ClinVar Miner

Submissions for variant NM_206933.3(USH2A):c.2299del (p.Glu767fs) (rs80338903)

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Total submissions: 20
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000623326 SCV000740743 likely pathogenic Inborn genetic diseases 2014-10-23 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: POSITIVE: Relevant Alteration(s) Detected
Baylor Genetics RCV000191141 SCV000245550 pathogenic Retinitis pigmentosa 39 2015-06-28 criteria provided, single submitter clinical testing This variant has been previously reported as disease-causing and was found once in our laboratory with 2 missense variants [G2224C, E3448K; phase undetermined] in a 32-year-old female with retinitis pigmentosa. Variant pathogenic in recessive state; heterozygotes are carriers.
CHLA Center for Personalized Medicine,Children's Hospital, Los Angeles RCV000735362 SCV000854516 pathogenic Short stature; Cognitive impairment; High palate; Distal arthrogryposis; Anxiety; Brisk reflexes; Dysautonomia; Abnormality of the upper limb; Multiple joint contractures; Dislocated radial head; Abnormality of upper limb joint; Chronic pain; Abnormality of upper limb bone criteria provided, single submitter clinical testing
Centre for Genomic Medicine, Manchester,Central Manchester University Hospitals RCV000210326 SCV000259101 pathogenic Retinal dystrophy 2015-01-30 no assertion criteria provided clinical testing
Counsyl RCV000002445 SCV000490145 pathogenic Usher syndrome, type 2A 2016-08-18 criteria provided, single submitter clinical testing
Counsyl RCV000191141 SCV000490146 pathogenic Retinitis pigmentosa 39 2016-08-18 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000254870 SCV000225952 pathogenic not provided 2016-10-14 criteria provided, single submitter clinical testing
GeneDx RCV000254870 SCV000321994 pathogenic not provided 2018-12-10 criteria provided, single submitter clinical testing The c.2299delG variant accounts for 16%-44% of USH2A variants and has been identified in patients with Usher syndrome type II, atypical Usher syndrome, and non-syndromic autosomal recessive retinitis pigmentosa (arRP) (Dreyer et al., 2001; Aller et al., 2004; Seyedahmadi et al., 2004; Aller et al., 2010). The c.2299delG variant causes a frameshift starting with codon Glutamic Acid 767, changes this amino acid to a Serine residue, and creates a premature Stop codon at position 21 of the new reading frame, denoted p.Glu767SerfsX21. This common variant is predicted to disrupt an exonic splicing enhancer and instead create an exonic splicing silencer in exon 13, thereby diminishing the splicing of exons 12 and 13 (Lenassi et al., 2014). The c.2299delG variant is observed in 55/34402 (0.16%) alleles from individuals of Latino background and in 12/8252 (0.15%) alleles from individuals of European American background in large population cohorts (Lek et al., 2016; Exome Variant Server). Based on currently available evidence, we interpret c.2299delG as a pathogenic variant.
GeneReviews RCV000032524 SCV000056187 pathologic Retinitis pigmentosa 2010-12-23 no assertion criteria provided curation Converted during submission to Pathogenic.
Human Genetics - Radboudumc,Radboudumc RCV000191141 SCV000804740 pathogenic Retinitis pigmentosa 39 2016-09-01 no assertion criteria provided clinical testing
Invitae RCV000254870 SCV000940875 pathogenic not provided 2018-12-27 criteria provided, single submitter 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. This variant is clearly defined as an Usher syndrome type II causative allele, accounting for 16-44% of disease alleles, and has also been reported in individuals affected with non-syndromic autosomal recessive retinitis pigmentosa (PMID: 9624053, 14970843, 15325563, 11402400, 25404053, 25097241). This variant is also known as 2314delG in the literature. ClinVar contains an entry for this variant (Variation ID: 2351). Loss-of-function variants in USH2A are known to be pathogenic (PMID: 10909849, 20507924, 24944099, 25649381). For these reasons, this variant has been classified as Pathogenic.
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000824793 SCV000065508 pathogenic Usher syndrome; Rare genetic deafness 2014-09-30 criteria provided, single submitter 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).
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet RCV000504641 SCV000926729 pathogenic Usher syndrome 2018-04-01 no assertion criteria provided research
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet RCV000032524 SCV000926730 pathogenic Retinitis pigmentosa 2018-04-01 no assertion criteria provided research
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet RCV000787895 SCV000926911 pathogenic Macular dystrophy 2018-04-01 no assertion criteria provided research
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet RCV000787897 SCV000926915 pathogenic Cone-rod dystrophy 2018-04-01 no assertion criteria provided research
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet RCV000787899 SCV000926917 pathogenic Congenital stationary night blindness 2018-04-01 no assertion criteria provided research
NIHR Bioresource Rare Diseases, University of Cambridge RCV000032524 SCV000598799 pathogenic Retinitis pigmentosa 2015-01-01 no assertion criteria provided research
NIHR Bioresource Rare Diseases, University of Cambridge RCV000504641 SCV000598800 pathogenic Usher syndrome 2015-01-01 no assertion criteria provided research
OMIM RCV000002445 SCV000022603 pathogenic Usher syndrome, type 2A 2009-12-01 no assertion criteria provided literature only

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