CDH4 p.Gln360Lys
c.1078C>A · VCV3830189
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.5226 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| AlphaMissense | 0.5226 | ambiguous |
|---|---|---|
| REVEL | 0.38 | indeterminate |
| SaProt | LLR -9.46 | tolerated |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.4 | GERP 2.1, phastCons 1 |
| Regional constraint | o/e 0.77 | unconstrained · MANE · 160 kb · p 4.6e-12 · regional, not allelic |
| Overall | ||
| CADD | 25.9 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
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
- CDH4
- Protein
- p.Gln360Lys
- Coding
- c.1078C>A
- MANE Select
- NM_001794
- Type
- single nucleotide variant
- Location
- chr20:61894937 (GRCh38)
- Gene constraint
- LOEUF 0.533 · pLI 0.54 (gnomAD)
- Structure
- AlphaFold pLDDT 79.02
- Residue 360
- the cadherin 2 domain
Similar variants
- CDH4 p.Thr396Met Uncertain significance ★★ ⚠ same type
- CDH4 p.Val580Ile Uncertain significance ★★ ⚠ same type
- CDH4 c.1629-8C>T Benign ★★ same type
- CDH4 c.2240-4A>G Benign ★★ same type
- CDH4 p.Ala33Thr Benign ★★ same type
- CDH4 p.Ala344= Benign/Likely benign ★★ same type
- CDH4 p.Asn283= Benign/Likely benign ★★ same type
- CDH4 p.Asn450= Benign/Likely 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/cdh4-p-gln360lys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown