CYBC1

cytochrome b-245 chaperone 1

Basic information

Region (hg38): 17:82440912-82450829

Previous symbols: [ "C17orf62" ]

Links

ENSG00000178927 ∙ NCBI:79415 ∙ OMIM:618334 ∙ HGNC:28672 ∙ Uniprot:Q9BQA9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• chronic granulomatous disease (Supportive), mode of inheritance: AR
• granulomatous disease, chronic, autosomal recessive, 5 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Granulomatous disease, chronic, autosomal recessive, 5	AR	Allergy/Immunology/Infectious	Surveillance for infections and infectious complications is indicated, and preventive measures (eg, antibacterial/antifungal prophylaxis, interferon gamma) may be beneficial; To treat fungal infections, specific antifungal drugs may be beneficial, and longer treatment courses (as well as specific considerations including coadministration with corticosteroids) may be indicated in individuals with CGD; In some instances, HSCT may be beneficial; Certain agents should be avoided, including material that would allow fungal spore inhalation	Allergy/Immunology/Infectious; Musculoskeletal	28600779; 30312704; 30361506

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYBC1 gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYBC1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	32	3	36
missense			48	2	2	52
nonsense	1					1
start loss			1			1
frameshift	1		2			3
inframe indel						0
splice donor/acceptor (+/-2bp)		2	1			3
splice region			1	3	1	5
non coding			24	46	16	86
Total	2	2	77	80	21

Variants in CYBC1

This is a list of pathogenic ClinVar variants found in the CYBC1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-82441021-C-T		not specified	Uncertain significance (Nov 15, 2024)
17-82441030-A-G		not specified	Uncertain significance (Jan 18, 2025)
17-82441061-A-C		not specified	Uncertain significance (Dec 16, 2024)
17-82441063-C-T		not specified	Likely benign (Nov 23, 2024)
17-82441081-C-T		not specified	Uncertain significance (Jun 01, 2023)
17-82441111-C-T		not specified	Uncertain significance (Mar 08, 2024)
17-82441125-C-G		not specified	Uncertain significance (May 15, 2024)
17-82441125-C-T		not specified	Uncertain significance (Dec 08, 2024)
17-82441129-C-T		not specified	Likely benign (Feb 12, 2025)
17-82441149-G-C		not specified	Uncertain significance (Feb 14, 2025)
17-82441204-C-G		not specified	Uncertain significance (Sep 11, 2024)
17-82441213-A-G		not specified	Uncertain significance (Jan 08, 2024)
17-82441216-A-C		not specified	Uncertain significance (Nov 21, 2022)
17-82441237-C-G		not specified	Uncertain significance (Jan 19, 2025)
17-82441243-G-T		not specified	Uncertain significance (Nov 17, 2022)
17-82441249-G-A		not specified	Uncertain significance (Nov 24, 2024)
17-82441835-A-G		not specified	Likely benign (Sep 12, 2023)
17-82441838-G-A		not specified	Uncertain significance (Dec 09, 2024)
17-82441854-G-A		not specified	Likely benign (Nov 30, 2022)
17-82441884-G-A		not specified	Likely benign (Sep 25, 2023)
17-82442242-C-T		not specified	Uncertain significance (Jan 04, 2025)
17-82442249-C-T		not specified	Uncertain significance (Jan 03, 2022)
17-82442293-G-A		not specified	Uncertain significance (Aug 13, 2021)
17-82442327-G-A		not specified	Uncertain significance (Dec 16, 2024)
17-82442330-T-A		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYBC1	protein_coding	protein_coding	ENST00000437807	6	8241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000603	0.738	125694	0	13	125707	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.469	96	110	0.874	0.00000666	1203
Missense in Polyphen		33	42.836	0.77037		474
Synonymous	-0.631	53	47.5	1.12	0.00000312	371
Loss of Function	0.926	6	9.00	0.667	3.82e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000701	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000622	0.0000616
Middle Eastern	0.000109	0.000109
South Asian	0.0000655	0.0000653
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for a stable expression of the CYBA and CYBB subunits of the cytochrome b-245 hetrodimer. Controls the phagocyte respiratory burst and is essential for innate immunity. {ECO:0000250|UniProtKB:Q3TYS2}.

Intolerance Scores

• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.0935
• hipred: N
• hipred_score: 0.292
• ghis: 0.549

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cybc1
• Phenotype: skeleton phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: innate immune response;respiratory burst after phagocytosis
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: protein binding