CYB561D2

cytochrome b561 family member D2, the group of Cytochrome b561

Basic information

Region (hg38): 3:50350844-50358460

Links

ENSG00000114395 ∙ NCBI:11068 ∙ OMIM:607068 ∙ HGNC:30253 ∙ Uniprot:O14569 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CYB561D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYB561D2 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	7	1	2

Variants in CYB561D2

This is a list of pathogenic ClinVar variants found in the CYB561D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-50350952-C-A			Benign (May 15, 2021)
3-50351176-C-A			Benign (May 13, 2021)
3-50353311-G-A		not specified	Uncertain significance (Dec 13, 2023)
3-50353325-C-T		not specified	Uncertain significance (Oct 06, 2023)
3-50353329-G-A		not specified	Uncertain significance (Jun 03, 2024)
3-50353430-C-T		not specified	Likely benign (Jul 14, 2023)
3-50353431-G-T		not specified	Uncertain significance (Dec 16, 2023)
3-50353466-G-A		not specified	Uncertain significance (May 16, 2023)
3-50353521-G-A		not specified	Uncertain significance (Apr 09, 2024)
3-50353533-C-T		not specified	Uncertain significance (Dec 12, 2023)
3-50353658-G-C		not specified	Uncertain significance (Apr 28, 2022)
3-50353722-A-T		not specified	Uncertain significance (Dec 28, 2023)
3-50355353-G-A		not specified	Uncertain significance (Feb 28, 2024)
3-50355356-G-A		not specified	Uncertain significance (May 31, 2023)
3-50355381-T-A		not specified	Uncertain significance (Apr 25, 2022)
3-50355416-G-A		not specified	Uncertain significance (Aug 16, 2022)
3-50358223-C-T		not specified	Uncertain significance (Apr 08, 2024)
3-50358329-G-C		not specified	Uncertain significance (Dec 09, 2023)
3-50358340-A-C		not specified	Uncertain significance (Oct 27, 2022)
3-50358396-G-C		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYB561D2	protein_coding	protein_coding	ENST00000418577	3	7766

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000138	0.661	125700	0	44	125744	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.970	97	128	0.759	0.00000736	1366
Missense in Polyphen		21	38.981	0.53872		434
Synonymous	-0.451	66	61.5	1.07	0.00000346	537
Loss of Function	0.817	7	9.75	0.718	6.44e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000419	0.000357
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.430
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.146
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyb561d2

Gene ontology

• Biological process: oxidation-reduction process
• Cellular component: endoplasmic reticulum;integral component of membrane;vesicle
• Molecular function: ferroxidase activity;heme binding;metal ion binding