ClinVar Miner

Submissions for variant NM_004004.6(GJB2):c.355GAG[1] (p.Glu120del)

dbSNP: rs80338947
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Total submissions: 18
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine,Mass General Brigham Personalized Medicine RCV000211776 SCV000061503 pathogenic Rare genetic deafness 2017-06-06 criteria provided, single submitter clinical testing The p.Glu120del variant in GJB2 has been reported in the homozygous state in mor e than ten probands and in the compound heterozygous state with another GJB2 pat hogenic variant in more than nine probands with hearing loss (Najmabadi 2005, Te kin 2003, Hismi 2006, Marlin 2005, Mani 2008, LMM data). This variant has been i dentified in 17/126016 European chromosomes by the Genome Aggregation Database ( gnomAD, http://gnomad.broadinstitute.org; dbSNP rs80338947); however, its freque ncy is low enough to be consistent with a recessive carrier frequency for autoso mal recessive nonsyndromic hearing loss. Functional studies indicate that the c hannels formed by the p.Glu120del mutant protein are inactive (Mani 2008). In su mmary, this variant meets criteria to be classified as pathogenic for autosomal recessive hearing loss. ACMG/AMP criteria applied: PM3_VeryStrong, PM2, PS2_Supp orting
Genetic Services Laboratory,University of Chicago RCV000146018 SCV000193170 pathogenic Hearing impairment 2013-02-08 criteria provided, single submitter clinical testing
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia RCV000018530 SCV000599747 pathogenic Autosomal recessive nonsyndromic hearing loss 1A 2017-05-09 criteria provided, single submitter clinical testing
GeneDx RCV000520132 SCV000617686 pathogenic not provided 2021-11-24 criteria provided, single submitter clinical testing In-frame deletion of one amino acid in the cytoplasmic loop, a non-repeat region; Published functional studies demonstrate c.358_360delGAG impairs the function of gap channels (Bruzzone et al., 2003; Mani et al., 2009); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 22975760, 29485809, 15070423, 11438992, 20609484, 10544226, 12673800, 15666300, 15967879, 16712961, 12505163, 18941476, 27573290, 27177978, 29501291, 31160754, 32747562, 33096615, 31589614, 33105617, 34581455, 34695157)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000018530 SCV000698248 pathogenic Autosomal recessive nonsyndromic hearing loss 1A 2016-12-27 criteria provided, single submitter clinical testing Variant summary: The GJB2 c.358_360delGAG (p.Glu120del) variant involves the deletion of one amino acid (Glu). One in silico tool predicts a damaging outcome for this variant. This variant was found in 8/121052 control chromosomes at a frequency of 0.0000661, which does not exceed the estimated maximal expected allele frequency of a pathogenic GJB2 variant (0.025). This variant has been reported as one of the most prevalent GJB2 pathogenic variant. Functional study showed GJB2 p.glu120del could not for homotypic gap-junction channels, thus lose the junctional conductance (Bruzzone_2003). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.
Athena Diagnostics Inc RCV000520132 SCV000841706 pathogenic not provided 2018-03-16 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV000018530 SCV000914613 pathogenic Autosomal recessive nonsyndromic hearing loss 1A 2018-10-18 criteria provided, single submitter clinical testing The GJB2 c.358_360delGAG (p.Glu120del) variant is an inframe deletion that has been reported in at least four studies in which it was found in at least 20 individuals with hearing loss, including seven homozygotes, 12 compound heterozygotes and on heterozygote in whom a second variant was not identified (Murgia et al. 2009; Tekin et al. 2003; Snoeckx et al. 2005; Mani et al. 2009). The p.Glu120del variant was absent from 120 control alleles and is reported at a frequency of 0.000135 in the European (non-Finnish) population of the Genome Aggregation Database. Functional studies conducted by two independent laboratories in Xenopus oocytes and HeLa cells revealed that compared with the wild type protein and negative control, the p.Glu120del variant resulted in the loss of gap junction channel function (Bruzzone et al. 2003; Mani et al. 2009). Further studies in HeLa cells revealed near-normal trafficking of the variant-containing protein to the cell membrane but reduced protein expression (Mani et al. 2009). Based on the collective evidence, the p.Glu120del variant is classified as pathogenic for autosomal recessive nonsyndromic hearing loss. