884.1

#	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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt EYA4 protein function. This variant has not been reported in the literature in individuals affected with EYA4-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 584 of the EYA4 protein (p.Cys584Arg).

#	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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