rs80338903

Variant names:

• chr1-216247094-TC-T
• rs80338903
• NM_206933.4:c.2299delG

Variant summary

Our verdict is Pathogenic. The variant received 15 ACMG points: 16P and 1B. PVS1 PP5_Very_Strong BS2_Supporting

The NM_206933.4(USH2A):​c.2299delG​(p.Glu767SerfsTer21) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000947 in 1,613,920 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: 𝑓 0.00050 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00099 (2 hom.)
• Consequence: USH2A NM_206933.4 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:53 O:2
• Conservation: PhyloP100: 1.75
• Publications: 183 publications found

Genes affected

USH2A (HGNC:12601): (usherin) This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

USH2A Gene-Disease associations (from GenCC):

• Usher syndrome type 2

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
• Usher syndrome type 2A

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae)
• retinitis pigmentosa 39

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• retinitis pigmentosa

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 15 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PP5: Variant 1-216247094-TC-T is Pathogenic according to our data. Variant chr1-216247094-TC-T is described in ClinVar as Pathogenic. ClinVar VariationId is 2351.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAdExome4 at 2 AD,AR geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USH2A	NM_206933.4	c.2299delG	p.Glu767SerfsTer21	frameshift_variant	Exon 13 of 72	ENST00000307340.8	NP_996816.3
USH2A	NM_007123.6	c.2299delG	p.Glu767SerfsTer21	frameshift_variant	Exon 13 of 21		NP_009054.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USH2A	ENST00000307340.8	c.2299delG	p.Glu767SerfsTer21	frameshift_variant	Exon 13 of 72	1	NM_206933.4	ENSP00000305941.3
USH2A	ENST00000366942.3	c.2299delG	p.Glu767SerfsTer21	frameshift_variant	Exon 13 of 21	1		ENSP00000355909.3
USH2A	ENST00000674083.1	c.2299delG	p.Glu767SerfsTer21	frameshift_variant	Exon 13 of 73			ENSP00000501296.1

Frequencies

GnomAD3 genomes AF: 0.000500 AC: 76 AN: 152122 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000882

Gnomad OTH AF: 0.000479

GnomAD2 exomes AF: 0.000757 AC: 190 AN: 250832 AF XY: 0.000723

Gnomad AFR exome AF: 0.000246

Gnomad AMR exome AF: 0.00179

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000998

Gnomad OTH exome AF: 0.00180

GnomAD4 exome AF: 0.000994 AC: 1453 AN: 1461798 Hom.: 2 Cov.: 31 AF XY: 0.000952 AC XY: 692 AN XY: 727208

African (AFR) AF: 0.000299 AC: 10 AN: 33476

American (AMR) AF: 0.00165 AC: 74 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39690

South Asian (SAS) AF: 0.0000116 AC: 1 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53414

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5766

European-Non Finnish (NFE) AF: 0.00119 AC: 1328 AN: 1111940

Other (OTH) AF: 0.000662 AC: 40 AN: 60394

GnomAD4 genome AF: 0.000500 AC: 76 AN: 152122 Hom.: 0 Cov.: 32 AF XY: 0.000444 AC XY: 33 AN XY: 74292

African (AFR) AF: 0.000121 AC: 5 AN: 41438

American (AMR) AF: 0.000655 AC: 10 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.000882 AC: 60 AN: 68018

Other (OTH) AF: 0.000479 AC: 1 AN: 2088

Alfa AF: 0.000582 Hom.: 0

Bravo AF: 0.000706

EpiCase AF: 0.00109

EpiControl AF: 0.000533

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:53 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Usher syndrome type 2A Pathogenic:13

Apr 09, 2024

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PVS1,PM3_VSTR,PP1_MOD -

Dec 17, 2019

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

NM_206933.2(USH2A):c.2299delG(aka E767Sfs*21) is classified as pathogenic in the context of USH2A-related disorders. Sources cited for classification include the following: PMID 10909849 and 24607488. Classification of NM_206933.2(USH2A):c.2299delG(aka E767Sfs*21)is based on the following criteria: The variant causes a premature termination codon that is expected to be targeted by nonsense-mediated mRNA decay and is reported in individuals with the relevant phenotype. Please note: this variant was assessed in the context of healthy population screening. -

Jun 10, 2024

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PVS1, PS3, PM3_Very Strong, PM6 -

Jul 17, 2023

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Usher syndrome, type 2A (MIM#276901). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD v2 <0.01 for a recessive condition (198 heterozygotes, 0 homozygotes). (SP) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Many NMD-predicted variants have been reported in patients with both retinitis pigmentosa and Usher syndrome (Decipher, ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant is one of the most common disease causing variants in the USH2A gene, and has been reported in patients with both Usher syndrome and retinitis pigmentosa (ClinVar, PMID: 29953849). (SP) 1206 - This variant has been shown to be paternally inherited. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Nov 04, 2023

Genome-Nilou Lab

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 07, 2022

Genetics and Molecular Pathology, SA Pathology

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The USH2A c.2299del variant is classified as PATHOGENIC (PVS1, PS4, PM3) This USH2A c.2299del variant is located in exon 13/72 and is predicted to cause a shift in the reading frame at codon 767 (PVS1). This recurrent variant has been reported as the most common USH2A pathogenic variant (PMID: 20301515, PMID:9624053, PMID:22135276, PMID:24607488) (PS4). This variant has been detected in trans with another pathogenic variant for this recessive condition in both this individual and in other reported cases in the literature (PM3) and has also been reported as pathogenic in a homozygous state. This variant is in dbSNP (rs80338903) and has been reported as pathogenic for Usher syndrome and Retinitis pigmentosa by other diagnostic laboratories in ClinVar (ClinVar Variation ID: 2351) and in the disease database HGMD (CD982997). -

Apr 03, 2020

Natera, Inc.

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jan 11, 2023

Illumina Laboratory Services, Illumina

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The USH2A c.2299del (p.Glu767SerfsTer21) variant results in the deletion of a nucleotide at position c.2299, causing a shift in the protein reading frame that is predicted to result in premature termination of the protein. Loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay is predicted, though RNA expression studies performed on nasal epithelial cells suggest that the c.2299del variant could alternately disrupt splicing, leading to skipping of exon 13 or exons 12 and 13 (PMID: 24607488). The c.2299del variant is the most common disease-causing variant in the USH2A gene, and is estimated to account for over 20% of disease-causing alleles among individuals with Usher syndrome type 2, but has also been reported in individuals with non-syndromic retinitis pigmentosa (PMID: 9624053; PMID: 20301515, GeneReviews NBK1341; PMID: 25649381; PMID: 29953849; PMID: 36011334). The highest frequency of this allele in the Genome Aggregation Database is 0.001778 in the Latino/Admixed American population (version 2.1.1). Based on the available evidence, the c.2299del (p.Glu767SerfsTer21) variant is classified as pathogenic for Usher syndrome type 2. -

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Genomics England Pilot Project, Genomics England

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 01, 2009

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Feb 01, 2019

Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 28, 2021

DBGen Ocular Genomics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Pathogenic:12

-

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jan 23, 2025

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.Glu767Serfs*21) in the USH2A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in USH2A are known to be pathogenic (PMID: 10729113, 10909849, 20507924, 25649381). This variant is present in population databases (rs80338903, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This premature translational stop signal has been observed in individuals with non-syndromic autosomal recessive retinitis pigmentosa and is a common Usher syndrome type II allele (PMID: 9624053, 11402400, 14970843, 15325563, 25097241, 25404053). This variant is also known as 2314delG. ClinVar contains an entry for this variant (Variation ID: 2351). 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. -

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Clinical Genetics, Academic Medical Center

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Oct 23, 2020

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 26, 2017

Knight Diagnostic Laboratories, Oregon Health and Sciences University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

USH2A: PM3:Very Strong, PVS1, PP1:Strong, PM2 -

-

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Oct 14, 2016

Eurofins Ntd Llc (ga)

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 24, 2021

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 19, 2018

Center for Personalized Medicine, Children's Hospital Los Angeles

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2020

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Frameshift 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; This variant is associated with the following publications: (PMID: 22581970, 9624053, 32141364, 27344577, 20145675, 29847639, 23352160, 18665195, 26872967, 12525556, 11402400, 24607488, 29151245, 25097241, 15325563, 14970843, 26969326, 24160897, 25404053, 27460420, 22135276, 23924366, 17296898, 25649381, 24944099, 22495311, 21234346, 21174530, 11311042, 10775529, 10729113, 26633545, 10909849, 23891399, 20301515, 15025721, 12112664, 19881469, 17405132, 10090909, 30337596, 28157192, 28838317, 29953849, 31231422, 31266775, 32581362, 31827275, 31980526, 32176120, 32036094, 32664777, 31589614, 33576794, 30755392, 32853555) -

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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Retinitis pigmentosa 39 Pathogenic:7

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Genomics England Pilot Project, Genomics England

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 04, 2023

Genome-Nilou Lab

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 30, 2024

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 01, 2016

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

May 22, 2022

3billion

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.070%). Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000002351). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -

Apr 08, 2021

Ocular Genomics Institute, Massachusetts Eye and Ear

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

The USH2A c.2299del variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PM3, PP1, PP3. Based on this evidence we have classified this variant as Pathogenic. -

Aug 18, 2016

Counsyl

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -

Usher syndrome Pathogenic:4

Jan 01, 2015

NIHR Bioresource Rare Diseases, University of Cambridge

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Oct 25, 2019

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: USH2A c.2299delG (p.Glu767SerfsX21) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 0.00076 in 250832 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in USH2A causing Usher syndrome (0.00076 vs 0.013), allowing no conclusion about variant significance. c.2299delG has been reported in the literature in multiple individuals affected with Usher syndrome. This variant appears to be a common USH2A mutation contributing to Usher Syndrome Type II (e.g. Aller_2004, Calzetti_2018 and Gene Reviews). Lenassi et al suggest that this change could disrupt an exonic splicing enhancer and create an exonic splicing silencer within exon 13 and therefore affect splicing of exons 12 and 13 of USH2A (Lenassi_2014). Nine ClinVar submitters (evaluation after 2014) cite this variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Jul 24, 2023

Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

Clinical significance based on ACMG v2.0 -

Apr 01, 2018

Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Retinitis pigmentosa Pathogenic:3 Other:1

Jan 01, 2015

NIHR Bioresource Rare Diseases, University of Cambridge

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Apr 01, 2021

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

The p.Glu767SerfsTer21 variant in USH2A was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PM3, PP1, PP3. Based on this evidence we have classified this variant as Pathogenic. If you have any questions about the classification please reach out to the Pierce Lab. -

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GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Apr 01, 2018

Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

USH2A-related disorder Pathogenic:3 Other:1

May 01, 2024

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The USH2A c.2299delG variant is predicted to result in a frameshift and premature protein termination (p.Glu767Serfs*21). This variant has been documented as causative for Usher syndrome (Eudy et al. 1998. PubMed ID: 9624053; Aller et al. 2010. PubMed ID: 20145675; Aparisi et al. 2014. PubMed ID: 25404053). This variant is reported in 0.18% of alleles in individuals of Latino descent in gnomAD. Frameshift variants in USH2A are expected to be pathogenic. This variant is interpreted as pathogenic. -

Jan 05, 2022

DASA

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2299del;p.(Glu767Serfs*21) is a null frameshift variant (NMD) in the USH2A gene and predicts alteration of the nonsense-mediate decay - NMD is present in a relevantexon to the transcript - PVS1. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID: 2351; PMID: 20301515; 31836858; 30718709; 29953849;25649381; 25404053; 23924366; 12525556) - PS4. The variant is present at low allele frequencies population databases (rs80338903– gnomAD 0.04996%; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2_supporting. The p.(Glu767Serfs*21) was detected in trans with a pathogenic variant (PMID: 31836858; 30718709; 29953849;25649381; 25404053; 23924366; 12525556) - PM3_strong. The variant co-segregated with disease in multiple affected family members (PMID: 23924366; 12525556) - PP1. In summary, the currently available evidence indicates that the variant is pathogenic. -

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UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

The c.2299delG (p.E767Sfs) variant is one of the most common pathogenic variants in USH2A and has been previously reported in multiple individuals with Usher syndrome type IIA or nonsyndromic retinitis pigmentosa (PMID: 18641288; 11402400; 15326663). -

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GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

Variant interpreted as Pathogenic and reported on 06-28-2019 by Lab or GTR ID 500188. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Retinal dystrophy Pathogenic:3

Jan 01, 2023

Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 15, 2019

Blueprint Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 30, 2015

Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Usher syndrome type 2 Pathogenic:1

May 14, 2023

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Inborn genetic diseases Pathogenic:1

Mar 03, 2020

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The alteration results in a premature stop codon: _x000D_ _x000D_ The c.2299delG (p.E767Sfs*21) alteration, located in exon 13 (coding exon 12) of the USH2A gene, consists of a deletion of one nucleotide at position 2299, causing a translational frameshift with a predicted alternate stop codon after 21 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. The alteration has been observed in affected individuals:_x000D_ _x000D_ The c.2299delG alteration is the most common alteration found in Usher syndrome type II (Ouyang, 2004; Baux, 2007). Based on the available evidence, this alteration is classified as pathogenic. -

Usher syndrome;C5680250:Rare genetic deafness Pathogenic:1

Sep 30, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Glu767fs variant in USH2A is a common pathogenic variant known to be assoc iated with Usher syndrome (Weston 2000, Dreyer 2000, Dreyer 2001, Najera 2002, O uyang 2004, Aller 2004). -

Macular dystrophy Pathogenic:1

Apr 01, 2018

Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

not specified Pathogenic:1

Jul 31, 2018

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Glu767fs variant (rs80338903) has been observed in multiple cohorts of patients with Usher Syndrome, Type II (selected references: Eudy 1998, Dreyer 2001, Aller 2010). It is one of the most common pathogenic alleles of USH2A, and it is estimated that this variant accounts for 16% (Weston 2000) to 76% (Ouyang 2004) of all pathogenic USH2A variant. This variant is listed in the Genome Aggregation Database (gnomAD) database with a frequency in Latino populations of 0.20% (identified in 34 out of 34,442 chromosomes). -

Usher syndrome type 2A;C3151138:Retinitis pigmentosa 39 Pathogenic:1

Jan 23, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cone-rod dystrophy Pathogenic:1

Apr 01, 2018

Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Congenital stationary night blindness Pathogenic:1

Apr 01, 2018

Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.7
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs80338903; hg19: chr1-216420436;