CLDN14 p.Ala5=
c.15C>T · rs387907416 · VCV64486
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00253%, nfe)
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 -3.1 | GERP -3.9 |
| Overall | ||
| CADD | 6.303 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00253%
European (non-Finnish) · 29/1,148,442 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00153%
Overall
0.00221%
31/1,399,862 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00253% | 39,601 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,148 |
| African / African-American | 0.00136% | 73,260 |
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.Ala5=
- Coding
- c.15C>T
- MANE Select
- NM_001146079
- dbSNP
- rs387907416
- Type
- single nucleotide variant
- Location
- chr21:36461681 (GRCh38)
- Gene constraint
- LOEUF 1.745 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 80.00
Similar variants
- 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
- CLDN14 p.Arg106Cys 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-ala5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown