NM_000503.6(EYA1):c.1650_1651dup (p.Tyr551fs) AND Branchiootic syndrome 1

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 8, 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:: RCV002254379.4

Allele description [Variation Report for NM_000503.6(EYA1):c.1650_1651dup (p.Tyr551fs)]

NM_000503.6(EYA1):c.1650_1651dup (p.Tyr551fs)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

8q13.3

Genomic location:

Preferred name:

NM_000503.6(EYA1):c.1650_1651dup (p.Tyr551fs)

HGVS:

NC_000008.11:g.71211203AC[3]
NG_011735.3:g.341925GT[3]
NM_000503.6:c.1650_1651dupMANE SELECT
NM_001288574.2:c.1632_1633dup
NM_001288575.2:c.1284_1285dup
NM_001370333.1:c.1737_1738dup
NM_001370334.1:c.1650_1651dup
NM_001370335.1:c.1650_1651dup
NM_001370336.1:c.1629_1630dup
NM_172058.4:c.1650_1651dup
NM_172059.5:c.1632_1633dup
NP_000494.2:p.Tyr551fs
NP_001275503.1:p.Tyr545fs
NP_001275504.1:p.Tyr429fs
NP_001357262.1:p.Tyr580fs
NP_001357263.1:p.Tyr551fs
NP_001357264.1:p.Tyr551fs
NP_001357265.1:p.Tyr544fs
NP_742055.1:p.Tyr551fs
NP_742056.2:p.Tyr545fs
NC_000008.10:g.72123438AC[3]

Protein change:

Y429fs

Links:

dbSNP: rs2128835296

NCBI 1000 Genomes Browser:

rs2128835296

Molecular consequence:

NM_000503.6:c.1650_1651dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001288574.2:c.1632_1633dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001288575.2:c.1284_1285dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370333.1:c.1737_1738dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370334.1:c.1650_1651dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370335.1:c.1650_1651dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370336.1:c.1629_1630dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_172058.4:c.1650_1651dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_172059.5:c.1632_1633dup - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Branchiootic syndrome 1 (BOS1)
Synonyms:: BO syndrome 1; Branchiootic dysplasia
Identifiers:: MONDO: MONDO:0011258; MedGen: C1865143; OMIM: 602588

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002525519	Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 8, 2022)	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

SCV002525519

Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 8, 2022)

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	unknown	yes	1	1	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 Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology, SCV002525519.1

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

Description

The c.1650_1651dup variant is not present in publicly available population databases like 1000 Genomes, Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC), Genome Aggregation Database (gnomAD), Indian Exome Database and in our in-house exome database. The variant was not previously reported to ClinVar, Human Genome Mutation Database (HGMD) and OMIM databases, in any affected individuals. In-silico pathogenicity prediction programs like MutationTaster2, CADD, Varsome etc. predicted this variant to be deleterious. The variant causes frameshift at the 551th aminoacid position of the wildtype transcript that creates a premature stop codon at the 555th position of the altered transcript which may translated into a truncated protein.

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

Last Updated: Dec 24, 2023

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