Is CYBA p.Arg164His (c.491G>A) pathogenic?

CYBA p.Arg164His (c.491G>A) is classified Uncertain significance in CYBA (ClinVar, Multiple submitters, 3 submitters; last evaluated 2022-07-30). AlphaMissense: likely pathogenic (0.7047); Ultra-rare (popmax 0.0597%, afr); Associated with granulomatous disease, chronic, autosomal recessive, cytochrome b-negative.

How common is CYBA p.Arg164His (c.491G>A) in the general population?

CYBA p.Arg164His (c.491G>A) is ultra-rare (popmax 0.0597%, afr) (gnomAD).

How is Chronic granulomatous disease inherited?

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

What do computational predictors say about CYBA p.Arg164His (c.491G>A)?

AlphaMissense predicts likely pathogenic (score 0.7047) — an in-silico prediction, not a clinical call.

CYBA p.Arg164His

Q: What condition is associated with CYBA p.Arg164His (c.491G>A)?

CYBA p.Arg164His (c.491G>A) is associated with granulomatous disease, chronic, autosomal recessive, cytochrome b-negative, chronic granulomatous disease (ClinVar).

c.491G>A · rs904612575 · VCV452090

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.7047 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0597%, afr)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

granulomatous disease, chronic, autosomal recessive, cytochrome b-negative

Computational evidence

Protein change
AlphaMissense	0.7047	likely pathogenic
REVEL	0.739	pathogenic-leaning
SaProt	LLR -7.99	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 0.48, phastCons 1
Regional constraint	o/e 1.20	unconstrained · MANE · 7,657 bp · p 0.00077 · regional, not allelic
Overall
CADD	28.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0597% African / African-American · 43/72,042 alleles

Filtering AF 0.0455% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0406%

Overall 0.006% 92/1,533,008 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0597%	1,675
European (non-Finnish)	0.0042%	23,824
South Asian	0.0012%	83,592

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: CYBA
Protein: p.Arg164His
Coding: c.491G>A
MANE Select: NM_000101
dbSNP: rs904612575
Type: single nucleotide variant
Location: chr16:88643450 (GRCh38)
Gene constraint: LOEUF 1.726 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.28 · 7 PDB
Residue 164: the 'disordered' region; an α-helix

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

Disease context

granulomatous disease, chronic, autosomal recessive, cytochrome b-negative — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: chronic granulomatous disease

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

CYBA p.Arg164Cys Uncertain significance ★★ ⚠ same residue
CYBA p.Arg164= Likely benign ★ same residue
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.369+1G>A 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-arg164his (accessed [today's date]).

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