CYBA p.Ala106fs
c.316dup · VCV4065592
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
chronic granulomatous disease
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 5 of 6 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.3, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CYBA
- Protein
- p.Ala106fs
- Coding
- c.316dup
- MANE Select
- NM_000101
- Type
- Duplication
- Location
- chr16:88646168 (GRCh38)
- Gene constraint
- LOEUF 1.726 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.28 · 7 PDB
- Residue 106
- an α-helix
Disease context
chronic granulomatous disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Chronic granulomatous disease (Orphanet):
- Inheritance
- Autosomal recessive, X-linked recessive
- Onset
- Adolescent, Adult, Childhood, Infancy
- Prevalence
- 1-9 / 1 000 000 (Worldwide)
Similar variants
- CYBA p.Arg56fs Pathogenic ★★ same condition
- CYBA c.128+2T>C Likely pathogenic ★★ same condition
- CYBA c.204-2A>G Pathogenic/Likely pathogenic ★★ same condition
- CYBA c.287+1G>T Pathogenic/Likely pathogenic ★★ same condition
- CYBA c.287+2T>C Pathogenic/Likely pathogenic ★★ same condition
- CYBA c.288-1G>T Pathogenic/Likely pathogenic ★★ same condition
- CYBA c.288-3_300del Likely pathogenic ★★ same condition
- CYBA c.58+2T>C Pathogenic/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/cyba-p-ala106fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown