rs111033271
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PP3_ModeratePP5_Very_Strong
The NM_022124.6(CDH23):c.6442G>A(p.Asp2148Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000898 in 1,613,806 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 Likely pathogenic (★★).
Frequency
Consequence
NM_022124.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152124Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000923 AC: 23AN: 249170Hom.: 0 AF XY: 0.0000814 AC XY: 11AN XY: 135216
GnomAD4 exome AF: 0.0000896 AC: 131AN: 1461682Hom.: 0 Cov.: 31 AF XY: 0.0000784 AC XY: 57AN XY: 727126
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152124Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74314
ClinVar
Submissions by phenotype
not provided Pathogenic:4
CDH23: PM3:Very Strong, PP1:Strong, PM2 -
This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 2148 of the CDH23 protein (p.Asp2148Asn). This variant is present in population databases (rs111033271, gnomAD 0.02%). This missense change has been observed in individual(s) with autosomal recessive deafness and/or Usher syndrome (PMID: 12075507, 12522556, 21940737, 27460420). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 4922). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on CDH23 protein function. For these reasons, this variant has been classified as Pathogenic. -
Identified with a second variant in additional patients with CDH23-related disorders in published literature, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes (PMID: 28000701, 27460420); 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: 12522556, 22652773, 33724713, 30531642, 21940737, 31816670, 15353998, 12075507, 27460420, 28000701, BuianovaA2024[Preprint]) -
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Autosomal recessive nonsyndromic hearing loss 12 Pathogenic:2
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The CDH23 c.6442G>A (p.Asp2148Asn) missense variant has been reported in three studies in which it is found in a total of eight individuals with hearing loss, including in two in a homozygous state, in five in a compound heterozygous state, and in one where zygosity was not specified (Astuto et al. 2002; De Brouwer et al. 2003; Schultz et al. 2011). This variant was also identified in 14 unaffected individuals in a heterozygous state. The p.Asp2148Asn variant was absent from a total of 296 controls and is reported at a frequency of 0.00015 in the European (non-Finnish) population of Exome Aggregation Consortium. Protein modelling studies revealed the Asp2148 residue is conserved and located in a calcium binding domain. Other aspartic acid to asparagine substitions associated with disease have been reported in these domains (de Brouwer et al. 2003). Based on the evidence, the p.Asp2148Asn variant is classified as pathogenic for autosomal recessive nonsyndromic hearing loss. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Autosomal recessive nonsyndromic hearing loss 12;C1832845:Usher syndrome type 1D;C4539685:Pituitary adenoma 5, multiple types Pathogenic:1
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CDH23-related disorder Pathogenic:1
The CDH23 c.6442G>A variant is predicted to result in the amino acid substitution p.Asp2148Asn. This variant has been reported in the homozygous and compound heterozygous state in multiple individuals with non-syndromic autosomal recessive deafness and Usher syndrome (Astuto et al. 2002. PubMed ID: 12075507; De Brouwer et al. 2003. PubMed ID: 12522556; Schultz et al. 2011. PubMed ID: 21940737; Bonnet et al. 2016. PubMed ID: 27460420; Li et al. 2021. PubMed ID: 33724713). Of note, this variant has been reported to segregate with disease in at least two families (De Brouwer et al. 2003. PubMed ID: 12522556; Schultz et al. 2011. PubMed ID: 21940737). This variant is reported in 0.019% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. -
Usher syndrome Pathogenic:1
Variant summary: CDH23 c.6442G>A (p.Asp2148Asn) results in a conservative amino acid change in 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 9.2e-05 in 249170 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CDH23 causing Usher Syndrome (9.2e-05 vs 0.0032), allowing no conclusion about variant significance. c.6442G>A has been reported in the literature in multiple individuals affected with Usher Syndrome and Nonsyndromic hearing loss (e.g. Astuto_2002, deBrouwer_2003, Schultz_2011, Bonnet_2016) and also observed to segregate with disease. These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 12075507, 27460420, 21940737, 12522556). ClinVar contains an entry for this variant (Variation ID: 4922). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pituitary adenoma 5, multiple types Pathogenic:1
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Autosomal recessive nonsyndromic hearing loss 12;C1848634:Usher syndrome type 2A Pathogenic:1
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Usher syndrome type 1D Pathogenic:1
This sequence variant is a single nucleotide substitution (G>A) at position 6442 of the coding sequence of the CDH23 gene that results in an aspartic acid to asparagine amino acid change at residue 2148 of the cadherin related 23 protein. This residue falls in the extracellular cadherin 20 domain of the protein (UniProt). This is a previously reported variant (ClinVar 4922) that has been observed in homozygous and compound heterozygous state in several individuals and families affected by hearing loss and/or Usher syndrome (PMID: 12522556, 28000701, 33724713, 12075507, 21940737, 27460420). This variant is present in 1454 of 1613806 alleles (0.008985%) in the gnomAD v4.0.0 population dataset. Multiple bioinformatic tools predict that this amino acid change would be damaging, and the Asp2148 residue at this position is highly conserved across the vertebrate species examined. Based upon the evidence, we consider this variant to be pathogenic. ACMG Criteria: PM2, PM3, PP1, PP3, PS4 -
Usher syndrome type 1 Pathogenic:1
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Rare genetic deafness Pathogenic:1
The p.Asp2148Asn variant in CDH23 has been previously reported in 1 individual with Usher syndrome who was compound heterozygous with p.Trp2811* (Bonnet 2016). It has also been reported in 4 additional individuals with hearing loss without evidence of retinitis pigmentosa and segregated in four affected relatives (Astuto 2002, de Brouwer 2003, Pennings 2004, Schultz 2003). In one study, the variant was identified in one Dutch patient who was homozygous, and in an American patient who was compound heterozygous with p.R2608H (reported as uncertain and likely benign in ClinVar) (Astuto 2002). In another large family with hearing loss, the p.Asp2148Asn variant was identified in four family members with hearing loss; two siblings were homozygous and two other individuals were compound heterozygous (with p.D1341N) (de Brouwer 2003, Pennings 2004). The variant was also reported in two siblings with hearing loss who were compound heterozygous with p.Arg1746Gln (Schultz 2011). This variant has been identified in 0.01% (25/128344) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis suggest that this variant may impact the protein. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal recessive hearing loss, and there could be a risk for Usher syndrome associated with this variant when present in compound heterozygosity with a loss of function variant as was reported in Bonnet 2016. ACMG/AMP criteria applied: PP1_Strong, PM3, PM2_Supporting, PP3. -
Retinal dystrophy Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at