CYB561

cytochrome b561, the group of Cytochrome b561

Basic information

Region (hg38): 17:63432303-63446354

Links

ENSG00000008283 ∙ NCBI:1534 ∙ OMIM:600019 ∙ HGNC:2571 ∙ Uniprot:P49447 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• orthostatic hypotension 2 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Orthostatic hypotension 2	AR	Biochemical; Cardiovascular	The condition may involve early-onset severe orthostatic hypotension, and medical managment (eg, with L-dihydroxyphenylserine) has been reported as beneficial	Biochemical; Cardiovascular	29343526

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYB561 gene.

• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYB561 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						0
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in CYB561

This is a list of pathogenic ClinVar variants found in the CYB561 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63434430-G-A		not specified	Uncertain significance (Feb 15, 2023)
17-63434457-G-C		not specified	Uncertain significance (Dec 12, 2023)
17-63434482-G-A		not specified	Uncertain significance (Aug 17, 2022)
17-63434508-T-C		not specified	Uncertain significance (Sep 22, 2022)
17-63434518-C-T		not specified	Uncertain significance (Jan 03, 2022)
17-63434552-G-A		CYB561-related disorder	Likely benign (Feb 26, 2020)
17-63435088-G-A		CYB561-related disorder	Likely benign (Apr 09, 2019)
17-63435135-C-T		not specified	Uncertain significance (Jul 25, 2023)
17-63435185-C-T		not specified	Uncertain significance (May 25, 2022)
17-63435186-G-A		not specified	Uncertain significance (Feb 28, 2023)
17-63435192-G-A		not specified	Uncertain significance (Nov 18, 2022)
17-63435210-C-G		not specified	Uncertain significance (Nov 17, 2022)
17-63435225-A-G		not specified	Uncertain significance (Aug 08, 2023)
17-63435231-A-G		not specified	Uncertain significance (Aug 08, 2023)
17-63435750-C-T		not specified	Uncertain significance (Oct 20, 2021)
17-63435756-C-T		not specified	Uncertain significance (Apr 22, 2022)
17-63435774-C-T		not specified	Uncertain significance (Jul 12, 2022)
17-63435775-G-A		CYB561-related disorder	Likely benign (Sep 17, 2019)
17-63436077-A-G		not specified	Uncertain significance (May 05, 2022)
17-63436093-C-T		Orthostatic hypotension 2	Pathogenic (Nov 14, 2018)
17-63436148-C-T		CYB561-related disorder	Benign (Jun 18, 2019)
17-63437417-C-T		Orthostatic hypotension 2	Pathogenic (Nov 14, 2018)
17-63437504-T-A		not specified	Uncertain significance (Oct 10, 2023)
17-63437524-G-A		CYB561-related disorder	Likely benign (Jun 07, 2019)
17-63440208-C-T		CYB561-related disorder	Benign (Feb 22, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYB561	protein_coding	protein_coding	ENST00000392976	5	14075

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.611	0.388	125694	0	9	125703	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.951	132	167	0.793	0.0000112	1589
Missense in Polyphen		44	61.3	0.71778		580
Synonymous	0.161	84	85.9	0.978	0.00000661	553
Loss of Function	2.61	2	11.6	0.173	5.81e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000269	0.0000264
Middle Eastern	0.000112	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Secretory vesicle-specific electron transport protein.

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.556
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.225
• hipred: N
• hipred_score: 0.469
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.613

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cyb561
• Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; pigmentation phenotype

Gene ontology

• Biological process: electron transport chain
• Cellular component: lysosomal membrane;integral component of membrane
• Molecular function: ferric-chelate reductase activity;protein binding;oxidoreductase activity;metal ion binding