STK4 p.Arg384=
c.1152G>A · VCV4759752
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
combined immunodeficiency due to STK4 deficiency
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 13.81 | 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
- STK4
- Protein
- p.Arg384=
- Coding
- c.1152G>A
- MANE Select
- NM_006282
- Type
- single nucleotide variant
- Location
- chr20:45024977 (GRCh38)
- Gene constraint
- LOEUF 0.6 · pLI 0.07 (gnomAD)
- Structure
- AlphaFold pLDDT 76.45 · 16 PDB
Disease context
combined immunodeficiency due to STK4 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Combined immunodeficiency due to STK4 deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood
Similar variants
- STK4 p.Arg115Ter Pathogenic/Likely pathogenic ★★ same condition
- STK4 p.Arg117Ter Pathogenic ★★ same condition
- STK4 p.Arg148Ter Pathogenic ★★ same condition
- STK4 p.Arg245Ter Pathogenic/Likely pathogenic ★★ same condition
- STK4 p.Ala391Val Uncertain significance ★★ ⚠ same condition
- STK4 p.Ala479Ser Uncertain significance ★★ ⚠ same condition
- STK4 p.Arg310Gln Uncertain significance ★★ ⚠ same condition
- STK4 p.Arg310Pro Uncertain significance ★★ ⚠ 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/stk4-p-arg384 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown