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NM_000503.6(EYA1):c.1523C>T (p.Ala508Val) AND multiple conditions

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Apr 8, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV004554820.2

Allele description [Variation Report for NM_000503.6(EYA1):c.1523C>T (p.Ala508Val)]

NM_000503.6(EYA1):c.1523C>T (p.Ala508Val)

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.1523C>T (p.Ala508Val)
HGVS:
  • NC_000008.11:g.71215461G>A
  • NG_011735.3:g.337670C>T
  • NM_000503.6:c.1523C>TMANE SELECT
  • NM_001288574.2:c.1505C>T
  • NM_001288575.2:c.1157C>T
  • NM_001370333.1:c.1610C>T
  • NM_001370334.1:c.1523C>T
  • NM_001370335.1:c.1523C>T
  • NM_001370336.1:c.1502C>T
  • NM_172058.4:c.1523C>T
  • NM_172059.5:c.1505C>T
  • NP_000494.2:p.Ala508Val
  • NP_001275503.1:p.Ala502Val
  • NP_001275504.1:p.Ala386Val
  • NP_001357262.1:p.Ala537Val
  • NP_001357263.1:p.Ala508Val
  • NP_001357264.1:p.Ala508Val
  • NP_001357265.1:p.Ala501Val
  • NP_742055.1:p.Ala508Val
  • NP_742056.2:p.Ala502Val
  • NC_000008.10:g.72127696G>A
  • NG_011735.2:g.151772C>T
  • NM_000503.5:c.1523C>T
Protein change:
A386V
Links:
dbSNP: rs754901033
NCBI 1000 Genomes Browser:
rs754901033
Molecular consequence:
  • NM_000503.6:c.1523C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001288574.2:c.1505C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001288575.2:c.1157C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370333.1:c.1610C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370334.1:c.1523C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370335.1:c.1523C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370336.1:c.1502C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172058.4:c.1523C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172059.5:c.1505C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Branchiootic syndrome 1 (BOS1)
Synonyms:
BO SYNDROME 1; BRANCHIOOTIC DYSPLASIA
Identifiers:
MONDO: MONDO:0011258; MedGen: C1865143; OMIM: 602588
Name:
Branchiootorenal syndrome 1
Identifiers:
MONDO: MONDO:0007236; MedGen: C4551702; Orphanet: 107; OMIM: 113650
Name:
Otofaciocervical syndrome 1 (OTFCS)
Identifiers:
MONDO: MONDO:0024532; MedGen: C3714941; OMIM: 166780

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005044095New York Genome Center - PrenatalSEQ
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Nov 19, 2021) 		inheritedclinical testing

Citation Link,

SCV005677289Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Apr 8, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedinheritedunknown1not providednot provided1not providedclinical 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 New York Genome Center - PrenatalSEQ, SCV005044095.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The c.1523C>T variant identified in EYA1 has previously been reported in ClinVar [ClinVar ID: 560446] as a Variant of Unknown Significance. The variant is observed in 11 alleles with no homozygotes across population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8) suggesting it is not a common benign variant in the populations represented in those databases. The predicted p.(Ala508Val) variant affects a conserved residue in exon 16 of this 18-exon gene, and in silico algorithms are in favor of a damaging effect (CADD v1.6= 27.9, REVEL= 0.965). Of note, there are nearby missense variants reported in literature in individuals with EYA1-related Branchiootorenal syndrome. Based on available evidence, this inherited c.1523C>T (p.(Ala508Val)) variant identified in EYA1 is reported as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV005677289.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jan 25, 2025