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Invitae RCV000520132 SCV000945066 pathogenic not provided 2021-11-27 criteria provided, single submitter clinical testing This variant, c.358_360del, results in the deletion of 1 amino acid(s) of the GJB2 protein (p.Glu120del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs80338947, gnomAD 0.01%). This variant has been observed in individuals with deafness (PMID: 10544226, 11438992, 15070423, 16712961, 18941476, 20553101, 20609484, 25214170). ClinVar contains an entry for this variant (Variation ID: 17006). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects GJB2 function (PMID: 12505163, 18941476). For these reasons, this variant has been classified as Pathogenic.
Myriad Women's Health, Inc. RCV000018530 SCV001193940 pathogenic Autosomal recessive nonsyndromic hearing loss 1A 2019-12-20 criteria provided, single submitter clinical testing NM_004004.5(GJB2):c.358_360delGAG(E120del) is classified as pathogenic in the context of GJB2-related DFNB1 nonsyndromic hearing loss and deafness. Sources cited for classification include the following: PMID 19371219, 18941476, 25012701, 22695344, and 12505163. Classification of NM_004004.5(GJB2):c.358_360delGAG(E120del) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.
INGEBI, INGEBI / CONICET RCV001257563 SCV001434017 pathogenic Nonsyndromic genetic hearing loss 2020-08-21 criteria provided, single submitter clinical testing Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: the filtering allele frequency of the c.358_360del variant in GJB2 which leads to p.(Glu120del) change is 0,008% (17/128492 European non-Finnish alleles with 95% CI) in Genome Aggregation Database (http://gnomad.broadinstitute.org; calculated by using inverse allele frequency at https://www.cardiodb.org/allelefrequencyapp/), which meets PM2_Supporting criteria. The c.358_360del variant is predicted to cause a protein length change due to an in-frame deletion that is not located in a repetitive region applying to PM4 rule. This variant was detected in trans with at least 4 pathogenic variants among different hearing loss patients (PMID: 1054426, 12673800, 15666300, 24158611) applying to PM3_VeryStrong criteria. Functional studies showed that p.Glu120del mutant did not induce the formation of homotypic junctional channel since the conductance levels measured did not exceed the background levels in Xenopus laevis oocytes (PMID:12505163). Besides, no dye transfer (Lucifer Yellow) was observed when p.Glu120del mutant was tested in HeLa cells (PMID:18941476) meeting PS3_Moderate rule. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive non-syndromic hearing loss: PM2_Supporting, PM4, PM3_VeryStrong, PS3_Moderate.
CeGaT Center for Human Genetics Tuebingen RCV000520132 SCV001747686 pathogenic not provided 2021-07-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000018530 SCV001810448 pathogenic Autosomal recessive nonsyndromic hearing loss 1A 2021-07-22 criteria provided, single submitter clinical testing
King Laboratory,University of Washington RCV000018530 SCV002059938 pathogenic Autosomal recessive nonsyndromic hearing loss 1A 2020-08-01 criteria provided, single submitter research GJB2 c.358_360delGAG, p.E120del was previously shown to be deficient in inducing formation of junctional channels (PMID: 18941476). It is homozygous in two children from a Palestinian family with pre-lingual nonsyndromic hearing loss (Abu Rayyan 2020). The variant is absent from 1300 Palestinian controls and present in 20/281644 alleles on gnomAD, all heterozygotes.
OMIM RCV000018530 SCV000038812 pathogenic Autosomal recessive nonsyndromic hearing loss 1A 1998-05-28 no assertion criteria provided literature only
GeneReviews RCV000018530 SCV000041045 not provided Autosomal recessive nonsyndromic hearing loss 1A no assertion provided literature only
Institut Pasteur du Maroc RCV000018530 SCV000267103 pathogenic Autosomal recessive nonsyndromic hearing loss 1A 2016-04-01 no assertion criteria provided clinical testing Pathogenic
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital RCV000678881 SCV000805074 pathogenic Hearing loss 2015-10-08 no assertion criteria provided clinical testing
Natera, Inc. RCV000018530 SCV001463374 pathogenic Autosomal recessive nonsyndromic hearing loss 1A 2020-09-16 no assertion criteria provided clinical testing

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