rs35887622

Description

This variant has required extensive investigation to determine its clinical significance. It does have high minor allele frequency in several populations (including 2.2% in the European Finnish population within ExAC). Conversely, there is significant literature evidence that this variant is pathogenic with a variable hearing phenotype.

The p.Met34Thr variant in GJB2 is well-established as a pathogenic variant. This variant, in homozygosity or in combination with another GJB2 variant, is common ly associated with mild to moderate hearing loss (Pollak 2007, Snoeckx 2005) and in rare cases, p.Met34Thr may even be associated with normal hearing. ACMG/AMP Criteria applied: PS4, PP1_Strong, PM3_VeryStrong.

PS1_Very strong, PS4_Strong, PM5_Moderate

The c.101T>C (p.Met34Thr) missense variant in the GJB2gene has been previously reported in numerous individuals with autosomal recessive Nonsyndromic hearing loss and has been shown to segregate with disease (Houseman et al., 2001; Bicego et al., 2006; Löppönen et al., 2012).This variant has been observed in trans with the well-characterized GJB2 c.35delG variant (Houseman et al., 2001; Bicego et al., 2006; Pollack et al., 2007). Multiple studies have shown this variant impairs proper assembly and function of the gap junction channel (Martin et al., 1999; D'Andrea et al., 2002; Bicego et al., 2006). The c.101T>C variant has been reported at low frequency in the three control population databases (Exome Sequencing Project [ESP], 1000 Genomes, and ExAC ); however, this variant has been observed as homozygous in 13 individuals in ExAC. Multiple lines of computational evidence predict a deleterious effect. In addition, multiple reputable diagnostic laboratories report this variant as pathogenic. Therefore, this collective evidence supports the classification of the c.101T>C (p.Met34Thr) as a recessive Likely Pathogenic variant for Nonsyndromic hearing loss.

The NM_004004.5(GJB2):c.101T>C missense variant was identified in exon 2of GJB2. This substitution is predicted to create a moderate amino acid change from a methionine to a threonine at amino acid position 34, NP_003995.2(GJB2):p.(Met34Thr). The methionine at this position has high conservation (100 vertebrates, UCSC). In silico software predictions of the pathogenicity of this variant are conflicting. It is situated in a transmembrane helix of theGJB2 protein. This variant has been observed in a population database at a frequency of 0.008% with 26 homozygotes observed (ExAC, GnomAD). However, this variant has been reported as a pathogenic variant in homozygous or compound heterozygous state, andbeen shown to segregate with disease in multiple families with hearing loss (ClinVar, Deafness variantion database, The connexin-deafness homepage). Based on current information and in association with the NM_004004.5(GJB2):c.550C>T variant, this variant has been classified as PATHOGENIC.

Variant summary: GJB2 c.101T>C (p.Met34Thr) results in a non-conservative amino acid change located in the Connexin, N-terminal (IPR013092) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0068 in 1604678 control chromosomes including 26 homozygotes. This frequency is not significantly higher than expected for a pathogenic variant in GJB2 causing Autosomal Recessive Non-Syndromic Hearing Loss, allowing no conclusion about variant significance. c.101T>C has been well reported in the literature in studies of individuals affected with hearing loss phenotypes (example, Houseman_2001 through Shen_2019). These data indicate that the variant is likely to be associated with disease. Many publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity measured as Cx26 hemichannel activated conductance following depolarization (example, Palmada_2006). Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation with conflicting assessments although a majority of these assessments support a pathogenic outcome. Furthermore, the ClinGen Hearing Loss Expert Panel has classified it as Pathogenic for autosomal recessive nonsyndromic hearing loss with variable expressivity and age-dependent penetrance (Shen_2019). Based on the evidence outlined above, the variant was classified as pathogenic.

NM_004004.5(GJB2):c.101T>C(M34T) is classified as pathogenic in the context of GJB2-related DFNB1 nonsyndromic hearing loss and deafness and is typically associated with bilateral mild to moderate hearing loss. Sources cited for classification include the following: PMID 10556284, 16849369, 15033936, 9716127, 23826813 and 16380907. Classification of NM_004004.5(GJB2):c.101T>C(M34T) 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.

The GJB2 pathogenic mild c.101T>C; p.Met34Thr variant (rs35887622) is reported in ClinVar (Variation ID: 17000), and observed in the Genome Aggregation Database with an overall allele frequency of 0.9 percent (2487/276420 alleles, including 26 homozygotes). This variant has been previously classified as benign based on population frequency data (Shearer 2014), and has been referred to as a variant with reduced penetrance (Feldmann 2004, Griffith 2000, Pollak 2007, Tang 2006). However, homozygosity for this variant has also been reported to co-segregate with mild to high frequency deafness (Hall 2012, Houseman 2001). Additionally, this variant has been to shown to have a variable phenotype within the same family (Lameiras 2015). Taken together, we consider this variant to be mildly pathogenic. References: Feldmann D et al. Clinical evidence of the nonpathogenic nature of the M34T variant in the connexin 26 gene. Eur J Hum Genet. 2004 Apr;12(4):279-84. PMID: 14694360. Griffith AJ et al. Autosomal recessive non-syndromic neurosensory deafness at DFNB1 not associated with the compound-heterozygous GJB2 (connexin 26) genotype M34T/167delT. Am J Hum Genet. 2000 Sep;67(3):745-9. PMID: 10903123. Pollak et al. M34T and V37I mutations in GJB2 associated hearing impairment: evidence for pathogenicity and reduced penetrance. Am J Med Genet A. 2007; 143A(21): 2534-2543. PMID: 17935238. Shearer AE et al. Utilizing ethnic-specific differences in minor allele frequency to recategorize reported pathogenic deafness variants. Am J Hum Genet. 2014 Oct 2;95(4):445-53. PMID: 25262649. Tang HY et al. DNA sequence analysis of GJB2, encoding connexin 26: observations from a population of hearing impaired cases and variable carrier rates, complex genotypes, and ethnic stratification of alleles among controls. Am J Med Genet A. 2006; 140(22): 2401-2415. PMID: 17041943.

Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: PS4, PP1_Strong, PM3, PP3.

This variant is one of the most common variants associated with autosomal recessive nonsyndromic hearing loss and is reported to have milder disease presentation and reduced penetrance in some families (PMID: 11134236, 16380907, 22668073). Therefore, the apparently high frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant is statistically more frequent in affected individuals than in the general population and/or healthy controls. Assessment of experimental evidence suggests this variant results in abnormal protein function. Experiments show this variant results in reduced cell to cell transfer of small molecules (PMID: 12176036, 12189493, 16300957, 16849369, 27884957). In multiple individuals, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic.

GJB2 NM_004004.5 exon 2 p.Met34Thr (c.101T>C): This variant has been reported in the literature in the homozygous or compound heterozygous state in several individuals with mild to severe nonsyndromic hearing loss, as well as in both affected and unaffected relatives, suggesting that this variant may have reduced penetrance or may act as a modifier of disease (Kelsell 1997 PMID:9139825, Houseman 2001 PMID:11134236, D'Andrea 2002 PMID:12176036, Feldmann 2004 PMID:14694360, Bicego 2006 PMID:16849369, Pollak 2007 PMID:17935238, Lopponen 2012 PMID:22668073, Lameiras 2015 PMID:26117665, Mikstiene 2016 PMID:26896187). This variant is also present in 2% (510/25108) of Finnish alleles in the Genome Aggregation Database, including 9 homozygotes (https://gnomad.broadinstitute.org/variant/13-20763620-A-G), which may indicate that it is a common variant or a risk allele in this population. This variant is also present in ClinVar, with classifications ranging from pathogenic to benign (Variation ID:17000). Evolutionary conservation and computational predictive tools for this variant are unclear. In vitro functional studies predict that this variant will lead to abnormal channel function (Martin 1999 PMID:10556284, D'Andrea 2002 PMID:12176036, Bicego 2006 PMID:16849369). However, at least one study did not demonstrate this (Oshima 2003 PMID:12384501). These studies may not accurately represent in vivo biological function. In summary, this variant is classified as pathogenic based on the data above.

The filtering allele frequency (the lower threshold of the 95% CI of 510/25108) of the c.101T>C (p.Met34Thr) variant in the GJB2 gene is 1.46% for European (non-Finnish) genomes in gnomAD. This is a high enough frequency that, in the absence of conflicting data, might warrant a benign classification based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1). However, based on the evidence outlined below, the ClinGen Hearing Loss Expert Panel believes that the evidence for the pathogenicity of this variant for nonsyndromic hearing loss outweighs its high allele frequency in population databases. Therefore, the BA1 code will not contribute to the overall classification. The homozygous genotype and compound heterozygous genotype with another variant in GJB2 have shown to be statistically enriched in patients with nonsyndromic sensorineural hearing loss compared to individuals representative of the general population in gnomAD and/or those who underwent carrier screening at Counsyl. (PS4; PMID: 31160754). This study also reported the variant in 27 homozygous affected probands, 17 affected probands with the p.Val37Ile variant in trans, 138 affected probands with a variant asserted to be P/LP in ClinVar, and 78 affected probands with a premature GJB2 termination codon in trans (PM3; PMID 31160754). The REVEL computational prediction analysis tool produced a score of 0.702, which is above the threshold necessary to apply PP3. Most dye transfer and electrical coupling assays support that the variant impacts protein function (PMID: 16849369, 12189493, 10556284, 16300957, 15033936, 12189493); however, some assays showed partial function (PMID: 27884957), and therefore this evidence was not counted. At least 16 segregations of the p.Met34Thr variant in family members have been described (PP1_Strong, PMID: 31160754, 10903123). Of note, the severity of hearing loss is known to be mild on average and there have been multiple accounts of incomplete penetrance of the variant in families/individuals with p.Met34Thr in a biallelic genotype. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive nonsyndromic genetic hearing lossbased on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PS4, PP1_Strong, PM3, PP3.

The GJB2 variant (c.101T>C; p.Met34Thr) was identified in several individuals with hearing loss and segregated in families with mild non-syndromic hearing loss (Lopponen et. al 2012; PMID 22668073) with functional studies supporting pathogenicity (Kelsell et al. 1997, PMID 9139825; Martin et al. 1999, PMID 10556284, Lopponen et. al 2012; PMID 22668073 and Shearer et al. 2014, PMID 2562649). However, this variant is quite prevalent in control databases (1049 alleles out of 122876 and 13 homozygotes in ExAC) and could be associated with reduced penetrance. Other clinical laboratories have classified this variant as pathogenic (SCV000061472 and SCV000112260) and variant of uncertain significance (SCV000193154).

Across a selection of literature, the GJB2 c.101T>C (p.Met34Thr) missense variant has been identified in at least 119 patients with an autosomal recessive form of nonsyndromic hearing loss. The variant was found in a homozygous state in 35 patients, in a compound heterozygous state in 66 patients (at least 59 of whom had a pathogenic deletion), and in a heterozygous state in 18 patients (Houseman et al, 2001; Feldmann et al. 2004; Snoeckx et al. 2005; Tang et al. 2006; Pollak et al. 2007; Löppönen et al. 2012; Dória et al. 2015; Mikstiene et al. 2016). This variant is generally associated with mild to moderate nonsyndromic hearing loss, and segregation was observed in a three-generation family (Löppönen et al. 2012). The p.Met34Thr variant was detected in 66 of 5380 control chromosomes mainly in a heterozygous state, and also in family members with normal audiograms, including in two with the variant in a homozygous state, in five with the variant in a compound heterozygous state, and in 23 with the variant in a heterozygous state (Feldmann et al. 2004; Löppönen et al. 2012). This conflicting evidence may be due to reduced penetrance, estimated at 10% in one study (Pollak et al. 2007), presence of other modifying factors (Houseman et al, 2001; Bicego et al. 2006), or due to an age-dependent effect (Pollak et al. 2007). Dória et al. (2015) suggest this variant may be a risk factor for nonsyndromic hearing loss. Functional studies suggest this variant affects intercellular channels based on dye transfer assays in transiently transfected HeLa cells (D'Andrea et al. 2002; Bicego et al. 2006), although at least one study did not observe this (Oshima et al. 2003). In addition, electrical conductance was decreased to 11% of wildtype in the presence of the p.Met34Thr variant (Bicego et al. 2006). The p.Met34Thr variant is reported at a frequency of 0.03535 in the Finnish population of the 1000 Genomes Project. Based on the evidence, the p.Met34Thr variant is classified as likely pathogenic for recessive nonsyndromic hearing loss. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The GJB2 p.M34T variant was identified in the literature in multiple individuals with by hearing loss, and is reported as a pathogenic variant for autosomal recessive nonsyndromic hearing loss with variable expressitivity and incomplete penetrance by the ClinGen Hearing Loss Expert Panel (Coco_2013_PMID_24611097; Doria_2015; Shen_2019_PMID_31160754). The variant was also found to segregate with disease in two Portuguese compound heterozygote siblings, although the siblings exhibited different phenotypes as one exhibited profound hearing loss, while the other sibling only had moderate hearing loss (Lameiras_2015_PMID_26117665). The variant was identified in dbSNP (ID: rs35887622) and ClinVar (classified as pathogenic by ClinGen Hearing Loss Variant Curation Expert Panel for Nonsyndromic hearing loss and deafness and 11 laboratories, as likely pathogenic by Knight Diagnostic Laboratories, as uncertain significance by Johns Hopkins and Division of Human Genetics, Children's Hospital of Philadelphia, as likely benign by Prevention Genetics, and as benign by Invitae). The variant was identified in control databases in 2538 of 282130 chromosomes (28 homozygous) at a frequency of 0.008996 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (Finnish) in 510 of 25108 chromosomes (freq: 0.02031), European (non-Finnish) in 1655 of 128490 chromosomes (freq: 0.01288), Other in 65 of 7214 chromosomes (freq: 0.00901), Ashkenazi Jewish in 82 of 10358 chromosomes (freq: 0.007917), Latino in 163 of 35426 chromosomes (freq: 0.004601) and African in 63 of 24968 chromosomes (freq: 0.002523), but was not observed in the East Asian or South Asian populations. The p.M34 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. Functional studies suggest that this variant alters gap junction function in Xenopus oocytes and mammalian cells (White_1998; Skerrett_2004_PMID_ 15033936; Martin_1999_PMID_ 10556284; Thonnissen_2002_PMID_ 12189493; Bicego_2006_PMID_ 16849369; Zonta_2014_PMID_ 24624091; D’Andrea_2002_PMID_ 12176036). In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

This variant was identified in compound heterozygosity with a second variant in GJB2 in a male patient with congenital bilateral moderate hearing loss.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

Case control studies suggest this variant is associated with hearing loss (Shen et al., 2019); homozygotes and compound heterozygotes with another GJB2 variant were statistically enriched in patients with autosomal recessive nonsyndromic hearing loss compared to the general population; Published in vitro functional studies support pathogenicity of the variant (Kelsell et al. 1997; Martin et al., 1999; Bicego et al., 2006), and in silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Classified as pathogenic by the ClinGen Hearing Loss Expert Panel, and noted to show variable expressivity and incomplete penetrance (SCV000927015.1; Landrum et al., 2016; Shen et al., 2019); This variant is associated with the following publications: (PMID: 31160754, 20083784, 23826813, 10903123, 16380907, 31980526, 31827275, 30344259, 31163360, 29773520, 30609409, 10830906, 9139825, 22855627, 25388846, 9600457, 17426645, 10888284, 22567861, 17935238, 27153395, 25262649, 11134236, 26896187, 26117665, 9716127, 20668687, 16300957, 12384501, 12189493, 16849369, 10556284, 11216656, 22995991, 22975760, 14694360, 10757647, 25214170, 15070423, 12176036, 21465647, 22668073, 30094485)

The GJB2 c.101T>C (p.M34T) variant has been reported as a mild (hypomorphic) variant that leads to mild to moderate hearing loss when found in the homozygous state or in trans with a more severe pathogenic GJB2 variant (PMID: 22668073; 11134236; 20708129; 17935238).

This variant was identified as compound heterozygous with NM_004004.6:c.35del:

Variant interpretted as Pathogenic and reported on 02-12-2019 by Lab or GTR ID 26957. 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.