CYB561D1

cytochrome b561 family member D1, the group of Cytochrome b561

Basic information

Region (hg38): 1:109494052-109502932

Links

ENSG00000174151 ∙ NCBI:284613 ∙ ∙ HGNC:26804 ∙ Uniprot:Q8N8Q1 ∙ 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 CYB561D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYB561D1 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		1
missense			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	3	0

Variants in CYB561D1

This is a list of pathogenic ClinVar variants found in the CYB561D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109494157-A-G		not specified	Likely benign (May 31, 2023)
1-109494171-C-T		not specified	Uncertain significance (Jun 06, 2023)
1-109494263-A-G		not specified	Uncertain significance (Oct 22, 2021)
1-109494540-G-A		not specified	Likely benign (Aug 01, 2022)
1-109494569-G-T		not specified	Uncertain significance (Jan 30, 2024)
1-109494570-G-C		not specified	Uncertain significance (Nov 09, 2021)
1-109494574-T-C		not specified	Likely benign (Nov 09, 2021)
1-109494580-A-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
1-109494594-T-C		not specified	Uncertain significance (May 26, 2022)
1-109494606-G-A		not specified	Uncertain significance (Oct 17, 2023)
1-109495761-C-T		not specified	Likely benign (Dec 10, 2024)
1-109495812-C-G		not specified	Uncertain significance (Nov 03, 2022)
1-109495820-G-A		not specified	Uncertain significance (May 23, 2023)
1-109495826-G-A		not specified	Uncertain significance (May 12, 2024)
1-109495840-C-T		not specified	Uncertain significance (Sep 11, 2024)
1-109495874-T-C		not specified	Uncertain significance (May 10, 2024)
1-109495889-G-T		not specified	Uncertain significance (Oct 12, 2022)
1-109495918-C-T		not specified	Uncertain significance (Mar 29, 2024)
1-109496015-T-C		not specified	Uncertain significance (Sep 03, 2024)
1-109496020-C-A		not specified	Uncertain significance (Dec 17, 2023)
1-109496036-T-C		not specified	Uncertain significance (Dec 03, 2021)
1-109496050-C-T		not specified	Uncertain significance (Jul 02, 2024)
1-109496108-C-T		not specified	Uncertain significance (Nov 10, 2024)
1-109496140-C-G		not specified	Uncertain significance (Jan 03, 2024)
1-109496195-C-T		not specified	Uncertain significance (Aug 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYB561D1	protein_coding	protein_coding	ENST00000369868	3	8881

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000718	0.520	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0703	137	135	1.02	0.00000710	1553
Missense in Polyphen		51	48.513	1.0513		584
Synonymous	-0.156	58	56.5	1.03	0.00000278	572
Loss of Function	0.521	7	8.65	0.809	4.56e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000554	0.000554
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.000294	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.315
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.294
• hipred: N
• hipred_score: 0.198
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.215

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyb561d1

Gene ontology

• Biological process: oxidation-reduction process
• Cellular component: integral component of membrane
• Molecular function: metal ion binding