YBEY

ybeY metalloendoribonuclease

Basic information

Region (hg38): 21:46286342-46297751

Previous symbols: [ "C21orf57" ]

Links

ENSG00000182362 ∙ NCBI:54059 ∙ OMIM:617461 ∙ HGNC:1299 ∙ Uniprot:P58557 ∙ 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 YBEY gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YBEY 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			10			10
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	10	0	2

Variants in YBEY

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

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

Position	Type	Phenotype	Significance	ClinVar
21-46286923-G-A		not specified	Uncertain significance (Sep 26, 2023)
21-46287082-A-G		not specified	Uncertain significance (Aug 02, 2021)
21-46287095-C-T		not specified	Uncertain significance (Nov 19, 2024)
21-46287125-T-TAAAAA		not specified	Benign (Mar 28, 2016)
21-46287136-T-A		not specified	Benign (Mar 29, 2016)
21-46291341-A-T		not specified	Uncertain significance (Oct 29, 2024)
21-46291368-T-G		not specified	Uncertain significance (Jun 17, 2024)
21-46291386-T-G		not specified	Uncertain significance (Dec 07, 2021)
21-46291428-G-A		not specified	Uncertain significance (Aug 12, 2021)
21-46291449-A-G		not specified	Uncertain significance (Aug 02, 2021)
21-46291454-G-C		not specified	Uncertain significance (Dec 13, 2022)
21-46296172-C-T		not specified	Uncertain significance (Feb 12, 2024)
21-46297544-C-G		not specified	Uncertain significance (Nov 10, 2024)
21-46297557-G-A		not specified	Uncertain significance (Mar 01, 2023)
21-46297557-G-T		not specified	Uncertain significance (Nov 11, 2024)
21-46297582-G-T		not specified	Uncertain significance (Oct 08, 2024)
21-46297594-G-A		not specified	Uncertain significance (Nov 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YBEY	protein_coding	protein_coding	ENST00000329319	4	11415

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-7	0.0625	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0149	83	83.4	0.995	0.00000403	1077
Missense in Polyphen		24	26.609	0.90194		330
Synonymous	1.13	27	35.5	0.760	0.00000204	321
Loss of Function	-0.983	9	6.33	1.42	2.66e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000705	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Single strand-specific metallo-endoribonuclease involved in rRNA maturation. {ECO:0000305|PubMed:28153719}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.216
• ghis: 0.433

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ybey

Gene ontology

• Biological process: rRNA processing;proteolysis;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: nucleus
• Molecular function: metalloendopeptidase activity;endoribonuclease activity;metal ion binding