CYBRD1

cytochrome b reductase 1, the group of Cytochrome b561

Basic information

Region (hg38): 2:171522247-171558129

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.

not_specified (33 variants)
CYBRD1-related_disorder (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. These statistics are base on transcript: NM_000024843.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar		4
missense			27 clinvar	3 clinvar		30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	7	0

Loading clinvar variants...

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