NM_004100.5(EYA4):c.2T>C (p.Met1Thr) AND Cardiovascular phenotype

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 15, 2023
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:: RCV003298208.2

Allele description [Variation Report for NM_004100.5(EYA4):c.2T>C (p.Met1Thr)]

NM_004100.5(EYA4):c.2T>C (p.Met1Thr)

Gene:

EYA4:EYA transcriptional coactivator and phosphatase 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q23.2

Genomic location:

Preferred name:

NM_004100.5(EYA4):c.2T>C (p.Met1Thr)

HGVS:

NC_000006.12:g.133274782T>C
NG_011596.2:g.38426T>C
NM_001301012.2:c.2T>C
NM_001301013.2:c.2T>C
NM_001370458.1:c.2T>C
NM_001370459.1:c.2T>C
NM_004100.5:c.2T>CMANE SELECT
NM_172103.4:c.2T>C
NM_172105.4:c.2T>C
NP_001287941.1:p.Met1Thr
NP_001287942.1:p.Met1Thr
NP_001357387.1:p.Met1Thr
NP_001357388.1:p.Met1Thr
NP_004091.3:p.Met1Thr
NP_742101.2:p.Met1Thr
NP_742103.1:p.Met1Thr
LRG_418t1:c.2T>C
LRG_418:g.38426T>C
LRG_418p1:p.Met1Thr
NC_000006.11:g.133595920T>C
NM_004100.4:c.2T>C

Protein change:

M1T

Links:

dbSNP: rs200593099

NCBI 1000 Genomes Browser:

rs200593099

Molecular consequence:

NM_001301012.2:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001301013.2:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001370458.1:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001370459.1:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_004100.5:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_172103.4:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_172105.4:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001301012.2:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001301013.2:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370458.1:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370459.1:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004100.5:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_172103.4:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_172105.4:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003989497	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (May 15, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003989497

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(May 15, 2023)

germline

clinical testing

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

Citation Link

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

Interpreting secondary cardiac disease variants in an exome cohort.

Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG; NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program..

Circ Cardiovasc Genet. 2013 Aug;6(4):337-46. doi: 10.1161/CIRCGENETICS.113.000039. Epub 2013 Jul 16.

PubMed [citation]

PMID:: 23861362
PMCID:: PMC3887521

Details of each submission

From Ambry Genetics, SCV003989497.3

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

Description

The p.M1? variant (also known as c.2T>C) is located in coding exon 1 of the EYA4 gene and results from a T to C substitution at nucleotide position 2. This alters the methionine residue at the initiation codon (ATG). Variations that modify the initiation codon (ATG) are expected to result in either loss of translation initiation, N-terminal truncation, or cause a shift in the mRNA reading frame; however, there is an in-frame methionine 29 amino acids from the initiation site, which may result in N-terminal truncation of unknown functional significance. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 7, 2024

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