CDH23 p.Tyr2000Ter
c.6000C>A · rs1564794944 · VCV599084
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Usher syndrome type 1D
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 46 of 70 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 40.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CDH23
- Protein
- p.Tyr2000Ter
- Coding
- c.6000C>A
- MANE Select
- NM_022124
- dbSNP
- rs1564794944
- Type
- single nucleotide variant
- Location
- chr10:71790364 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2000
- the cadherin 19 domain
Similar variants
- CDH23 p.Arg2029Trp Pathogenic ★★★ ⚠ same condition
- CDH23 p.Glu956Lys Pathogenic ★★★ same condition
- CDH23 p.Pro240Leu Pathogenic ★★★ same condition
- CDH23 c.1515-12G>A Uncertain significance ★★★ same condition
- CDH23 p.Ala3190Val Uncertain significance ★★★ ⚠ same condition
- CDH23 p.Arg3189Trp Uncertain significance ★★★ ⚠ same condition
- CDH23 p.Asp2695Asn Uncertain significance ★★★ ⚠ same condition
- CDH23 p.Pro2205Leu Uncertain significance ★★★ same condition
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-tyr2000ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown