rs121909196
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_000503.6(EYA1):c.1319G>A(p.Arg440Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_000503.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EYA1 | NM_000503.6 | c.1319G>A | p.Arg440Gln | missense_variant | Exon 14 of 18 | ENST00000340726.8 | NP_000494.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Branchiootorenal syndrome 1 Pathogenic:2
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Branchiootic syndrome 1 Pathogenic:1
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EYA1-related disorder Pathogenic:1
The EYA1 c.1319G>A variant is predicted to result in the amino acid substitution p.Arg440Gln. This variant is also referred to as c.1220G>A or R407Q in the literature, corresponding to NM_172060. It has been reported in individuals with branchio-oto-renal syndrome (see, for example, Kumar et al. 1997. PubMed ID: 10464653; Orten et al. 2008. PubMed ID: 18220287; Mann et al. 2019. PubMed ID: 30655312), including some in whom it was reported de novo (Masuda et al. 2022. PubMed ID: 35046468; Cho et al. 2024. PubMed ID: 39125727). An in vivo experimental study indicated this variant affected development of the otic vesicle and vestibulocochlear nerve in Xenopus laevis embryos (referred to as R435Q, Li et al. 2010. PubMed ID: 19951260). An additional study indicated this variant protein was able to translocate into the nucleus with similar efficiency to wild type (Musharraf et al. 2014. PubMed ID: 24489909). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as pathogenic. -
Branchiooculofacial syndrome Pathogenic:1
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Melnick-Fraser syndrome Pathogenic:1
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 440 of the EYA1 protein (p.Arg440Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with branchiootorenal syndrome (PMID: 10464653, 15146463, 18220287, 21280147, 28832562). Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this EYA1 variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 10,567 individuals referred to our laboratory for EYA1 testing. This variant is also known as c.1220G>A (p.Arg407Gln). ClinVar contains an entry for this variant (Variation ID: 7935). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt EYA1 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects EYA1 function (PMID: 19951260, 24489909). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -
Rare genetic deafness Pathogenic:1
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Branchiootic syndrome 1;C3714941:Otofaciocervical syndrome 1;C4551702:Branchiootorenal syndrome 1 Pathogenic:1
PM2+PS4+PP1_Strong+PM1+PS3_Moderate+PP3 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at