CLDN16 p.Phe55fs
c.165del · VCV3359186
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
renal hypomagnesemia 3
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 2 of 5 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -0.25, phastCons 0.94 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CLDN16
- Protein
- p.Phe55fs
- Coding
- c.165del
- MANE Select
- NM_006580
- Type
- Deletion
- Location
- chr3:190402384 (GRCh38)
- Gene constraint
- LOEUF 0.837 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.74
- Residue 55
- a UniProt-annotated variant site (in homg3; retained in the endoplasmic reticulum and targeted for proteasomal degradation)
Similar variants
- CLDN16 p.Phe55= Benign/Likely benign ★★ same residue
- CLDN16 c.-45del Benign/Likely benign ★★ same condition
- CLDN16 c.218_382del Likely pathogenic ★ same condition
- CLDN16 c.219_382+2del Likely pathogenic ★ same condition
- CLDN16 p.Asn53fs Likely pathogenic ★ same condition
- CLDN16 c.(?_598 Pathogenic same condition
- CLDN16 p.Gly157fs Pathogenic same condition
- CLDN16 c.217+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/cldn16-p-phe55fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown