CLDN14 p.Pro28=
c.84G>A · rs778927942 · VCV2900965
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0121%, afr)
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 -3.5 | GERP -4.1 |
| Overall | ||
| CADD | 7.834 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0121%
African / African-American · 9/74,634 alleles
Filtering AF
0.00626%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00469%
Overall
0.0053%
85/1,602,280 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0121% | 8,293 |
| East Asian | 0.0113% | 8,830 |
| Remaining individualsnot grpmax-eligible | 0.00644% | 15,522 |
| European (non-Finnish) | 0.00553% | 18,077 |
| South Asian | 0.00224% | 44,689 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CLDN14
- Protein
- p.Pro28=
- Coding
- c.84G>A
- MANE Select
- NM_001146079
- dbSNP
- rs778927942
- Type
- single nucleotide variant
- Location
- chr21:36461612 (GRCh38)
- Gene constraint
- LOEUF 1.745 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 80.00
Similar variants
- CLDN14 p.Pro28Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- CLDN14 p.Arg81His Pathogenic/Likely pathogenic ★★ same type
- CLDN14 p.Cys97Ter Pathogenic/Likely pathogenic ★★ same type
- CLDN14 p.Trp30Ter Pathogenic/Likely pathogenic ★★ same type
- CLDN14 c.*107G>A Uncertain significance ★★ same type
- CLDN14 p.Ala196Val Uncertain significance ★★ ⚠ same type
- CLDN14 p.Ala72Val Uncertain significance ★★ ⚠ same type
- CLDN14 p.Ala98Thr Uncertain significance ★★ ⚠ 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/cldn14-p-pro28 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown