The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_022124.6(CDH23):c.380A>G (p.Asp127Gly)

CA10576804

228491 (ClinVar)

Gene: CDH23
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 637bd8ea-a91f-4012-9a60-43d0bfce68ad
Approved on: 2023-06-27
Published on: 2023-06-30

HGVS expressions

NM_022124.6:c.380A>G
NM_022124.6(CDH23):c.380A>G (p.Asp127Gly)
NC_000010.11:g.71511163A>G
CM000672.2:g.71511163A>G
NC_000010.10:g.73270920A>G
CM000672.1:g.73270920A>G
NC_000010.9:g.72940926A>G
NG_008835.1:g.119217A>G
ENST00000224721.12:c.380A>G
ENST00000398809.9:c.380A>G
ENST00000442677.4:n.380A>G
ENST00000646131.1:n.44A>G
ENST00000224721.10:c.380A>G
ENST00000299366.11:c.380A>G
ENST00000398809.8:c.380A>G
ENST00000398842.7:c.203A>G
ENST00000461841.7:c.380A>G
ENST00000616684.4:c.380A>G
ENST00000622827.4:c.380A>G
NM_001171930.1:c.380A>G
NM_001171931.1:c.380A>G
NM_001171932.1:c.380A>G
NM_022124.5:c.380A>G
NM_052836.3:c.380A>G
NR_120672.1:n.143+615T>C
NM_001171930.2:c.380A>G
NM_001171931.2:c.380A>G
NM_052836.4:c.380A>G
NM_001171932.2:c.380A>G
More

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP4 PP3 PM3
Not Met criteria codes 22
BS2 BS4 BS3 BS1 BP5 BP7 BP2 BP3 BP1 BP4 PS2 PS4 PS3 PS1 PP1 PP2 BA1 PM6 PVS1 PM1 PM4 PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDH23, COCH, GJB2, KCNQ4, MYO6, MYO7A, SLC26A4, TECTA and USH2A Version 2

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.380A>G (NM_022124.6(CDH23):c.380A>G (p.Asp127Gly)) variant in CDH23 is a missense variant predicted to cause substitution of aspartate by glycine at amino acid 127. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.796 which is above the threshold of 0.7, evidence that correlates with impact to CDH23 function (PP3). This variant has been detected in one individual with autosomal recessive Usher syndrome. For this individual, they were compound heterozygous for the variant and a pathogenic variant (NM_022124.6(CDH23):c.1949dup (p.Leu651fs) (SCV000271345.2) ) and this individual was confirmed in trans by family testing (1.0 point, PM3; LMM internal data). The patient with the variant had congenital severe-profound hearing loss with vestibular complications and ophthalmology-related issues, features highly specific to Usher syndrome (LMM Internal Data; PP4). This variant was re-reviewed on 1.18.2023 and because no additional evidence is available, professional judgment was used to retain this variant as likely pathogenic for autosomal recessive Usher syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP. In summary, this variant is classified as likely pathogenic for autosomal recessive Usher Syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM2_supporting, PP3, PM3, PP4 (ClinGen Hearing Loss VCEP Specifications Version 2; 6/27/2022).
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP4
The patient with the variant had congenital severe-profound hearing loss with vestibular complications and ophthalmology-related issues, features highly specific to Usher syndrome (Laboratory for Molecular Medicine Internal Data; PP4).
PP3
REVEL score is 0.796, which is above 0.7, the threshold for pathogenicity set by the hearing loss VCEP. Amino acid is very well-conserved. The results from three in silico predictors/lines of evidence (PolyPhen, REVEL score, conservation) provide evidence that correlates with impact to CDH23 function (PP3).
PM3
This variant was detected in trans with NM_022124.5:c.1949_1950insC (p.Leu651fs)(a pathogenic variant) in CDH23 in a patient with Usher Syndrome (Laboratory for Molecular Medicine Internal Data).
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
The variant is absent from gnomAD.
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
REVEL score is 0.796.
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
The variant is absent from gnomAD.
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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