NM_004004.6(GJB2):c.35del (p.Gly12fs) AND Autosomal recessive nonsyndromic hearing loss 1A
- Germline classification:
- Pathogenic (32 submissions)
- Last evaluated:
- Jul 23, 2024
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000018527.99
Allele description [Variation Report for NM_004004.6(GJB2):c.35del (p.Gly12fs)]
NM_004004.6(GJB2):c.35del (p.Gly12fs)
- Gene:
- GJB2:gap junction protein beta 2 [Gene - OMIM - HGNC]
- Variant type:
- Deletion
- Cytogenetic location:
- 13q12.11
- Genomic location:
- Preferred name:
- NM_004004.6(GJB2):c.35del (p.Gly12fs)
- Other names:
- NM_004004.5(GJB2):c.35delG(p.Gly12Valfs); NM_004004.5(GJB2):c.35delG
- HGVS:
- NC_000013.11:g.20189552del
- NG_008358.1:g.8429del
- NM_004004.6:c.35delMANE SELECT
- NP_003995.2:p.Gly12fs
- LRG_1350t1:c.35del
- LRG_1350:g.8429del
- LRG_1350p1:p.Gly12fs
- NC_000013.10:g.20763686del
- NC_000013.10:g.20763686delC
- NC_000013.10:g.20763686delC
- NC_000013.10:g.20763691del
- NC_000013.10:g.20763691del
- NC_000013.10:g.20763691delC
- NC_000013.11:g.20189547delC
- NM_004004.5:c.35delG
- NM_004004.6:c.35delGMANE SELECT
- c.35delG
- c.35delG (p.Gly12Valfs*2)
- p.(Gly12Valfs*2)
- p.Gly12Valfs*2
- p.Gly12ValfsX2
- p.Gly12fs
This HGVS expression did not pass validation- Protein change:
- G12fs
- Links:
- OMIM: 121011.0005; dbSNP: rs80338939
- NCBI 1000 Genomes Browser:
- rs80338939
- Observations:
- 14
Condition(s)
- Name:
- Autosomal recessive nonsyndromic hearing loss 1A (DFNB1A)
- Synonyms:
- Deafness nonsyndromic, Connexin 26 linked; Deafness, autosomal recessive 1A; DFNB 1 Nonsyndromic Hearing Loss and Deafness; See all synonyms [MedGen]
- Identifiers:
- MONDO: MONDO:0009076; MedGen: C2673759; Orphanet: 90636; OMIM: 220290
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000038809 | OMIM | no assertion criteria provided | Pathogenic (Oct 5, 2012) | germline | literature only | PubMed (33) |
SCV000041047 | GeneReviews | no classification provided | not provided | unknown | literature only | PubMed (31) |
SCV000223930 | Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 14, 2016) | germline | clinical testing | |
SCV000238466 | Division of Human Genetics, Children's Hospital of Philadelphia - CSER-PediSeq | no assertion criteria provided | Pathogenic (Mar 20, 2015) | maternal | research | |
SCV000698250 | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) | Pathogenic (Aug 8, 2017) | germline | clinical testing | PubMed (7) LabCorp Variant Classification Summary - May 2015.docx, |
SCV000746336 | Genomic Research Center, Shahid Beheshti University of Medical Sciences | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Aug 7, 2018) | inherited | clinical testing | |
SCV000902318 | Genetic Testing Center for Deafness, Department of Otolaryngology Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital | no assertion criteria provided | Pathogenic (Feb 26, 2019) | inherited | case-control | |
SCV000915629 | Illumina Laboratory Services, Illumina | criteria provided, single submitter (ICSL Variant Classification Criteria 09 May 2019) | Pathogenic (Dec 4, 2018) | germline | clinical testing | |
SCV000928370 | Laboratory of Medical Genetics, National & Kapodistrian University of Athens | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jun 26, 2018) | germline | clinical testing | |
SCV001138912 | Mendelics | criteria provided, single submitter (Mendelics Assertion Criteria 2017) | Pathogenic (May 28, 2019) | unknown | clinical testing | |
SCV001149786 | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | criteria provided, single submitter (Classification criteria August 2017) | Pathogenic (Sep 28, 2018) | inherited, germline | clinical testing | |
SCV001193910 | Myriad Genetics, Inc. | criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019)) | Pathogenic (Oct 18, 2019) | unknown | clinical testing | |
SCV001244783 | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jun 20, 2017) | unknown | clinical testing | |
SCV001251502 | UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill - NSIGHT-NC NEXUS | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | germline | research | |
SCV001429469 | Institute of Human Genetics, University of Leipzig Medical Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jul 23, 2024) | unknown | clinical testing | |
SCV001455333 | Natera, Inc. | no assertion criteria provided | Pathogenic (Sep 16, 2020) | germline | clinical testing | |
SCV001593117 | Genome-Nilou Lab | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 19, 2021) | germline | clinical testing | |
SCV001745839 | Center of Genomic medicine, Geneva, University Hospital of Geneva | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Nov 8, 2018) | inherited | clinical testing | |
SCV001985050 | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Oct 28, 2021) | unknown | clinical testing | |
SCV002058591 | 3billion | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 3, 2022) | germline | clinical testing | PubMed (1) PMID:12176036, |
SCV002515328 | Daryl Scott Lab, Baylor College of Medicine | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Feb 1, 2022) | biparental | clinical testing | |
SCV002580972 | MGZ Medical Genetics Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jul 18, 2022) | germline | clinical testing | |
SCV003807233 | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 10, 2023) | germline | clinical testing | |
SCV003926558 | UAEU Genomics Laboratory, United Arab Emirates University | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 23, 2022) | germline | research | |
SCV003932690 | Clinical Genetics Laboratory, Skane University Hospital Lund | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jul 18, 2024) | germline | clinical testing | |
SCV003935282 | Integrating Genomics into Medicine, Frazer Institute, University Of Queensland | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jun 2, 2023) | germline | clinical testing | |
SCV004171600 | Zotz-Klimas Genetics Lab, MVZ Zotz Klimas | no assertion criteria provided | Pathogenic (Nov 24, 2023) | germline | clinical testing | |
SCV004175439 | Genetics and Molecular Pathology, SA Pathology
| criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (May 11, 2023) | germline | clinical testing | |
SCV004231802 | Clinical Genomics Laboratory, Stanford Medicine | no assertion criteria provided | Pathogenic (Jun 24, 2021) | germline | clinical testing | |
SCV004806830 | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 26, 2024) | germline | clinical testing | |
SCV005049570 | Diagnostics Centre, Carl Von Ossietzky University Oldenburg | no assertion criteria provided | Pathogenic (Nov 8, 2023) | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | biparental | yes | 1 | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | no | 35 | not provided | not provided | not provided | not provided | clinical testing |
not provided | maternal | yes | not provided | not provided | not provided | not provided | not provided | research |
not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
not provided | unknown | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
not provided | germline | yes | 130 | not provided | not provided | 3 | not provided | clinical testing, research |
not provided | inherited | yes | 7 | 1 | not provided | 1 | yes | clinical testing, case-control |
not provided | unknown | yes | 13 | 13 | not provided | not provided | not provided | clinical testing |
not provided | unknown | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
Persian | germline | yes | 1 | not provided | not provided | not provided | not provided | clinical testing |
Citations
PubMed
Connexin 26 gene linked to a dominant deafness.
Denoyelle F, Lina-Granade G, Plauchu H, Bruzzone R, Chaïb H, Lévi-Acobas F, Weil D, Petit C.
Nature. 1998 May 28;393(6683):319-20. No abstract available.
- PMID:
- 9620796
de Zwart-Storm EA, Hamm H, Stoevesandt J, Steijlen PM, Martin PE, van Geel M, van Steensel MA.
J Med Genet. 2008 Mar;45(3):161-6. Epub 2007 Nov 9.
