CYB561A3

cytochrome b561 family member A3, the group of Cytochrome b561

Basic information

Region (hg38): 11:61348754-61362283

Previous symbols: [ "CYBASC3" ]

Links

ENSG00000162144 ∙ NCBI:220002 ∙ OMIM:618757 ∙ HGNC:23014 ∙ Uniprot:Q8NBI2 ∙ 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 CYB561A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYB561A3 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	10	2	0

Variants in CYB561A3

This is a list of pathogenic ClinVar variants found in the CYB561A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61351014-G-C		not specified	Uncertain significance (Aug 12, 2021)
11-61351023-G-A		not specified	Uncertain significance (Feb 14, 2023)
11-61353088-G-A		not specified	Uncertain significance (Jan 18, 2023)
11-61353792-C-T		not specified	Uncertain significance (Jan 19, 2022)
11-61353843-T-C		not specified	Uncertain significance (Dec 07, 2021)
11-61353858-G-A		not specified	Uncertain significance (May 27, 2022)
11-61353965-G-A		not specified	Uncertain significance (Nov 09, 2021)
11-61356532-C-T		not specified	Uncertain significance (Feb 28, 2024)
11-61356670-G-A		not specified	Uncertain significance (Mar 25, 2024)
11-61356701-G-A		not specified	Likely benign (Nov 10, 2021)
11-61356722-C-T		not specified	Likely benign (Aug 04, 2021)
11-61356725-A-G		not specified	Uncertain significance (Jan 31, 2022)
11-61357219-T-C		not specified	Uncertain significance (Dec 01, 2022)
11-61362038-TCTC-T		Familial aplasia of the vermis	Uncertain significance (Jun 14, 2016)
11-61362042-C-T		Familial aplasia of the vermis	Uncertain significance (Jun 14, 2016)
11-61362081-A-C		Familial aplasia of the vermis	Uncertain significance (Jun 14, 2016)
11-61362210-A-C		Familial aplasia of the vermis	Uncertain significance (Jun 14, 2016)
11-61362252-A-G		Familial aplasia of the vermis	Likely benign (Jun 14, 2016)
11-61362256-C-A		Familial aplasia of the vermis	Uncertain significance (Jun 14, 2016)
11-61362266-G-A		Familial aplasia of the vermis	Uncertain significance (Jun 14, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYB561A3	protein_coding	protein_coding	ENST00000426130	6	13555

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0110	0.952	125733	0	13	125746	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.898	122	153	0.796	0.00000886	1674
Missense in Polyphen		44	58.687	0.74973		677
Synonymous	0.0202	67	67.2	0.997	0.00000418	546
Loss of Function	1.81	5	11.7	0.429	4.98e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000151	0.000151
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ferric-chelate reductase that reduces Fe(3+) to Fe(2+) before its transport from the endosome to the cytoplasm. Probably uses ascorbate as electron donor (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.288
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyb561a3
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: oxidation-reduction process
• Cellular component: lysosomal membrane;integral component of membrane;late endosome membrane
• Molecular function: protein binding;oxidoreductase activity;metal ion binding