ZNF804B

Summary

ZNF804B (zinc finger protein 804B, HGNC:21958) is a protein-coding gene on chromosome 7q21.13, encoding Zinc finger protein 804B (A4D1E1).

Predicted to enable zinc ion binding activity. Predicted to be active in nucleus.

Source: NCBI Gene 219578 — RefSeq curated summary.

At a glance

• GWAS associations: 17
• Clinical variants (ClinVar): 210 total
• MANE Select transcript: NM_181646

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21958
Approved symbol	ZNF804B
Name	zinc finger protein 804B
Location	7q21.13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32110
Ensembl gene	ENSG00000182348
Ensembl biotype	protein_coding
Entrez	219578

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000333190, ENST00000611114

RefSeq mRNA: 1 — MANE Select: NM_181646 NM_181646

CCDS: CCDS5613

Canonical transcript exons

ENST00000333190 — 4 exons

Exon	Start	End
ENSE00001300488	88759700	88760084
ENSE00001324621	89218155	89218295
ENSE00002318419	89333363	89338528
ENSE00002454319	89327344	89327474

Expression profiles

Bgee: expression breadth broad, 24 present calls, max score 71.89.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2651 / max 41.3376, expressed in 137 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
79425	0.1364	69
79424	0.0789	48
79422	0.0317	14
79423	0.0181	6

Top tissues by expression

123 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	71.89	silver quality
left lobe of thyroid gland	UBERON:0001120	66.47	gold quality
thyroid gland	UBERON:0002046	66.29	gold quality
right lobe of thyroid gland	UBERON:0001119	65.94	gold quality
superior frontal gyrus	UBERON:0002661	55.43	gold quality
prefrontal cortex	UBERON:0000451	54.25	gold quality
cortical plate	UBERON:0005343	50.18	gold quality
primary visual cortex	UBERON:0002436	46.91	silver quality
body of pancreas	UBERON:0001150	46.65	gold quality
frontal cortex	UBERON:0001870	46.41	gold quality
corpus callosum	UBERON:0002336	44.99	gold quality
adult mammalian kidney	UBERON:0000082	44.06	gold quality
lymph node	UBERON:0000029	44.00	gold quality
kidney	UBERON:0002113	42.76	gold quality
placenta	UBERON:0001987	42.13	silver quality
pancreas	UBERON:0001264	41.38	gold quality
sural nerve	UBERON:0015488	40.92	gold quality
vermiform appendix	UBERON:0001154	40.83	silver quality
bone marrow cell	CL:0002092	40.12	gold quality
cerebral cortex	UBERON:0000956	40.05	gold quality
Brodmann (1909) area 9	UBERON:0013540	38.27	silver quality
dorsolateral prefrontal cortex	UBERON:0009834	37.36	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ganglionic eminence	UBERON:0004023	37.15	gold quality
anterior cingulate cortex	UBERON:0009835	36.54	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
bone marrow	UBERON:0002371	35.94	gold quality
cortex of kidney	UBERON:0001225	34.90	gold quality
monocyte	CL:0000576	34.37	gold quality
brain	UBERON:0000955	33.81	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	2230.99
E-HCAD-25	yes	854.37
E-ANND-3	yes	4.75

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTCF

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf804b	ENSDARG00000103396
mus_musculus	Zfp804b	ENSMUSG00000092094
rattus_norvegicus	Zfp804b	ENSRNOG00000031306

Paralogs (2): ZNF804A (ENSG00000170396), GPATCH8 (ENSG00000186566)

Protein

Protein identifiers

Zinc finger protein 804B — A4D1E1 (reviewed: A4D1E1)

All UniProt accessions (2): A4D1E1, A0A087WUA7

RefSeq proteins (1): NP_857597* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR052445	ZNF804A-like/GPATCH8	Family

UniProt features (11 total): sequence variant 7, chain 1, zinc finger region 1, sequence conflict 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A4D1E1-F1	43.04	0.06

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 22 (showing top): RRAGTTGT_UNKNOWN, AACTTT_UNKNOWN, YATGNWAAT_OCT_C, LAKE_ADULT_KIDNEY_C3_PROXIMAL_TUBULE_EPITHELIAL_CELLS_S1_S2, LAKE_ADULT_KIDNEY_C5_PROXIMAL_TUBULE_EPITHELIAL_CELLS_STRESS_INFLAM, DESCARTES_MAIN_FETAL_BIPOLAR_CELLS, DESCARTES_FETAL_ADRENAL_SCHWANN_CELLS, DESCARTES_FETAL_EYE_BIPOLAR_CELLS, DESCARTES_FETAL_MUSCLE_SCHWANN_CELLS, DESCARTES_FETAL_PLACENTA_STROMAL_CELLS, DESCARTES_FETAL_SPLEEN_STROMAL_CELLS, ZA_UNIPROT_Q9UM89_UNREVIEWED_GENES_TARGET_GENES, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_2H_ACT_CD4_TCELL_DN, GSE17974_2H_VS_72H_UNTREATED_IN_VITRO_CD4_TCELL_UP, GSE2706_R848_VS_LPS_2H_STIM_DC_DN

GO Biological Process (0):

GO Molecular Function (2): zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