- PMID:
- 17993581
Details of each submission
From OMIM, SCV000038809.5
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (33) |
Description
A mutation consisting of deletion of 1 guanine (G) in a run of 6 guanines extending from position 30 to position 35 in the GJB2 gene has been observed by several groups. Some referred to the deleted nucleotide as 30G (the first of the 6 Gs), whereas others referred to it as 35G. The second mutation found by Carrasquillo et al. (1997) to be responsible for nonsyndromic recessive deafness (DFNB1A; 220290) in a Muslim-Israeli village in the lower Galilee was a deletion of a guanine residue at cDNA position 35 (35delG), causing a frameshift of the coding sequence leading to premature chain termination at the twelfth amino acid. The mutation was on a different haplotype from the W77R mutation (121011.0004). Zelante et al. (1997) found a very high frequency of the 35delG mutation in Spanish, Italian, and Israeli autosomal recessive neurosensory deafness patients, in whom it accounted for approximately 50% of cases. This might be interpreted as evidence for an ancient deletion mutation that had spread in Europe and Middle-East; however, the mutation identified in the inbred group by Carrasquillo et al. (1997) was shown by haplotype analysis to be of recent origin and on different haplotypes from those identified by Zelante et al. (1997). Thus, these mutations are all likely different, independent and recurrent, and arise due to the run of Gs being a mutation hotspot. Haplotype analysis of 35delG mutations in different populations can be used to address this question definitively.
Denoyelle et al. (1997) found that the 30delG mutation accounted for approximately 70% of CX26 mutant alleles in a study of 65 Caucasian families with prelingual deafness originating from various countries. The high frequency of this mutation may recommend it for genetic counseling in families with a single deaf child. Denoyelle et al. (1997) made the significant observation that only moderate hearing loss was found in some individuals homozygous for the 30delG mutation.
Among 82 families from Italy and Spain with recessive nonsyndromic deafness and 54 unrelated individuals with apparently sporadic congenital deafness, Estivill et al. (1998) found mutations in the GJB2 gene in 49% of participants with recessive deafness and 37% of sporadic cases. The 35delG mutation accounted for 85% of GJB2 mutations, and 6 other mutations accounted for 6% of alleles; no changes in the coding region of GJD2 were detected in 9% of DFNB1 alleles. The carrier frequency of the 35delG mutation in the general population was 1 in 31 (95% CI, 1 in 19 to 1 in 87).
Morell et al. (1998) found a prevalence of 0.73% for heterozygosity for the 30delG mutation in Ashkenazi Jews. Audiologic examination of carriers of the mutant allele who had normal hearing showed subtle differences in their otoacoustic emissions, suggesting that the expression of mutations in GJB2 may be semidominant.
Reporting from Iowa, Green et al. (1999) found that of 52 sequential probands referred for congenital sensorineural hearing loss, 22 (42%) were found to have GJB2 mutations. They identified the 35delG mutation in 29 of the 41 mutant alleles. Of the probands' sibs, all homozygotes and compound heterozygotes had deafness. They found 35delG heterozygosity in 14 of 560 controls, for a carrier rate of 2.5%. The carrier rate for all recessive deafness-causing GJB2 mutations was determined to be 3.01%. Calculated sensitivity and specificity values for a screening test based on the 35delG mutation alone were 96.9% and 97.4%, respectively, and observed values were 94% and 97%, respectively.
Antoniadi et al. (1999) analyzed 395 voluntary healthy Greek blood donors for the 35delG mutation of the GJB2 gene. They detected 14 heterozygotes, giving a carrier frequency of 3.5% in the Greek population. With an incidence of prelingual deafness of about 1 in 1,000 children, homozygosity for the 35delG mutation should account for about 30% of all cases. The discovery of this very common mutation in the most common form of genetic hearing loss should enable easy DNA diagnosis, carrier detection, and prenatal diagnosis.
Because of the high frequency of carriers of the 35delG mutation in the Greek population reported by Antoniadi et al. (1999), it is perhaps not surprising that pseudodominant inheritance was observed in 2 families reported by Pampanos et al. (2000).
In a study of 35 Japanese families with bilateral sensorineural hearing loss, Abe et al. (2000) found no individuals with this mutation. In addition, they found a high prevalence of a novel frameshift mutation (121011.0014) in these families.
Kudo et al. (2000) found no cases of the 30delG allele among 39 Japanese patients with prelingual deafness.
