ZNF33A

protein-coding

zinc finger protein 33A, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable transcription cis-regulatory region binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF33
ZNF11A

MANE transcript

NM_006954.2

Inheritance

—

ClinVar variants

U:117B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr10:38,010,650-38,065,088

External References & Databases

Ensembl (ENSG00000189180)

Transcript & Mutation Effects

hg38 • Region Span ~54.4 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 ZNF33A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 120

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006954.2. 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			1 clinvar	1 clinvar		2
missense			115 clinvar	5 clinvar		120
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	117	6	0	123

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 55 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006954.2	RefSeq	NP_008885.1	4	MANE Select
ENST00000432900.7	Ensembl	ENSP00000402467.3	4	MANE Select
NM_001278170.2	RefSeq	NP_001265099.1	4	Standard
NM_001278171.2	RefSeq	NP_001265100.1	1	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

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374618
Coding exons: 4
Length: 54439
Individuals with no LoFs: 125584
Homozygous LoFs: 0
Heterozygous LoFs: 164
Defined: 125748
p: 0.000652

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.376	429	408	1.05	0.0000185	5441
Missense (PolyPhen)		134	134.36	0.99733		1741
Synonymous	-0.856	161	148	1.09	0.00000700	1363
Loss of Function	1.71	18	27.7	0.649	0.00000123	416

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0021	0.0021	notable
Latino/Admixed American	0.00046	0.00046	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0010	0.0010	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00061	0.00060	rare
South Asian	0.00082	0.00082	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0738

Intolerance Scores

LoFtool: 0.918
RVIS EVS: 0.18
RVIS percentile EVS: 66.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.468

Gene Damage Prediction

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