ZBED3

zinc finger BED-type containing 3, the group of Zinc fingers BED-type|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 5:77072071-77087285

Links

ENSG00000132846 ∙ NCBI:84327 ∙ OMIM:615250 ∙ HGNC:20711 ∙ Uniprot:Q96IU2 ∙ 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 ZBED3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBED3 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			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	2	0

Variants in ZBED3

This is a list of pathogenic ClinVar variants found in the ZBED3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-77077251-G-A		not specified	Likely benign (Nov 30, 2022)
5-77077343-G-C			Likely benign (Mar 01, 2023)
5-77077424-C-T		not specified	Uncertain significance (May 24, 2023)
5-77077545-C-T		not specified	Uncertain significance (Mar 17, 2023)
5-77077593-C-T		not specified	Uncertain significance (Dec 17, 2023)
5-77077644-C-G		not specified	Uncertain significance (Nov 18, 2023)
5-77077649-C-G		not specified	Uncertain significance (Nov 12, 2021)
5-77077655-T-A		not specified	Uncertain significance (Nov 17, 2021)
5-77077658-T-G		not specified	Uncertain significance (Sep 21, 2021)
5-77077661-C-G		not specified	Uncertain significance (Aug 09, 2021)
5-77077662-C-G		not specified	Uncertain significance (Aug 09, 2021)
5-77077683-A-G		not specified	Uncertain significance (Aug 30, 2021)
5-77077701-C-T		not specified	Uncertain significance (Jan 11, 2023)
5-77077859-G-T		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBED3	protein_coding	protein_coding	ENST00000255198	1	15252

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0825	0.568	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.910	19	33.9	0.560	0.00000166	1394
Missense in Polyphen		5	7.5559	0.66173		414
Synonymous	0.909	11	15.6	0.707	8.11e-7	527
Loss of Function	-0.204	1	0.802	1.25	3.52e-8	33

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a positive regulator in the activation of the canonical Wnt/beta-catenin signaling pathway by stabilizing cytoplasmic beta-catenin. Involved in transcription activation of Wnt target gene expression (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.101

Haploinsufficiency Scores

• pHI: 0.0956
• hipred: N
• hipred_score: 0.238

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.418

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbed3

Gene ontology

• Biological process: negative regulation of protein phosphorylation;Wnt signaling pathway;positive regulation of transcription by RNA polymerase II;protein stabilization;positive regulation of canonical Wnt signaling pathway
• Cellular component: cytosol;membrane
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding