CDHR1 p.Trp504Ter
c.1511G>A · rs74902839 · VCV1453319
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
CDHR1-related disorders
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 14 of 17 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 4.7, phastCons 1 |
| Overall | ||
| CADD | 49.0 | 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
- CDHR1
- Protein
- p.Trp504Ter
- Coding
- c.1511G>A
- MANE Select
- NM_033100
- dbSNP
- rs74902839
- Type
- single nucleotide variant
- Location
- chr10:84211673 (GRCh38)
- Gene constraint
- LOEUF 1.004 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.79
- Residue 504
- the cadherin 5 domain
Disease context
CDHR1-related disorders
Similar variants
- CDHR1 c.1168-1G>C Pathogenic/Likely pathogenic ★★ same condition
- CDHR1 c.1321-1G>A Likely pathogenic ★★ same condition
- CDHR1 c.1485+2T>C Pathogenic ★★ same condition
- CDHR1 c.1485+2T>G Pathogenic ★★ same condition
- CDHR1 c.1554-2A>C Pathogenic/Likely pathogenic ★★ same condition
- CDHR1 c.297+1G>T Pathogenic ★★ same condition
- CDHR1 c.526-1G>A Likely pathogenic ★★ same condition
- CDHR1 c.55+1G>A Likely pathogenic ★★ 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/cdhr1-p-trp504ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown