rs763721044
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PP3_Strong
The NM_022124.6(CDH23):c.7903G>T(p.Val2635Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,662 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 Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
CDH23
NM_022124.6 missense
NM_022124.6 missense
Scores
6
7
2
Clinical Significance
Conservation
PhyloP100: 9.96
Genes affected
CDH23 (HGNC:13733): (cadherin related 23) This gene is a member of the cadherin superfamily, whose genes encode calcium dependent cell-cell adhesion glycoproteins. The encoded protein is thought to be involved in stereocilia organization and hair bundle formation. The gene is located in a region containing the human deafness loci DFNB12 and USH1D. Usher syndrome 1D and nonsyndromic autosomal recessive deafness DFNB12 are caused by allelic mutations of this cadherin-like gene. Upregulation of this gene may also be associated with breast cancer. Alternative splice variants encoding different isoforms have been described. [provided by RefSeq, May 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.946
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.7903G>T | p.Val2635Phe | missense_variant | 56/70 | ENST00000224721.12 | |
CDH23 | NM_001171933.1 | c.1183G>T | p.Val395Phe | missense_variant | 9/23 | ||
CDH23 | NM_001171934.1 | c.1183G>T | p.Val395Phe | missense_variant | 9/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.7903G>T | p.Val2635Phe | missense_variant | 56/70 | 5 | NM_022124.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248118Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134738
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GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461458Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726986
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ClinVar
Significance: Uncertain significance
Submissions summary: Pathogenic:1Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Autosomal recessive nonsyndromic hearing loss 12 Pathogenic:1
Pathogenic, no assertion criteria provided | research | Laboratory of Prof. Karen Avraham, Tel Aviv University | Feb 19, 2016 | Congenital, profound HL - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 24, 2014 | The p.Val2635Phe variant in CDH23 has been previously reported in 3 Jewish-Alger ian individuals with hearing loss (Brownstein 2011, Idan 2013). The variant was identified in the homozygous state in two of these individuals and was present i n the heterozygous state in the third individual who did not carry a second CDH2 3 variant on the other allele. The variant apparently segregated with the hearin g loss in affected family members in two pedigrees; however one family was consa nguineous (which increases the presence of homozygous variants in offspring irre spective of their clinical significance) and, although consanguinity was not rep orted for the second family, all affected family members, including two affected apparently unrelated spouses, were homozygous for the variant. The variant was not identified in 106 ethnically-matched controls; however, this sample size is too small to accurately determine the population frequency of the variant. Given that the variant has only been seen in the homozygous state and was not observe d in compound heterozygosity with a known CDH23 pathogenic variant in affected i ndividuals, as well as the fact that these families all have a unique shared anc estry with limited control data, the information in these studies does not provi de sufficient evidence to assume that the p.Val2635Phe variant is causative for hearing loss. The p.Val2635Phe variant has also been identified in 4/10962 of La tino chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadins titute.org), but this frequency is not high enough to rule out a pathogenic role . Computational prediction tools and conservation analysis suggest that this var iant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, due to insufficient data to support pathog enicity, and the limited evidence and control data presented in the studies abov e, the clinical significance of the p.Val2635Phe variant in CDH23 is uncertain. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 27, 2022 | This sequence change replaces valine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 2635 of the CDH23 protein (p.Val2635Phe). This variant is present in population databases (rs763721044, gnomAD 0.01%). This missense change has been observed in individual(s) with deafness (PMID: 19888295, 21917145). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 228503). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;T;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Sift4G
Uncertain
D;.;D;D
Polyphen
1.0
.;D;.;.
Vest4
MutPred
Loss of sheet (P = 0.0315);Loss of sheet (P = 0.0315);.;.;
MVP
MPC
0.72
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at