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Variant: NM_022124.6(CDH23):c.6614C>T (p.Pro2205Leu)

CA137541

46014 (ClinVar)

Gene: CDH23
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: f49b45e9-308a-4c2f-8941-4ed41c897a1b
Approved on: 2023-11-15
Published on: 2024-01-10

HGVS expressions

NM_022124.6:c.6614C>T
NM_022124.6(CDH23):c.6614C>T (p.Pro2205Leu)
NC_000010.11:g.71793542C>T
CM000672.2:g.71793542C>T
NC_000010.10:g.73553299C>T
CM000672.1:g.73553299C>T
NC_000010.9:g.73223305C>T
NG_008835.1:g.401596C>T
ENST00000224721.12:c.6614C>T
ENST00000224721.10:c.6629C>T
ENST00000622827.4:c.6614C>T
NM_022124.5:c.6614C>T

Uncertain Significance

Met criteria codes 3
PP1 PM3 PM2_Supporting
Not Met criteria codes 1
PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The variant c.6614C>T (NM_022124.6(CDH23):c.6614C>T (p.Pro2205Leu)) in CDH23 is a missense variant predicted to cause substitution of proline by leucine at amino acid 2205 (p.Pro2205Leu). The highest population minor allele frequency in gnomAD v4.0.0 is 0.000002920 (8/1179896 alleles) in the European (non-Finnish) population, which is lower than the ClinGen Hearing Loss VCEP threshold (<0.00007) for PM2_Supporting, meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.342, which is neither above nor below the thresholds predicting a damaging or benign impact on CDH23 function. This variant has been detected in at least 8 individuals with autosomal recessive hearing loss. All of these individuals were homozygous for the variant (1.0 pts; PMIDs: 28501645, 32747562 & LMM Internal Data (SCV000062934.5); PM3). There was a common haplotype found between five affected individuals from three families, one of which had three affected siblings, including a set of twins. Personal communication confirmed the three siblings were sequenced; however, it was not apparent whether the twins were dizygotic or monozygotic and therefore only one twin was counted toward segregation (PP1_Supporting; 28501645). In summary, this variant meets the criteria to be classified as uncertain significance for autosomal recessive Usher syndrome, based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP (PM2_Supporting, PM3, PP1_Supporting; Version 2; 11/15/23).
Met criteria codes
PP1
The variant has been reported to segregate with autosomal recessive hearing loss in 5 affected individuals, two of whom are twins, from 3 families who share a common haplotype (PP1_Supporting; PMID: 28501645).
PM3
This variant has been detected in at least 8 individuals with autosomal recessive hearing loss. All of these individuals were homozygous for the variant (1.0 pts; PMIDs: 28501645, 32747562 & LMM Internal Data (SCV000062934.5); PM3).
PM2_Supporting
The highest major allele frequency in gnomAD v4.0.0 is 8/1179896 alleles (0.000006780) in the European (non-Finnish) population, which is lower than the ClinGen Hearing Loss VCEP threshold of 0.00007, meeting this criterion (PM2_supporting).
Not Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.342, which is neither above nor below the thresholds predicting a damaging or benign impact on CDH23 function.
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