rs774518779
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM5PP3_StrongPP5_Very_Strong
The ENST00000382848.5(GJB2):c.506G>A(p.Cys169Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C169R) has been classified as Likely pathogenic.
Frequency
Consequence
ENST00000382848.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GJB2 | NM_004004.6 | c.506G>A | p.Cys169Tyr | missense_variant | 2/2 | ENST00000382848.5 | NP_003995.2 | |
GJB2 | XM_011535049.3 | c.506G>A | p.Cys169Tyr | missense_variant | 2/2 | XP_011533351.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GJB2 | ENST00000382848.5 | c.506G>A | p.Cys169Tyr | missense_variant | 2/2 | 1 | NM_004004.6 | ENSP00000372299 | P1 | |
GJB2 | ENST00000382844.2 | c.506G>A | p.Cys169Tyr | missense_variant | 1/1 | ENSP00000372295 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251060Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135736
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461760Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727166
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Autosomal recessive nonsyndromic hearing loss 1A Pathogenic:3Uncertain:1
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jun 20, 2017 | Variant summary: The GJB2 c.506G>A (p.Cys169Tyr) variant involves the alteration of a conserved nucleotide. "Cys169 is one of the six extracellular cysteine residues which are conserved in all connexin isoforms. These six cysteines form three disulfide bridges, which are likely to play an important role in guiding the correct folding of the connexin protein and the docking of the two hexameric hemichannels in the extracellular region" via Zonta_2015. 4/4 in silico tools predict a damaging outcome. A functional study, Zonta_2015 supports these predictions and showed that the variant "At the cellular level, our results show that the mutant protein fails to form junctional channels in HeLa transfectants despite being correctly targeted to the plasma membrane. At the molecular level, this effect can be accounted for by disruption of the disulfide bridge that Cys169 forms with Cys64 in the wild-type structure (Cx26WT)." This variant was found in 2/121012 control chromosomes at a frequency of 0.0000165, which does not exceed the estimated maximal expected allele frequency of a pathogenic GJB2 variant (0.025). Multiple publications have cited the variant in homozygous affected individuals, in addition a heterozygous affected individual, which a second mutation was not indicated to have been found. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Genetic Diagnostics Department, Viafet Genomics Laboratory | Aug 23, 2021 | As part of Carrier Screening testing performed at Viafet Genomics Laboratory, this variant was identified in a heterozygous state in 2 family members who are not affected with this condition. This variant has been identified in a homozygous state in several patients affected with hearing loss (PMIDs: 24551843 and 25628337). In addition, functional studies have revealed that this variant fails to form junctional channels in vitro despite being correctly targeted to the plasma membrane (PMID: 25628337). - |
Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Uncertain significance, flagged submission | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 26, 2024 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jun 17, 2022 | Published functional studies demonstrate a damaging effect as the p.(C169Y) variant results in disruption of junction channel formation, and disrupts the disulfide bridge that typically forms between the C169 and C64 residues (Zonta et al., 2015); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24551843, 25388846, 15365987, 34354426, 22103400, 25628337) - |
Autosomal dominant keratitis-ichthyosis-hearing loss syndrome;C0265964:Mutilating keratoderma;C0266004:Knuckle pads, deafness AND leukonychia syndrome;C1835672:Palmoplantar keratoderma-deafness syndrome;C1844678:X-linked mixed hearing loss with perilymphatic gusher;C1865234:Ichthyosis, hystrix-like, with hearing loss;C2673759:Autosomal recessive nonsyndromic hearing loss 1A;C2675750:Autosomal dominant nonsyndromic hearing loss 3A Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Rare genetic deafness Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 23, 2022 | The p.Cys169Tyr variant in GJB2 has been reported in three homozygous and two heterozygous individuals with hearing loss and segregated with disease in seven affected individuals from three families (Zonta 2015 PMID: 25628337, Birkenhäger 2014 PMID: 24551843, Azaiez 2004 PMID: 15365987, Mahfood 2021 PMID: 34354426). It has also been identified in 0.00176% (2/113464) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org) and reported in ClinVar (Variation ID 265481). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. This variant disrupts one of six conserved cysteine residues that form intramolecular disulfide bonds and are critical for intercellular channel formation (Zonta 2015 PMID: 25628337, Birkenhäger 2014 PMID: 24551843, Dahl 1991 PMID: 1707811). In vitro functional studies provide some evidence that this variant impacts protein function by obliterating the formation of gap junction plaques at points of cell-to-cell contact (Zonta 2015 PMID: 25628337); however, these types of assays may not accurately represent biological function. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive hearing loss. ACMG/AMP Criteria applied: PP1_Strong; PM1; PM3; PM2_Supporting; PP3; PS3_Supporting. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at