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NM_000503.6(EYA1):c.896C>A (p.Ser299Ter) AND Rare genetic deafness

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 5, 2015
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:
RCV000219278.4

Allele description [Variation Report for NM_000503.6(EYA1):c.896C>A (p.Ser299Ter)]

NM_000503.6(EYA1):c.896C>A (p.Ser299Ter)

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.896C>A (p.Ser299Ter)
HGVS:
  • NC_000008.11:g.71271828G>T
  • NG_011735.3:g.281303C>A
  • NM_000503.6:c.896C>AMANE SELECT
  • NM_001288574.2:c.878C>A
  • NM_001288575.2:c.530C>A
  • NM_001370333.1:c.983C>A
  • NM_001370334.1:c.896C>A
  • NM_001370335.1:c.896C>A
  • NM_001370336.1:c.965C>A
  • NM_172058.4:c.896C>A
  • NM_172059.5:c.968C>A
  • NP_000494.2:p.Ser299Ter
  • NP_001275503.1:p.Ser293Ter
  • NP_001275504.1:p.Ser177Ter
  • NP_001357262.1:p.Ser328Ter
  • NP_001357263.1:p.Ser299Ter
  • NP_001357264.1:p.Ser299Ter
  • NP_001357265.1:p.Ser322Ter
  • NP_742055.1:p.Ser299Ter
  • NP_742056.2:p.Ser323Ter
  • NC_000008.10:g.72184063G>T
  • NG_011735.2:g.95405C>A
  • NM_172058.2:c.896C>A
  • p.Ser299X
Protein change:
S177*
Links:
dbSNP: rs876657691
NCBI 1000 Genomes Browser:
rs876657691
Molecular consequence:
  • NM_000503.6:c.896C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001288574.2:c.878C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001288575.2:c.530C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001370333.1:c.983C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001370334.1:c.896C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001370335.1:c.896C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001370336.1:c.965C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_172058.4:c.896C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_172059.5:c.968C>A - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Rare genetic deafness
Identifiers:
MedGen: C5680250; Orphanet: 96210

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000271368Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Pathogenic
(Nov 5, 2015) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000271368.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The p.Ser299X variant in EYA1 has not been previously reported in individuals wi th Branchio-oto-renal syndrome or in large population studies. This nonsense var iant leads to a premature termination codon at position 299, which is predicted to lead to a truncated or absent protein. Heterozygous loss of function of the E YA1 gene is an established disease mechanism in Branchio-oto-renal syndrome. In summary, this variant meets our criteria to be classified as pathogenic for Bran chio-oto-renal syndrome in an autosomal dominant manner based on the predicted i mpact to the protein.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

Last Updated: Dec 24, 2023