CDH23 p.Ser2155fs
c.6463_6464del · VCV4816091
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Usher syndrome type 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 48 of 70 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CDH23
- Protein
- p.Ser2155fs
- Coding
- c.6463_6464del
- MANE Select
- NM_022124
- Type
- Microsatellite
- Location
- chr10:71793386 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2155
- the cadherin 20 domain
Disease context
Usher syndrome type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Usher syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Worldwide)
Similar variants
- CDH23 p.Ser2155= Conflicting classifications of pathogenicity ★ same residue
- CDH23 p.Gly2156fs Pathogenic/Likely pathogenic ★★ same condition
- CDH23 p.Phe2664del Pathogenic/Likely pathogenic ★★ same condition
- CDH23 p.Val2274fs Likely pathogenic ★★ same condition
- CDH23 p.Lys2775del Uncertain significance ★★ same condition
- CDH23 p.Ser2155Leu Uncertain significance ★★ same residue
- CDH23 p.Glu96fs Likely pathogenic ★ same condition
- CDH23 p.Ser2155Ter Likely pathogenic ★ same residue
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cdh23-p-ser2155fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown