Granulomatous disease, chronic, X-linked: genes and variants

Genes linked to Granulomatous disease, chronic, X-linked

• CYBB: NADPH oxidase 2

  It generates the catalytic electron flow that allows phagocytes to produce microbicidal reactive oxygen species during the respiratory burst. Loss-of-function variants cause X-linked chronic granulomatous disease with severe susceptibility to bacterial and fungal infection.

  36 disease-causing and 99 uncertain variants in CYBB are linked to Granulomatous disease, chronic, X-linked.

Where Granulomatous disease, chronic, X-linked variants cluster

• CYBB Transmembrane (positions 47–72): 3 of 36 disease-causing changes, 1.8× more than its size predicts.

Known disease-causing variants in Granulomatous disease, chronic, X-linked

Uncertain variants in Granulomatous disease, chronic, X-linked that look disease-causing

Which prediction tools work for Granulomatous disease, chronic, X-linked

How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).

• CATVariant: 97 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• PolyPhen-2: 95 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• SIFT: 89 out of 100

Same protein, different disease

• Granulomatous disease, chronic, X-linked, variant is also caused by CYBB variants; they fall mostly in different places as the Granulomatous disease, chronic, X-linked variants (3 disease-causing).

Diseases related to Granulomatous disease, chronic, X-linked

• Chronic granulomatous disease, also linked to CYBB
• X-linked Mendelian susceptibility to mycobacterial diseases due to CYBB deficiency, also linked to CYBB

Frequently asked questions

Which genes are linked to Granulomatous disease, chronic, X-linked?

In CATVariant, Granulomatous disease, chronic, X-linked is linked to 1 analyzed protein: CYBB (NADPH oxidase 2).

How many genetic variants are linked to Granulomatous disease, chronic, X-linked?

162 variants: 36 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 99 are of uncertain significance or have conflicting reports.

Which uncertain variants in Granulomatous disease, chronic, X-linked look disease-causing?

2 uncertain variants reach the likely-pathogenic range of the ACMG/AMP points scale on computable evidence, for example CYBB A57S and CYBB T362K. These are leads for expert review, not diagnoses.

Which variant effect predictor works best for Granulomatous disease, chronic, X-linked?

Among tools not trained on clinical labels, SIFT separates this disease's known disease-causing variants from harmless ones best (AUROC 0.89, based on 29 disease-causing and 27 harmless variants).

About this data

Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.

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