10-71712674-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3

The NM_022124.6(CDH23):​c.3230C>G​(p.Pro1077Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1077L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

CDH23
NM_022124.6 missense

Scores

4
9
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.88
Variant links:
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]
C10orf105 (HGNC:20304): (chromosome 10 open reading frame 105) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 ACMG points.

PM1
In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 6 uncertain in NM_022124.6
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.836

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CDH23NM_022124.6 linkuse as main transcriptc.3230C>G p.Pro1077Arg missense_variant 28/70 ENST00000224721.12
C10orf105NM_001164375.3 linkuse as main transcriptc.*3262G>C 3_prime_UTR_variant 2/2 ENST00000441508.4
CDH23NM_001171930.2 linkuse as main transcriptc.3230C>G p.Pro1077Arg missense_variant 28/32
C10orf105NM_001168390.2 linkuse as main transcriptc.*3262G>C 3_prime_UTR_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CDH23ENST00000224721.12 linkuse as main transcriptc.3230C>G p.Pro1077Arg missense_variant 28/705 NM_022124.6 P1Q9H251-1
C10orf105ENST00000441508.4 linkuse as main transcriptc.*3262G>C 3_prime_UTR_variant 2/21 NM_001164375.3 P1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingInvitaeFeb 28, 2022In 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. 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 C65"). This variant has not been reported in the literature in individuals affected with CDH23-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 1077 of the CDH23 protein (p.Pro1077Arg). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.34
BayesDel_addAF
Pathogenic
0.36
D
BayesDel_noAF
Pathogenic
0.28
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.026
T;T;T;T;.
Eigen
Uncertain
0.61
Eigen_PC
Uncertain
0.61
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.87
D;D;D;D;D
M_CAP
Pathogenic
0.43
D
MetaRNN
Pathogenic
0.84
D;D;D;D;D
MetaSVM
Uncertain
-0.24
T
MutationAssessor
Benign
0.070
.;.;N;.;.
MutationTaster
Benign
1.0
D;D;D;D
PrimateAI
Uncertain
0.52
T
REVEL
Benign
0.25
Sift4G
Uncertain
0.0040
D;D;.;D;.
Polyphen
0.73
.;.;P;.;.
Vest4
0.90
MutPred
0.58
Loss of methylation at K1080 (P = 0.0405);Loss of methylation at K1080 (P = 0.0405);Loss of methylation at K1080 (P = 0.0405);Loss of methylation at K1080 (P = 0.0405);Loss of methylation at K1080 (P = 0.0405);
MVP
0.90
ClinPred
0.96
D
GERP RS
4.9
Varity_R
0.35
gMVP
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-73472431; API