chr8-71271802-G-A

Variant names:

• chr8-71271802-G-A
• rs121909195
• NM_000503.6:c.922C>T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000503.6(EYA1):​c.922C>T​(p.Arg308*) variant causes a stop gained change. The variant allele was found at a frequency of 0.000000684 in 1,461,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: EYA1 NM_000503.6 stop_gained
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 3.62

Genes affected

EYA1 (HGNC:3519): (EYA transcriptional coactivator and phosphatase 1) This gene encodes a member of the eyes absent (EYA) family of proteins. The encoded protein may play a role in the developing kidney, branchial arches, eye, and ear. Mutations of this gene have been associated with branchiootorenal dysplasia syndrome, branchiootic syndrome, and sporadic cases of congenital cataracts and ocular anterior segment anomalies. A similar protein in mice can act as a transcriptional activator. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Dec 2013]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 8-71271802-G-A is Pathogenic according to our data. Variant chr8-71271802-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 7929.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-71271802-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EYA1	NM_000503.6	c.922C>T	p.Arg308*	stop_gained	Exon 10 of 18	ENST00000340726.8	NP_000494.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EYA1	ENST00000340726.8	c.922C>T	p.Arg308*	stop_gained	Exon 10 of 18	1	NM_000503.6	ENSP00000342626.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461878 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727238

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

EYA1-related disorder Pathogenic:1

Feb 02, 2023

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The EYA1 c.922C>T variant is predicted to result in premature protein termination (p.Arg308*). This variant has been reported in individuals with branchio-oto-renal syndrome (referred to as Arg275Term, Abdelhak et al. 1997. PubMed ID: 9020840; Orten et al. 2008. PubMed ID: 18220287; Unzaki et al. 2018. PubMed ID: 29500469). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Nonsense variants in EYA1 are expected to be pathogenic. Given all the evidence, we interpret c.922C>T (p.Arg308*) as pathogenic. -

Melnick-Fraser syndrome Pathogenic:1

Nov 11, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Arg308*) in the EYA1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in EYA1 are known to be pathogenic (PMID: 10464653, 18220287). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with branchiootorenal syndrome (PMID: 9020840, 18220287, 29500469). 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 p.R275*. ClinVar contains an entry for this variant (Variation ID: 7929). For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:1

Sep 20, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Identified in multiple unrelated patients with features consistent with EYA1-related branchiootorenal spectrum disorder referred for genetic testing at GeneDx and in published literature (PMID: 9020840, 18220287); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 31738409, 24803398, 9020840, 18220287, 35939872) -

Branchiootorenal syndrome 1 Pathogenic:1

Feb 01, 1997

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Rare genetic deafness Pathogenic:1

Sep 17, 2011

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Arg308X variant in EYA1 has been reported in the literature in 5 individuals affected with branchio-oto-renal syndrome (BOR) or BOR related symptoms (Abdelh ak 1997, Orten 2008). This variant reportedly segregated with the clinical featu re of BOR in one family (Abdelhak 1997). This variant leads to a premature stop codon at position 308, which is predicted to lead to a truncated or absent prote in. In summary, this variant meets our criteria to be classified as pathogenic. -

Branchiootic syndrome 1;C3714941:Otofaciocervical syndrome 1;C4551702:Branchiootorenal syndrome 1 Pathogenic:1

May 16, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.62
CADD	Pathogenic	41
DANN	Uncertain	1.0
Eigen	Pathogenic	0.77
Eigen_PC	Uncertain	0.64
FATHMM_MKL	Uncertain	0.89	D
Vest4		0.81
GERP RS		4.8

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs121909195; hg19: chr8-72184037; COSMIC: COSV58172873; COSMIC: COSV58172873;