ZNF45

protein-coding

zinc finger protein 45, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription factor activity. Predicted to be involved in DNA-templated transcription and regulation of DNA-templated transcription. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF13

MANE transcript

NM_003425.4

Inheritance

—

ClinVar variants

U:85B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr19:43,912,624-43,935,282

External References & Databases

Ensembl (ENSG00000124459)

Transcript & Mutation Effects

hg38 • Region Span ~22.7 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 ZNF45 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 88

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003425.4. 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						0
missense			85 clinvar	3 clinvar		88
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	85	3	0	88

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 181 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003425.4	RefSeq	NP_003416.1	4	MANE Select
ENST00000269973.10	Ensembl	ENSP00000269973.4	4	MANE Select
ENST00000588140.1	Ensembl	ENSP00000467551.1	3	Standard
ENST00000589703.5	Ensembl	ENSP00000468579.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription, DNA-templated
regulation of transcription by RNA polymerase II
transcription initiation from RNA polymerase II promoter
multicellular organism development

Molecular Function

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

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000269973
Coding exons: 4
Length: 22650
Individuals with no LoFs: 125670
Homozygous LoFs: 0
Heterozygous LoFs: 76
Defined: 125746
p: 0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.880	313	360	0.869	0.0000179	4506
Missense (PolyPhen)		152	190.47	0.79804		2268
Synonymous	-0.217	129	126	1.02	0.00000590	1204
Loss of Function	2.44	15	29.3	0.513	0.00000169	372

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00038	0.00038	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00034	0.00034	rare
South Asian	0.00036	0.00036	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.845
RVIS EVS: 0.45
RVIS percentile EVS: 77.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.850

Gene Damage Prediction

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