ZBED4

protein-coding

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

Gene summary

Enables identical protein binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_014838.3

Inheritance

—

ClinVar variants

P:1U:165B:22

Top phenotype

Short stature

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr22:49,853,844-49,897,383

External References & Databases

Ensembl (ENSG00000100426)

Transcript & Mutation Effects

hg38 • Region Span ~43.5 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 ZBED4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 175

not providedTotal: 8

Short statureTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014838.3. 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	1 clinvar	5 clinvar	8
missense			163 clinvar	15 clinvar	1 clinvar	179
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	165	16	6	188

Highest pathogenic variant AF is 0.0000041141766

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014838.3	RefSeq	NP_055653.2	1	MANE Select
ENST00000216268.6	Ensembl	ENSP00000216268.4	1	MANE Select
ENST00000850559.1	Ensembl	ENSP00000520851.1	1	Standard
ENST00000850559.2	Ensembl	ENSP00000520851.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding
metal ion binding
protein dimerization activity

Cellular Component

nucleus
nucleoplasm
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000216268
Coding exons: 1
Length: 36237
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125746
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.26	560	732	0.765	0.0000468	7702
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.0287
RVIS EVS: -1.31
RVIS percentile EVS: 4.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.220

Gene Damage Prediction

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