ZNF404

protein-coding

zinc finger protein 404, 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. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001033719.3

Inheritance

—

ClinVar variants

U:82B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr19:43,872,365-43,901,385

External References & Databases

Ensembl (ENSG00000176222)

Transcript & Mutation Effects

hg38 • Region Span ~29.0 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 ZNF404 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 84

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001033719.3. 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			1 clinvar	3 clinvar		4
missense			80 clinvar	4 clinvar		84
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	82	7	0	89

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001033719.3	RefSeq	NP_001028891.2	3	MANE Select
ENST00000587539.2	Ensembl	ENSP00000466051.1	3	MANE Select
ENST00000591815.2	Ensembl	ENSP00000521059.1	3	Standard
ENST00000591815.3	Ensembl	ENSP00000521059.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000587539
Coding exons: 3
Length: 29023
Individuals with no LoFs: 125253
Homozygous LoFs: 0
Heterozygous LoFs: 135
Defined: 125388
p: 0.000538

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.992	243	291	0.836	0.0000139	3699
Missense (PolyPhen)		83	97.716	0.8494		1261
Synonymous	0.884	83	93.9	0.884	0.00000442	912
Loss of Function	0.975	14	18.5	0.756	8.99e-7	282

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00046	0.00044	rare
Latino/Admixed American	0.00099	0.00098	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.0025	0.0025	notable
Finnish	0.00066	0.00065	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00033	0.00033	rare
Other	0.00051	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.00146

Gene Damage Prediction

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