Gasparini et al. (2000) analyzed the 35delG mutation in 3,270 random controls from 17 European countries. They detected a carrier frequency of 1 in 35 in southern Europe and 1 in 79 in central and northern Europe. In addition, 35delG was detected in 5 of 376 Jewish subjects of different origins, but was absent in other non-European populations.
In a study of 560 persons from 5 ethnic groups of Russia, Anichkina et al. (2001) found the 35delG mutation in 12 chromosomes, giving a carrier frequency of 1 in 47. These results demonstrated that the 35delG mutation is present not only in western but also in eastern European (Finno-Ugric and Turkic) populations.
In a study of 76 Austrian patients with sensorineural hearing loss, Loffler et al. (2001) found that the 35delG mutation accounted for 65.4% of GJB2 mutant alleles among 13 patients with biallelic GJB2 mutations. A 35delG carrier frequency of 1 in 112 (0.9%) was observed among 672 blood donors from Tirol (West-Austria).
Van Laer et al. (2001) studied 35 Belgian, 30 British, and 49 American patients with nonsyndromic hearing impairment who were homozygous for the 35delG mutation and 70 Belgian, 30 British, and 50 American normal hearing controls. Four single-nucleotide polymorphisms mapped in the immediate vicinity of the GJB2 gene, and 2 positioned some distance from it were analyzed. Significant differences between the genotypes of patients and controls for the 5 SNPs closest to the GJB2 gene were found, with nearly complete association of 1 SNP allele with the 35delG mutation. Van Laer et al. (2001) concluded that the 35delG mutation is derived from a common, albeit ancient, founder.
Oliveira et al. (2002) added Brazil to the countries in which the 35delG mutation is a frequent cause of deafness.
In a study in Italy of 179 patients with hearing loss, Gualandi et al. (2002) found that the 35delG mutation accounted for 22.1% of analyzed chromosomes in sporadic cases and 39.4% in familial cases; 35delG prevalence reached 41% in autosomal recessive and 44.4% in pseudodominant pedigrees. In a high proportion of 35delG heterozygous hearing loss patients (52%), no second GJB2 mutation was detected.
D'Andrea et al. (2002) showed that the 35delG mutation, which they identified in almost 90% of an affected Italian population, resulted in no CX26 expression following transient transfection in HeLa cells. Furthermore, there was no dye transfer between clusters of cells expressing this mutation.
De Brouwer et al. (2003) performed a genetic analysis of a large consanguineous family that was previously described by Marres and Cremers (1989). Patients in 1 branch of the family were homozygous for the 35delG mutation in the GJB2 gene, whereas patients in 2 other branches carried mutations in the CDH23 gene (605516.0008-605516.0009) causing DFNB12 (601386).
Del Castillo et al. (2002) reported 2 Spanish individuals with severe hearing loss who were found to be compound heterozygous for the 35delG mutation and a 309-kb deletion in the GJB6 gene (604418.0004), consistent with digenic inheritance (see 220290). The GJB6 deletion truncating the GJB6 gene was shown to be the accompanying mutation in approximately 50% of deaf GJB2 heterozygotes in a cohort of Spanish patients, thus becoming second only to 35delG at GJB2 as the most frequent mutation causing prelingual hearing impairment in Spain.
Rothrock et al. (2003) presented evidence that the 35delG mutation arose in European and Middle Eastern populations from a single mutational event on a founder chromosome. They felt that the high frequency does not represent a mutation hotspot. They found the same, relatively rare, polymorphism associated with the 35delG mutation immediately upstream of the first exon of GJB2 in all populations studied including those in Italy, Brazil, and North America.
Salvinelli et al. (2003) reported a low frequency of the 35delG mutation in Sicilians with hearing loss, whereas it had previously been reported to be responsible for most nonsyndromic recessive deafness in American and European populations. Only 5 of 53 probands with familial deafness were homozygous for 35delG; another 5 were heterozygous for 35delG and 2 more were compound heterozygous for 35delG and 167delT (121011.0010).
Lucotte and Pinna (2003) reported a frequency of 35delG heterozygotes of 3.35% in Corsica. This value was lower than that in continental Italy but similar to values reported for Sardinia and for Greece.
