ZNF404 zinc finger protein 404 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ZNF404provided by HGNC
Official Full Name: zinc finger protein 404provided by HGNC
Primary source: HGNC:HGNC:19417
See related: Ensembl:ENSG00000176222 AllianceGenome:HGNC:19417
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
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. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Mar 2025]
Expression: Ubiquitous expression in brain (RPKM 3.0), testis (RPKM 2.6) and 25 other tissues See more
Orthologs: all
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Genomic context

Location:: 19q13.31

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (43872365..43883964, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (46695264..46706862, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (44376517..44388116, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The deleterious SNPs localized in STXBP4 and ZNF404 genes were identified which might play a role in breast cancer development by dysregulating its gene expression.
Title: Computational Analysis of Breast Cancer GWAS Loci Identifies the Putative Deleterious Effect of STXBP4 and ZNF404 Gene Variants.
We used The Cancer Genome Atlas breast cancer patient data to identify ANKLE1 and ZNF404 as the target genes of candidate TF binding site SNPs in the 19p13.11 and 19q13.31 GWAS-identified loci. These SNPs are associated with the expression of ZNF404 and ANKLE1 in breast tissue.
Title: Identification of breast cancer associated variants that modulate transcription factor binding.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
The correlation between reading and mathematics ability at age twelve has a substantial genetic component. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: zinc finger protein 404

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001033719.3 → NP_001028891.2 zinc finger protein 404

See identical proteins and their annotated locations for NP_001028891.2

Status: VALIDATED

Source sequence(s)

AC011508, BC101333, BQ188692

Consensus CDS

CCDS59394.1

UniProtKB/Swiss-Prot

A4FU30, K7ELF2, Q494X3

Related

ENSP00000466051.1, ENST00000587539.2

Conserved Domains (6) summary

smart00349
Location:6 → 51

KRAB; krueppel associated box

COG5048
Location:106 → 510

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:357 → 377

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam01352
Location:6 → 45

KRAB; KRAB box

pfam13465
Location:482 → 506

zf-H2C2_2; Zinc-finger double domain

pfam14353
Location:413 → 458

CpXC; CpXC protein