ZNF133

protein-coding

zinc finger protein 133, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF150

MANE transcript

NM_001352452.2

Inheritance

—

ClinVar variants

U:68B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr20:18,288,283-18,316,996

External References & Databases

Ensembl (ENSG00000125846)

Transcript & Mutation Effects

hg38 • Region Span ~28.7 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 ZNF133 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001352452.2. 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					2 clinvar	2
missense			68 clinvar	4 clinvar		72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	68	4	2	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 195 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001352452.2	RefSeq	NP_001339381.2	3	MANE Select
ENST00000425686.3	Ensembl	ENSP00000406638.2	3	MANE Select
NM_001083330.4	RefSeq	NP_001076799.2	3	Standard
NM_001282995.3	RefSeq	NP_001269924.2	3	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 by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377671
Coding exons: 3
Length: 28520
Individuals with no LoFs: 125713
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 125741
p: 0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.01	269	379	0.710	0.0000214	4272
Missense (PolyPhen)		76	152.08	0.49974		1773
Synonymous	1.03	139	155	0.895	0.00000940	1265
Loss of Function	3.01	9	25.3	0.355	0.00000168	266

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation as a repressor.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.689
RVIS EVS: -0.04
RVIS percentile EVS: 50.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.678

Gene Damage Prediction

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