Is CYBB p.Phe563fs (c.1689del) pathogenic?

CYBB p.Phe563fs (c.1689del) is classified Pathogenic in CYBB (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-14). Absent from gnomAD; Associated with granulomatous disease, chronic, X-linked.

What condition is associated with CYBB p.Phe563fs (c.1689del)?

CYBB p.Phe563fs (c.1689del) is associated with granulomatous disease, chronic, X-linked (ClinVar).

How common is CYBB p.Phe563fs (c.1689del) in the general population?

CYBB p.Phe563fs (c.1689del) is absent from gnomAD (gnomAD).

How is Chronic granulomatous disease inherited?

Typically Autosomal recessive, X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CYBB p.Phe563fs

c.1689del · rs1602186299 · VCV646155

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

granulomatous disease, chronic, X-linked

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (13 of 13) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.8	GERP 1.7, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CYBB
Protein: p.Phe563fs
Coding: c.1689del
MANE Select: NM_000397
dbSNP: rs1602186299
Type: Deletion
Location: chrX:37810893 (GRCh38)
Structure: AlphaFold pLDDT 90.29 · 6 PDB
Residue 563: a β-strand

Full CYBB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

granulomatous disease, chronic, X-linked — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Chronic granulomatous disease (Orphanet):

Inheritance: Autosomal recessive, X-linked recessive
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

CYBB p.Phe563= Benign/Likely benign ★★ same residue
CYBB p.Glu347fs Pathogenic ★★ same condition
CYBB p.Glu540fs Likely pathogenic ★★ same condition
CYBB p.Val27fs Pathogenic ★★ same condition
CYBB p.Val321fs Pathogenic ★★ same condition
CYBB c.1150_1151+2del Pathogenic ★ same condition
CYBB c.141+1del Pathogenic ★ same condition
CYBB c.37_45+2del 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/cybb-p-phe563fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown