ClinVar Miner

Submissions for variant NM_004004.6(GJB2):c.101T>C (p.Met34Thr) (rs35887622)

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Total submissions: 30
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Hearing Loss Variant Curation Expert Panel RCV000211758 SCV000927015 pathogenic Nonsyndromic hearing loss and deafness 2019-06-24 reviewed by expert panel curation 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.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000844701 SCV000061472 pathogenic Rare genetic deafness 2011-06-10 criteria provided, single submitter clinical testing 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.
Genetic Services Laboratory, University of Chicago RCV000018523 SCV000193154 pathogenic Deafness, autosomal recessive 1A 2016-02-17 criteria provided, single submitter clinical testing
Molecular Otolaryngology and Renal Research Laboratories,University of Iowa Hospital and Clinics RCV000018523 SCV000264324 pathogenic Deafness, autosomal recessive 1A 2015-10-21 criteria provided, single submitter clinical testing 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.
PreventionGenetics,PreventionGenetics RCV000168670 SCV000309913 likely pathogenic not specified 2019-11-22 criteria provided, single submitter clinical testing
GeneDx RCV000080364 SCV000321726 pathogenic not provided 2018-12-11 criteria provided, single submitter clinical testing The M34T pathogenic variant in the GJB2 gene has been reported extensively in association with autosomal recessive non-syndromic sensorineural hearing loss (NSHL) and is associated with a milder severity and later onset of hearing loss compared to other reported pathogenic variants in the GJB2 gene (Wilcox et al., 2000; Houseman et al., 2001; Snoeckx et al., 2005). Heterozygous carriers of the M34T variant without another GJB2/GJB6 pathogenic variant are typically unaffected (Kenna et al., 2010). M34T is a common GJB2 variant especially in the European population, possibly with reduced penetrance (Pollak et al. 2007), as the variant is observed in 517/25,782 alleles (2.0%) from individuals of European Finnish ancestry, including multiple unrelated homozygous individuals, in large population cohorts (Lek et al., 2016). The M34T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Functional in vitro studies have supported pathogenicity of M34T (Kelsell et al. 1997; Martin et al., 1999; Bicego et al., 2006). Missense variants at the same codon (M34I/R/L/V) and in nearby residues (I30V/N, F31I, R32L/C/S, and others) have been reported in the Human Gene Mutation Database in association with hearing loss (Stenson et al., 2014), supporting the functional importance of this region of the protein. In summary, we interpret M34T as a pathogenic variant.
Illumina Clinical Services Laboratory,Illumina RCV000300311 SCV000383040 likely benign Mutilating keratoderma 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000487479 SCV000383041 likely benign Deafness, autosomal dominant 3a 2017-04-27 criteria provided, single submitter clinical testing 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.
Illumina Clinical Services Laboratory,Illumina RCV000260287 SCV000383042 likely benign Keratitis ichthyosis and deafness syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000018523 SCV000383043 likely pathogenic Deafness, autosomal recessive 1A 2017-06-12 criteria provided, single submitter clinical testing 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.
Illumina Clinical Services Laboratory,Illumina RCV000379337 SCV000383044 likely benign Hystrix-like ichthyosis with deafness 2017-04-27 criteria provided, single submitter clinical testing 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.
Knight Diagnostic Laboratories, Oregon Health and Sciences University RCV000018523 SCV000538034 likely pathogenic Deafness, autosomal recessive 1A 2016-03-14 criteria provided, single submitter clinical testing 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.
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia RCV000018523 SCV000599729 uncertain significance Deafness, autosomal recessive 1A 2017-05-09 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000168670 SCV000603813 pathogenic not specified 2018-08-31 criteria provided, single submitter clinical testing 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. 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. 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. 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. 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.
Integrated Genetics/Laboratory Corporation of America RCV000018523 SCV000698223 pathogenic Deafness, autosomal recessive 1A 2020-02-24 criteria provided, single submitter clinical testing 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.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000080364 SCV000700273 pathogenic not provided 2016-12-13 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000080364 SCV000841697 pathogenic not provided 2017-09-19 criteria provided, single submitter clinical testing
Invitae RCV000080364 SCV001105249 benign not provided 2019-12-31 criteria provided, single submitter clinical testing
Mendelics RCV000018523 SCV001138911 pathogenic Deafness, autosomal recessive 1A 2019-05-28 criteria provided, single submitter clinical testing
Baylor Genetics RCV001004397 SCV001163369 pathogenic Deafness, autosomal recessive 1A; Deafness, autosomal recessive 1b criteria provided, single submitter clinical testing
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV001027827 SCV001190447 pathogenic Deafness, autosomal recessive 1A; Mutilating keratoderma; Hystrix-like ichthyosis with deafness; Keratitis-ichthyosis-deafness syndrome, autosomal dominant; Palmoplantar keratoderma-deafness syndrome; Knuckle pads, deafness AND leukonychia syndrome; Deafness, autosomal dominant 3a 2019-11-14 criteria provided, single submitter clinical testing 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.
Myriad Women's Health, Inc. RCV000018523 SCV001194149 pathogenic Deafness, autosomal recessive 1A 2019-12-26 criteria provided, single submitter clinical testing 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.
Victorian Clinical Genetics Services,Murdoch Childrens Research Institute RCV000018523 SCV001244778 pathogenic Deafness, autosomal recessive 1A 2017-07-12 criteria provided, single submitter clinical testing 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.
UNC Molecular Genetics Laboratory,University of North Carolina at Chapel Hill RCV000018523 SCV001251549 pathogenic Deafness, autosomal recessive 1A criteria provided, single submitter research 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).
OMIM RCV000018523 SCV000038805 pathogenic Deafness, autosomal recessive 1A 2014-10-02 no assertion criteria provided literature only
GeneReviews RCV000018523 SCV000041038 pathologic Deafness, autosomal recessive 1A 2011-07-14 no assertion criteria provided curation Converted during submission to Pathogenic.
Division of Human Genetics,Children's Hospital of Philadelphia RCV000018523 SCV000238468 pathogenic Deafness, autosomal recessive 1A 2015-06-10 no assertion criteria provided research 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).
GeneReviews RCV000487479 SCV000574679 benign Deafness, autosomal dominant 3a 2016-12-22 no assertion criteria provided literature only
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital RCV000678866 SCV000805059 uncertain significance Hearing loss 2017-12-29 no assertion criteria provided clinical testing
GenomeConnect, ClinGen RCV000487479 SCV001423221 not provided Deafness, autosomal dominant 3a no assertion provided phenotyping only 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.

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