ZBTB45

protein-coding

zinc finger and BTB domain containing 45, the group of Zinc fingers C2H2-type|BTB domain containing

Gene summary

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II; regulation of cytokine production; and regulation of immune system process. Predicted to be located in nucleus. Predicted to be active in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF499

MANE transcript

NM_001316979.2

Inheritance

—

ClinVar variants

U:85B:6

Top phenotype

ZBTB45-related condition

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr19:58,513,530-58,538,911

External References & Databases

Ensembl (ENSG00000119574)

Transcript & Mutation Effects

hg38 • Region Span ~25.4 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 ZBTB45 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 3

ZBTB45-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001316979.2. 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				3 clinvar	1 clinvar	4
missense			85 clinvar	2 clinvar		87
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	85	5	1	91

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001316979.2	RefSeq	NP_001303908.1	2	MANE Select
ENST00000594051.6	Ensembl	ENSP00000469089.1	2	MANE Select
NM_001316978.2	RefSeq	NP_001303907.1	2	Standard
NM_001316981.2	RefSeq	NP_001303910.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
nervous system development

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000594051
Coding exons: 2
Length: 25382
Individuals with no LoFs: 125690
Homozygous LoFs: 0
Heterozygous LoFs: 47
Defined: 125737
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.36	287	360	0.798	0.0000245	3228
Missense (PolyPhen)		96	145.56	0.6595		1297
Synonymous	-1.93	195	164	1.19	0.0000124	1177
Loss of Function	1.22	9	13.9	0.648	8.32e-7	129

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00033	0.00031	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00027	rare
Finnish	0.000096	0.000092	rare
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.000066	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation (Probable). In the central nervous system, may play a role in glial cell differentiation (By similarity). {ECO:0000250|UniProtKB:Q52KG4, ECO:0000305}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.397
RVIS EVS: -0.38
RVIS percentile EVS: 28.01

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.869

Gene Damage Prediction

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