ZBED4

zinc finger BED-type containing 4, the group of Zinc fingers BED-type

Basic information

Region (hg38): 22:49853844-49897383

Links

ENSG00000100426 ∙ NCBI:9889 ∙ OMIM:612552 ∙ HGNC:20721 ∙ Uniprot:O75132 ∙ 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 ZBED4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBED4 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					5	5
missense			98	10	1	109
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	98	10	6

Variants in ZBED4

This is a list of pathogenic ClinVar variants found in the ZBED4 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-49883676-T-G		not specified	Uncertain significance (Mar 06, 2025)
22-49883677-G-C		not specified	Uncertain significance (May 17, 2023)
22-49883699-G-A		not specified	Likely benign (Sep 16, 2021)
22-49883708-G-A		not specified	Uncertain significance (Nov 13, 2024)
22-49883729-A-C		not specified	Uncertain significance (Mar 13, 2023)
22-49883817-C-T		not specified	Uncertain significance (Aug 31, 2022)
22-49883825-G-A		not specified	Uncertain significance (Oct 26, 2021)
22-49883834-C-T		Short stature	Pathogenic (Nov 18, 2001)
22-49883838-C-T		not specified	Uncertain significance (Dec 01, 2022)
22-49883839-G-A			Benign (Apr 03, 2018)
22-49883868-A-G		not specified	Uncertain significance (Nov 07, 2022)
22-49883874-C-T		not specified	Uncertain significance (Sep 03, 2024)
22-49883889-C-T		not specified	Uncertain significance (Apr 04, 2023)
22-49883990-C-T		not specified	Uncertain significance (Sep 29, 2023)
22-49884035-T-A		not specified	Uncertain significance (Jan 03, 2024)
22-49884071-A-G		not specified	Uncertain significance (Feb 26, 2024)
22-49884084-A-G		not specified	Uncertain significance (Oct 31, 2022)
22-49884204-C-T		not specified	Uncertain significance (Feb 15, 2025)
22-49884213-C-T		not specified	Uncertain significance (Feb 16, 2023)
22-49884221-C-T		not specified	Uncertain significance (Nov 25, 2024)
22-49884248-G-A		not specified	Likely benign (Dec 19, 2022)
22-49884249-C-T		not specified	Uncertain significance (Feb 27, 2025)
22-49884312-C-T		not specified	Uncertain significance (Sep 22, 2023)
22-49884344-T-C		not specified	Uncertain significance (Aug 04, 2023)
22-49884377-A-G		not specified	Likely benign (Jan 17, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBED4	protein_coding	protein_coding	ENST00000216268	1	36237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.507	0.493	125732	0	14	125746	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.26	560	732	0.765	0.0000468	7702
Missense in Polyphen		132	248.87	0.5304		2612
Synonymous	-1.78	372	331	1.12	0.0000249	2340
Loss of Function	4.14	7	32.5	0.215	0.00000171	384

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000910	0.0000907
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000937	0.0000924
European (Non-Finnish)	0.0000710	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.0287
• rvis_EVS: -1.31
• rvis_percentile_EVS: 4.82

Haploinsufficiency Scores

• pHI: 0.150
• hipred: Y
• hipred_score: 0.662
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.220

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbed4
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding;protein dimerization activity