Alvarez et al. (2005) screened the GJB2 gene in 34 Spanish Romani (gypsy) families with autosomal recessive nonsyndromic hearing loss and found mutations in 50%. The predominant allele was W24X (121011.0003), accounting for 79% of DFNB1 alleles; 35delG was the second most common allele (17%).
Wilch et al. (2006) described a large kindred of German descent in which they found a novel allele of the GJB2 gene that segregated with deafness when present in trans with the 35delG allele of GJB2. Qualitative PCR-based allele-specific expression assays showed that expression of both GJB2 and GJB6 from the novel allele was dramatically reduced. The findings suggested possible coregulation of GJB2 and GJB6, which are closely situated on 13q. The DFNB1 locus (220290) encompasses GJB2 and GJB6. The 2 genes lie within 30 kb of each other and their products are coexpressed in the cochlea. Wilch et al. (2010) reported follow-up of the family reported by Wilch et al. (2006) in which 4 deaf individuals were heterozygous for the 35delG allele. Array CGH of these patients identified a common 131.4-kb deletion on chromosome 13 that was carried in trans with the 35delG mutation. The deletion was not found in 160 control individuals or in 528 patients with hearing loss and a heterozygous GJB2 or GJB6 mutation. The proximal breakpoint of the deletion lies more than 100 kb upstream of the transcriptional start sites of GJB2 and GJB6, leaving both of those genes intact. Wilch et al. (2010) suggested that the deleted region contains a distant cis-regulatory region that controls GJB2 and GJB6 expression.
Lezirovitz et al. (2006) identified a homozygous 35delG mutation in the GJB2 gene in 2 Brazilian sibs with profound congenital sensorineural deafness. A third sib with a milder form of progressive hearing loss beginning in childhood was also homozygous for the mutation, suggesting phenotypic variability. One of the sibs with profound deafness also had oculocutaneous albinism type IV (OCA4; 606574) caused by a homozygous mutation in the MATP gene (606202.0009). Lezirovitz et al. (2006) concluded that congenital deafness and oculocutaneous albinism due to mutations in 2 different genes as seen in their Brazilian family suggested a similar coincident inheritance of 2 separate recessive disorders in the Sephardic family reported by Ziprkowski and Adam (1964) (see 220900).
By haplotype analysis of 60 unrelated Greek individuals homozygous for the 35delG mutation and 60 Greek hearing controls, Kokotas et al. (2008) found evidence that the mutation was due to a common founder effect. The mutation was estimated to have occurred about 700 generations or approximately 14,000 years ago.
Hilgert et al. (2009) noted that the hearing loss associated with homozygosity for the 35delG mutation shows marked phenotypic variability, ranging from mild to profound. A genomewide association study of 255 individuals homozygous for 35delG, followed by a replication study of 297 samples, yielded 9 SNPs that showed significant association with mild/moderate hearing loss compared to profound hearing loss (p values between 3 x 10(-3) and 1 x 10(-4)). Although these SNPs may reflect a small modifying effect on the phenotype, Hilgert et al. (2009) concluded that the overall results suggested that the phenotypic variability in this subset of patients cannot be explained by the effect of 1 major modifier gene.
Ammar-Khodja et al. (2009) found that the 35delG mutation was the most common mutant allele in deaf individuals in Algeria, representing 76% of mutant alleles at the DFNB1 locus identified in 25 families. Fifteen families with nonsyndromic deafness were homozygous for this mutation, 2 were compound heterozygous for 35delG and another pathogenic mutation in the GJB2 gene, and 3 were heterozygous for the 35delG mutation. One patient who was heterozygous for the mutation was found to have Usher syndrome (276900) due to a homozygous mutation in the MYO7A gene (276903).
Among 1,510 Schmiedeleut (S-leut) Hutterites from the United States, Chong et al. (2012) found 54 heterozygotes and no homozygotes for the 35delG mutation in the GJB2 gene, for a frequency of 0.036, or 1 in 28. The population frequency of this allele in other populations is about 1 in 40 (Kenneson et al., 2002).
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From GeneReviews, SCV000041047.3
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (31) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | not provided | not provided | not provided | Assert pathogenicity | not provided | not provided | not provided | not provided |
From Knight Diagnostic Laboratories, Oregon Health and Sciences University - CSER-NextGen, SCV000223930.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
The c.35delG (p.Gly12Valfs*2) frameshift variant introduces a premature stop codon, leading to the truncation of the Connexin 26 protein. The c.35delG variant represents the most common pathogenic variant in Caucasian patients with genetic sensorineural deafness (Carrasquillo et al. 1997; Denoyelle et al. 1997; Zelante et al. 1997; Green et al. 1999; Gasparini et al. 2000; Kenneson et al. 2002; Bouwer et al. 2007). Therefore, this collective evidence supports the classification of the c.35delG (p.Gly12Valfs*2) as a Pathogenic variant for Nonsyndromic hearing loss.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | no | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Division of Human Genetics, Children's Hospital of Philadelphia - CSER-PediSeq, SCV000238466.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | PubMed (9) |
Description
The GJB2 variant (c.35delG, p.Gly12Valfs*2) identified in this patient is a frameshift variant, reported to be the most common pathogenic variant in individuals with European ancestry (Carrasquillo et al. 1997, PMID: 9328482; Denoyelle et al. 1997, PMID: 9336442; Zelante et al. 1997, PMID: 9285800; Green et al. 1999, PMID: 10376574; Gasparini et al. 2000, PMID: 10713883; Kenneson et al. 2002, PMID: 12172392; Bouwer et al. 2007, PMID: 18294064).
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | maternal | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, SCV000599723.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 104 | not provided | not provided | clinical testing | not provided |
2 | not provided | 35 | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 104 | not provided | not provided | not provided | |
2 | germline | no | not provided | not provided | not provided | 35 | not provided | not provided | not provided |
From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698250.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (7) |
Description
Variant summary: The GJB2 c.35delG (p.Gly12Valfs) variant results in a premature termination codon, predicted to cause a truncated or absent GJB2 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (e.g., c.71G>A [p.Trp24X], c.131G>A [p.Trp44X], and c.167delT [p.Leu56fs). This variant was found in 733/122042 control chromosomes (3 homozygotes) including ExAC at a frequency of 0.0060061, which does not exceed the estimated maximal expected allele frequency of a pathogenic GJB2 variant (0.025). This variant is known to be the most common pathogenic GJB2 variant worldwide that causes autosomal recessive nonsyndromic hearing loss. Immunochemistry studies showed that the variant does not produce detectable protein and prevents normal intercellular molecular transfer (D'Andrea_BBRC_2002). Multiple clinical diagnostic laboratories/reputable databases have classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000746336.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 3 | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | inherited | yes | not provided | not provided | not provided | 3 | not provided | not provided | not provided |
From Genetic Testing Center for Deafness, Department of Otolaryngology Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, SCV000902318.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | yes | case-control | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | inherited | yes | not provided | not provided | not provided | 1 | not provided | 1 | not provided |
From Illumina Laboratory Services, Illumina, SCV000915629.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (5) |
Description
The GJB2 c.35delG (p.Gly12ValfsTer2) variant, which results in a frameshift and is predicted to result in premature termination of the protein, is one of the most common variants associated with the recessive form of nonsyndromic hearing loss, DFNB1, with more than half of all persons of northern European ancestry with two identifiable GJB2 mutations being homozygous for this variant (Scott et al. 1998). Across a small selection of the available literature, the p.Gly12ValfsTer2 variant has been identified in a homozygous state in 89 individuals with hearing loss, in a compound heterozygous state in 23 affected individuals, and in a heterozygous state in 11 affected individuals in whom a second variant was not identified (Zelante et al. 1997; Estivill et al. 1998; Murgia et al. 1999; Snoeckx et al. 2005). The p.Gly12ValfsTer2 variant was identified in a total of ten of 800 control chromosomes and is reported at a frequency of 0.0152 in the Utah residents with Northern and Western European ancestry population of the 1000 Genomes Project which is consistent with the carrier frequency for p.Gly12ValfsTer2 (Snoeckx et al. 2005). Based on the potential impact of frameshift variants and the evidence from the literature the p.Gly12ValfsTer2 variant is classified as pathogenic for recessive nonsyndromic hearing loss. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV000928370.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
PVS1, PS3, PM1, PP5
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Mendelics, SCV001138912.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV001149786.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | not provided |
2 | not provided | 1 | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | inherited | yes | 1 | blood | not provided | 1 | not provided | not provided | not provided | |
2 | germline | yes | 1 | blood | not provided | 1 | not provided | not provided | not provided |
From Myriad Genetics, Inc., SCV001193910.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (5) |
Description
NM_004004.5(GJB2):c.35delG(aka p.G12Vfs*2) is classified as pathogenic in the context of GJB2-related DFNB1 nonsyndromic hearing loss and deafness. Sources cited for classification include the following: PMID 12176036, 24158611, 19371219, 15967879, 16380907. Classification of NM_004004.5(GJB2):c.35delG(aka p.G12Vfs*2) is based on the following criteria: The variant causes a premature termination codon that is not expected to be targeted by nonsense-mediated mRNA decay; however, literature evidence strongly supports pathogenicity. Please note: this variant was assessed in the context of healthy population screening.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV001244783.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 13 | not provided | not provided | clinical testing | PubMed (1) |
Description
A homozygous deletion variant was identified, NM_004004.5(GJB2):c.35delG in exon 2 of the GJB2 gene.This deletion creates a frameshift from amino acid position 12, introducing a stop codon 2 residues downstream, NP_003995.2(GJB2):p.(Gly12Valfs*2). This results in loss of protein function through truncation (majority of the protein).This variant is present in the gnomAD population database at a frequency of 0.6%. It has been previously reported to be the most common pathogenic variant in deaf individuals with European ancestry (ClinVar). In addition, other truncating variants downstream of c.35delG in GJB2 have been reported as pathogenic in individuals with deafness (ClinVar). Based on current information, this variant has been classified as PATHOGENIC.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | 13 | not provided | 13 | not provided |
From UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill - NSIGHT-NC NEXUS, SCV001251502.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 2 | not provided | not provided | research | PubMed (6) |
Description
The GJB2 c.35delG (p.G12fs) frameshift variant is reported as the most common pathogenic variant associated with autosomal recessive nonsyndromic hearing loss (PMID: 9285800; 9328482; 9819448; 12176036; 20301449).
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 2 | not provided | not provided | not provided |
From Institute of Human Genetics, University of Leipzig Medical Center, SCV001429469.9
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
Criteria applied: PVS1,PM3_VSTR,PS4
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Natera, Inc., SCV001455333.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Genome-Nilou Lab, SCV001593117.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | Persian | 1 | not provided | not provided | clinical testing | PubMed (1) |
Description
We found this variant in a patient with hearing impairment in a homozygous state.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Center of Genomic medicine, Geneva, University Hospital of Geneva, SCV001745839.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 2 | not provided | not provided | clinical testing | PubMed (1) |
Description
This variant was identified in compound heterozygosity with a second variant in GJB2 in 2 different male patients with congenital bilateral moderate hearing loss.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | inherited | yes | not provided | not provided | not provided | 2 | not provided | not provided | not provided |
From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne, SCV001985050.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From 3billion, SCV002058591.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
Description
Frameshift: predicted to result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated region (PVS1_S). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 12176036, PS3_S). The variant has been observed in multiple (>3) similarly affected unrelated individuals(PMID: 25999548, 26969326, PS4_S). The variant has been reported multiple times as an established pathogenic/likely pathogenic variant (ClinVar ID: VCV000017004, PMID:9285800, 3billion dataset). The same variant was previously reported several times in trans with another pathogenic variant in this gene (PMID: 26445815, PM3_VS). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided |
From Daryl Scott Lab, Baylor College of Medicine, SCV002515328.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (2) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | biparental | yes | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From MGZ Medical Genetics Center, SCV002580972.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 17 | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 17 | not provided | not provided | not provided |
From Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein, SCV003807233.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
Description
ACMG classification criteria: PVS1 very strong, PS4 strong, PM3 very strong
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided |
From UAEU Genomics Laboratory, United Arab Emirates University, SCV003926558.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | research | PubMed (10) |
Description
The frameshift deletion NM_004004.6(GJB2):c.35delG (p.Gly12Valfs*2) is reported to be the most common pathogenic variant in GJB2 associated with Autosomal Recessive Deafness 1A (DFNB1A) across different ethnic groups and reported in homozygous and compound heterozygous states (PubMed: 9285800, 10422812, 10713883, 11313751, 11483639, 26445815). This variant has been curated as Pathogenic by ClinGen hearing loss Expert panel members (PMID: 30311386). Though this variant is observed in 1027/111668 (0.92%) alleles in the gnomAD database, studies suggests that the carrier frequency of this variant can reach up to 2%-4% (PMID: 16380907). The p.Gly12Valfs*2 variant is predicted to cause loss of normal protein function through protein truncation caused a frameshift mutation. Published in vitro functional studies demonstrated that the variation leads to the absence of functional protein and activity (PubMed: 12176036). For these reasons, this variant has been classified as Pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV003932690.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
PVS1, PM3_VS, PS4
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Integrating Genomics into Medicine, Frazer Institute, University Of Queensland, SCV003935282.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Zotz-Klimas Genetics Lab, MVZ Zotz Klimas, SCV004171600.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Genetics and Molecular Pathology, SA Pathology, SCV004175439.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Clinical Genomics Laboratory, Stanford Medicine, SCV004231802.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | 1 | not provided | not provided | clinical testing | not provided |
Description
The p.Gly12Valfs*2 variant in the GJB2 gene is a well reported cause of nonsyndromic hearing loss. This variant was determined to be in trans with other pathogenic variants (p.Val37Ile, p.Met34Thr), consistent with autosomal recessive inheritance (Sloan-Heggen et al., 2016). The presence of this variant with an established disease-causing variant on the opposite allele increases suspicion for its pathogenicity. The p.Gly12Valfs*2 variant has also been identified in 1,217/127,068 European chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Although this variant has been seen in the general population, its frequency is consistent with a recessive carrier frequency for hearing loss. This variant results in a 1 bp deletion, which causes a shift in the protein reading frame, leading to a premature termination codon 2 amino acids downstream. Loss of function is an established mechanism of disease for the GJB2 gene. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Gly12Valfs*2 variant as pathogenic for autosomal recessive nonsyndromic hearing loss based on the information above. [ACMG evidence codes used: PVS1; PM3_verystrong]
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004806830.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Diagnostics Centre, Carl Von Ossietzky University Oldenburg, SCV005049570.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 2 | not provided | not provided | clinical testing | PubMed (3) |
Description
The variant GJB2: c.35delG, p.Gly12Valfs*2, which is located in the coding exon 2 of the GJB2 gene, results from a deletion of a base at nucleotide position c.35. The variant causes a frameshift that results in the replace of a glycine by a valine at protein position 12, followed by a premature translation stop codon after two amino acids. Degradation of the truncated gene product due to non-sense mediated decay is not predicted. However, a large part of the protein is lost, including the functionally relevant connexin domain.The variant was described in an Italian study as the most common GJB2 variant associated with autosomal recessive non-syndromic hearing loss (PMID: 12176036). Multiple studies showed an increased prevalence on individuals affected with hearing loss (PMID: 26969326, 25999548). A cell culture-based functional study showed that the altered gene product is no longer detectable and leads to a loss of function of GJB2 (PMID: 12176036). The variant is not considered rare in the overall population (allele frequency= 0.007050 in gnomAD, v4.1.0). The variant has been consistently classified as Pathogenic in more than 80 entries in ClinVar (ClinvarID: 17004). The ClinGen Expert panel for hearing disorders classified this variant as Pathogenic despite the comparatively high allele frequency. In summary, the variant is classified as Pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 2 | not provided | not provided | not provided |
Flagged submissions
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000599723 | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV000599723 appears to be redundant with SCV000257945. (DGD Variant Analysis Guidelines) | Pathogenic (May 9, 2017) | germline | clinical testing |
Last Updated: Oct 26, 2024