CYBRD1

cytochrome b reductase 1, the group of Cytochrome b561

Basic information

Region (hg38): 2:171522246-171558129

Links

ENSG00000071967 ∙ NCBI:79901 ∙ OMIM:605745 ∙ HGNC:20797 ∙ Uniprot:Q53TN4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary hemochromatosis (Strong), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYBRD1 gene.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYBRD1 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			11		1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in CYBRD1

This is a list of pathogenic ClinVar variants found in the CYBRD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-171522561-T-C		not specified	Uncertain significance (Jun 30, 2022)
2-171522589-C-T		CYBRD1-related disorder	Likely benign (Feb 03, 2022)
2-171522648-C-G		not specified	Uncertain significance (Oct 26, 2021)
2-171522718-T-G		not specified	Uncertain significance (Apr 12, 2023)
2-171522720-G-A		not specified	Uncertain significance (Apr 22, 2022)
2-171522723-T-C		not specified	Uncertain significance (Jan 18, 2023)
2-171541669-C-T		not specified	Uncertain significance (Dec 17, 2023)
2-171541677-C-T		not specified	Uncertain significance (Sep 14, 2022)
2-171541683-A-G		not specified	Uncertain significance (Dec 21, 2023)
2-171541734-A-G		not specified	Uncertain significance (Jun 21, 2022)
2-171541759-T-C		not specified	Uncertain significance (Mar 29, 2023)
2-171553387-G-A		not specified	Likely benign (Mar 07, 2024)
2-171553470-T-C		not specified	Uncertain significance (Jul 09, 2021)
2-171553471-G-A		not specified	Uncertain significance (May 16, 2023)
2-171554550-C-T		not specified	Uncertain significance (Dec 07, 2023)
2-171554604-C-A		not specified	Uncertain significance (Sep 27, 2021)
2-171554632-G-A		not specified	Likely benign (Nov 28, 2023)
2-171554763-G-A			Benign (Sep 04, 2018)
2-171554814-G-A		not specified	Uncertain significance (Dec 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYBRD1	protein_coding	protein_coding	ENST00000321348	4	35887

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0116	0.954	125717	0	15	125732	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.589	139	160	0.869	0.00000787	1838
Missense in Polyphen		37	54.41	0.68002		635
Synonymous	-0.924	75	65.5	1.15	0.00000357	597
Loss of Function	1.83	5	11.8	0.424	5.92e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000231
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ferric-chelate reductase that reduces Fe(3+) to Fe(2+). Present at the brush border of duodenal enterocytes where it probably reduces dietary Fe(3+) thereby facilitating its transport into the mucosal cells. Uses ascorbate as electron donor. May be involved in extracellular ascorbate recycling in erythrocyte membranes. May also act as a ferrireductase in airway epithelial cells. {ECO:0000269|PubMed:16521311, ECO:0000269|PubMed:16521312, ECO:0000269|PubMed:17068337, ECO:0000269|PubMed:19673882}.
• Pathway: Mineral absorption - Homo sapiens (human);Transport of small molecules;Iron uptake and transport (Consensus)

Recessive Scores

• pRec: 0.183

Intolerance Scores

• loftool: 0.317
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.93

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.305
• ghis: 0.389

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cybrd1
• Phenotype: homeostasis/metabolism 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); liver/biliary system phenotype

Gene ontology

• Biological process: cellular iron ion homeostasis;response to iron ion;oxidation-reduction process
• Cellular component: lysosomal membrane;plasma membrane;integral component of membrane;brush border membrane;extracellular exosome
• Molecular function: ferric-chelate reductase activity;protein binding;oxidoreductase activity;oxidoreductase activity, oxidizing metal ions;metal ion binding