Submissions for variant NM_024009.3(GJB3):c.652_663del (p.Leu218_Asp221del)

dbSNP: rs727503069

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000150744	SCV000198184	likely benign	not specified	2015-02-27	criteria provided, single submitter	clinical testing	p.Leu218_Asp221del in exon 2 of GJB3: This variant is not expected to have clini cal significance because the region affected by this 4 amino acid in-frame delet ion is poorly conserved across mammals and evolutionarily distant species. In ad dition, in a family with erythrokeratodermia variabalis (EKV) without hearing lo ss, this variant was detected in both affected and unaffected family members, wh ile a variant that arose de novo on the same allele (in cis) in one individual s egregated with disease in her children, indicating that the de novo variant is c ausative for the EKV, and the p.Leu218_Asp221del is unrelated to the disease (Ri chard 2000). This variant has also been identified in 2/8250 European American c hromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/E VS/).
Eurofins Ntd Llc (ga)	RCV000724547	SCV000227516	uncertain significance	not provided	2015-01-22	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000724547	SCV000885522	likely benign	not provided	2017-12-29	criteria provided, single submitter	clinical testing	The GJB3 p.Leu218_Asp221del variant (rs727503069) has not been reported in association with hearing loss or deafness, but it has been identified in a family with erythrokeratodermia variabilis without hearing loss; however, this variant was identified in both affected and unaffected individuals whereas another variant that was on the same allele (in cis) and arose de novo in one individual was found only in affected family members (Richard 2000). Collectively, these observations suggest that the p.Leu218_Asp221del is not responsible for disease. Furthermore, the four amino acids that are removed by this in-frame deletion are poorly conserved (UCSC). The p.Leu218_Asp221del variant is listed in the Genome Aggregation Database (gnomAD) browser with an allele frequency of 0.14% in the Ashkenazi Jewish population (identified in 14 out of 10,148 chromosomes), and is found in the ClinVar database (Variant ID: 163536). Based on the available evidence, the p.Leu218_Asp221del variant is classified as likely benign.
CeGaT Center for Human Genetics Tuebingen	RCV000724547	SCV001147226	likely benign	not provided	2018-06-01	criteria provided, single submitter	clinical testing
GeneDx	RCV000724547	SCV001831915	likely benign	not provided	2021-05-14	criteria provided, single submitter	clinical testing	Observed in both affected and unaffected individuals in a family with erythrokeratodermia variabilis in published literature; affected patients also harbored a de novo variant on the same allele (in cis) (Richard et al., 2000); In-frame deletion of 4 amino acids in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 10798362)
Invitae	RCV000724547	SCV002144433	uncertain significance	not provided	2023-12-15	criteria provided, single submitter	clinical testing	This variant, c.652_663del, results in the deletion of 4 amino acid(s) of the GJB3 protein (p.Leu218_Asp221del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs768372993, gnomAD 0.1%). This variant has been observed in individual(s) with clinical features of autosomal dominant erythrokeratodermia variabilis (PMID: 10798362). This variant is also known as 652del12, ∆LHKD218-221. ClinVar contains an entry for this variant (Variation ID: 163536). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.