YBEY

protein-coding

ybeY metalloendoribonuclease

Gene summary

This gene encodes a highly conserved metalloprotein. A similar protein in bacteria acts as an endoribonuclease, and is thought to function in ribosomal RNA maturation and ribosome assembly. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

Previous symbols:

C21orf57

MANE transcript

NM_001314025.2

Inheritance

—

ClinVar variants

U:24B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.42

Max pathogenic AF

—

Genomic locus

chr21:46,286,342-46,297,751

External References & Databases

Ensembl (ENSG00000182362)

Transcript & Mutation Effects

hg38 • Region Span ~11.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to YBEY variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 21

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001314025.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			20 clinvar	1 clinvar		21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	24	1	0	25

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 78 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001314025.2	RefSeq	NP_001300954.1	4	MANE Select
ENST00000397701.9	Ensembl	ENSP00000380813.4	4	MANE Select
NM_001006114.3	RefSeq	NP_001006114.1	2	Standard
NM_001314022.2	RefSeq	NP_001300951.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

rRNA processing
proteolysis
RNA phosphodiester bond hydrolysis, endonucleolytic

Molecular Function

metalloendopeptidase activity
endoribonuclease activity
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000329319
Coding exons: 4
Length: 11415
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125748
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0149	83	83.4	0.995	0.00000403	1077
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000070	0.000070	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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