NM_000503.6(EYA1):c.1044T>G (p.Tyr348Ter) AND Branchiootorenal syndrome 1

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Nov 30, 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:: RCV000625536.5

Allele description [Variation Report for NM_000503.6(EYA1):c.1044T>G (p.Tyr348Ter)]

NM_000503.6(EYA1):c.1044T>G (p.Tyr348Ter)

Gene:

EYA1:EYA transcriptional coactivator and phosphatase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q13.3

Genomic location:

Preferred name:

NM_000503.6(EYA1):c.1044T>G (p.Tyr348Ter)

Other names:

p.Tyr348Ter

HGVS:

NC_000008.11:g.71269746A>C
NG_011735.3:g.283385T>G
NM_000503.6:c.1044T>GMANE SELECT
NM_001288574.2:c.1026T>G
NM_001288575.2:c.678T>G
NM_001370333.1:c.1131T>G
NM_001370334.1:c.1044T>G
NM_001370335.1:c.1044T>G
NM_001370336.1:c.1113T>G
NM_172058.4:c.1044T>G
NM_172059.5:c.1116T>G
NP_000494.2:p.Tyr348Ter
NP_001275503.1:p.Tyr342Ter
NP_001275504.1:p.Tyr226Ter
NP_001357262.1:p.Tyr377Ter
NP_001357263.1:p.Tyr348Ter
NP_001357264.1:p.Tyr348Ter
NP_001357265.1:p.Tyr371Ter
NP_742055.1:p.Tyr348Ter
NP_742056.2:p.Tyr372Ter
NC_000008.10:g.72181981A>C
NG_011735.2:g.97487T>G
NM_000503.5:c.1044T>G

Protein change:

Y226*

Links:

dbSNP: rs1554615511

NCBI 1000 Genomes Browser:

rs1554615511

Molecular consequence:

NM_000503.6:c.1044T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001288574.2:c.1026T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001288575.2:c.678T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001370333.1:c.1131T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001370334.1:c.1044T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001370335.1:c.1044T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001370336.1:c.1113T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_172058.4:c.1044T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_172059.5:c.1116T>G - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Branchiootorenal syndrome 1
Identifiers:: MONDO: MONDO:0007236; MedGen: C4551702; Orphanet: 107; OMIM: 113650

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000746031	Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare	no assertion criteria provided	Pathogenic (Sep 18, 2017)	germline	clinical testing
SCV004171703	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 30, 2023)	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

SCV000746031

Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare

no assertion criteria provided

Pathogenic
(Sep 18, 2017)

germline

clinical testing

SCV004171703

Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 30, 2023)

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	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare, SCV000746031.1

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

#	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 Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV004171703.1

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

Description

A heterozygous nonsense variant in exon 11 of the EYA1 gene that results in a stop codon and premature truncation of the protein at codon 348 was detected. The observed variant is reported as Pathogenic in ClinVar database. This variant has not been reported in the 1000 genomes, gnomAD (v3.1), gnomAD (v2.1) and topmed, databases. The in silico prediction of the variant is damaging by MutationTaster2. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as likely pathogenic.

#	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		1	not provided	not provided	not provided

Last Updated: Mar 30, 2024

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