CDH13 p.Val476=
c.1428C>G · VCV4535134
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.026 | GERP -2.2, phastCons 0.93 |
| Overall | ||
| CADD | 5.505 | PHRED · no single calibrated threshold — expert panels disagree |
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
- CDH13
- Protein
- p.Val476=
- Coding
- c.1428C>G
- MANE Select
- NM_001257
- Type
- single nucleotide variant
- Location
- chr16:83678351 (GRCh38)
- Gene constraint
- LOEUF 0.456 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.19 · 1 PDB
- Residue 476
- the cadherin 3 domain
Similar variants
- CDH13 c.1102-6T>C Benign ★★ same type
- CDH13 c.1284+90A>G Benign ★★ same type
- CDH13 c.1539-109T>C Benign ★★ same type
- CDH13 c.1681+64T>C Benign ★★ same type
- CDH13 c.1682-151C>T Benign ★★ same type
- CDH13 c.1682-180G>A Benign ★★ same type
- CDH13 c.1682-59A>G Benign ★★ same type
- CDH13 c.1682-62G>A Benign ★★ same type
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/cdh13-p-val476 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown