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NM_000503.6(EYA1):c.340T>C (p.Phe114Leu) AND Branchiootorenal syndrome 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 12, 2019
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:
RCV001212522.1

Allele description [Variation Report for NM_000503.6(EYA1):c.340T>C (p.Phe114Leu)]

NM_000503.6(EYA1):c.340T>C (p.Phe114Leu)

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.340T>C (p.Phe114Leu)
HGVS:
  • NC_000008.11:g.71321812A>G
  • NG_011735.2:g.45421T>C
  • NG_011735.3:g.231319T>C
  • NM_000503.6:c.340T>CMANE SELECT
  • NM_001288574.2:c.337T>C
  • NM_001288575.2:c.-12T>C
  • NM_001370333.1:c.427T>C
  • NM_001370334.1:c.340T>C
  • NM_001370335.1:c.340T>C
  • NM_001370336.1:c.424T>C
  • NM_172058.4:c.340T>C
  • NM_172059.5:c.427T>C
  • NP_000494.2:p.Phe114Leu
  • NP_001275503.1:p.Phe113Leu
  • NP_001357262.1:p.Phe143Leu
  • NP_001357263.1:p.Phe114Leu
  • NP_001357264.1:p.Phe114Leu
  • NP_001357265.1:p.Phe142Leu
  • NP_742055.1:p.Phe114Leu
  • NP_742056.2:p.Phe143Leu
  • NC_000008.10:g.72234047A>G
  • NM_000503.5:c.340T>C
Protein change:
F113L
Links:
dbSNP: rs772521196
NCBI 1000 Genomes Browser:
rs772521196
Molecular consequence:
  • NM_001288575.2:c.-12T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000503.6:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001288574.2:c.337T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370333.1:c.427T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370334.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370335.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370336.1:c.424T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172058.4:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172059.5:c.427T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001384108Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 12, 2019) 		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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001384108.1

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

Description

This sequence change replaces phenylalanine with leucine at codon 114 of the EYA1 protein (p.Phe114Leu). The phenylalanine residue is moderately conserved and there is a small physicochemical difference between phenylalanine and leucine. This variant is present in population databases (rs772521196, ExAC 0.009%). This variant has not been reported in the literature in individuals with EYA1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 23, 2022