702 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF804B	TEX47	Q8TBZ9	643
ZNF804B	TMEM253	P0C7T8	476
ZNF804B	ELAPOR2	A8MWY0	475
ZNF804B	SLC35F3	Q8IY50	420
ZNF804B	RIMS4	Q9H426	403
ZNF804B	CLBA1	Q96F83	396
ZNF804B	OR10V1	Q8NGI7	395
ZNF804B	DEF8	Q6ZN54	393
ZNF804B	AKAP6	Q13023	378
ZNF804B	OR4F16	Q6IEY1	377
ZNF804B	OR8K5	Q8NH50	375
ZNF804B	TPST1	O60507	374
ZNF804B	ALG10	Q5BKT4	371
ZNF804B	STEAP2	Q8NFT2	369
ZNF804B	OR10G8	Q8NGN5	369
ZNF804B	NTNG1	Q9Y2I2	369

IntAct

2 interactions, top by confidence:

A	B	Type	Score
ZNF804B	KRT8	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (5): ZNF804B (Affinity Capture-MS), KRT8 (Proximity Label-MS), ZNF804B (Positive Genetic), ZNF804B (Protein-RNA), ZNF804B (Affinity Capture-MS)

ESM2 similar proteins: A0A140LI88, A4D1E1, D3Z987, D3ZUC6, E5FYH0, E5FYH1, E9Q3S4, F6ULY3, F7DF15, G3S077, G7H7V7, G7NY55, O35923, O54952, O88491, O95405, P38398, P48754, P51587, P97929, Q0VBV7, Q0VGT4, Q2M3C7, Q3V089, Q56UN5, Q5DTT3, Q5F2C3, Q5VWN6, Q61493, Q68DQ2, Q6J6I8, Q6J6I9, Q6J6J0, Q6NSW3, Q6ZP01, Q7TSY8, Q7Z570, Q80U44, Q864S8, Q864U1

Diamond homologs: A2A6A1, A2AKY4, A4D1E1, Q7Z570, Q9UKJ3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

210 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	172
Likely benign	19
Benign	15

Top pathogenic / likely-pathogenic (0)

SpliceAI

3947 predictions. Top by Δscore:

Variant	Effect	Δscore
7:88786708:G:GT	donor_gain	1.0000
7:89218151:A:AG	acceptor_gain	1.0000
7:89218151:AAAG:A	acceptor_gain	1.0000
7:89218152:A:G	acceptor_gain	1.0000
7:89218152:AAG:A	acceptor_gain	1.0000
7:89218153:A:AG	acceptor_gain	1.0000
7:89218153:A:AT	acceptor_loss	1.0000
7:89218153:AG:A	acceptor_gain	1.0000
7:89218154:G:GG	acceptor_gain	1.0000
7:89218154:G:GT	acceptor_loss	1.0000
7:89218154:GG:G	acceptor_gain	1.0000
7:89218154:GGA:G	acceptor_gain	1.0000
7:89218154:GGAT:G	acceptor_gain	1.0000
7:89218154:GGATT:G	acceptor_gain	1.0000
7:89218291:AGCAG:A	donor_loss	1.0000
7:89218292:GCAG:G	donor_gain	1.0000
7:89218293:CAG:C	donor_loss	1.0000
7:89218294:AGGTA:A	donor_loss	1.0000
7:89218295:GG:G	donor_loss	1.0000
7:89218296:GTAA:G	donor_loss	1.0000
7:89218297:T:G	donor_loss	1.0000
7:88761890:ACTTT:A	acceptor_gain	0.9900
7:88761894:T:TA	acceptor_gain	0.9900
7:88795044:CTT:C	acceptor_gain	0.9900
7:88795047:C:CC	acceptor_gain	0.9900
7:88795862:G:GT	donor_gain	0.9900
7:88918958:G:GT	donor_gain	0.9900
7:88919001:T:G	donor_gain	0.9900
7:88947484:G:GT	donor_gain	0.9900
7:88947485:G:T	donor_gain	0.9900

AlphaMissense

9012 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:89327371:T:C	F93L	1.000
7:89327373:T:A	F93L	1.000
7:89327373:T:G	F93L	1.000
7:89218215:T:C	C57R	0.999
7:89218216:G:A	C57Y	0.999
7:89218217:T:G	C57W	0.999
7:89218224:T:A	C60S	0.999
7:89218224:T:C	C60R	0.999
7:89218225:G:A	C60Y	0.999
7:89218225:G:C	C60S	0.999
7:89218225:G:T	C60F	0.999
7:89218226:T:G	C60W	0.999
7:89218254:T:C	F70L	0.999
7:89218255:T:C	F70S	0.999
7:89218255:T:G	F70C	0.999
7:89218256:T:A	F70L	0.999
7:89218256:T:G	F70L	0.999
7:89218263:C:G	H73D	0.999
7:89218265:T:A	H73Q	0.999
7:89218265:T:G	H73Q	0.999
7:89218272:T:C	S76P	0.999
7:89218287:C:G	H81D	0.999
7:89218292:G:C	K82N	0.999
7:89218292:G:T	K82N	0.999
7:89327346:A:C	R84S	0.999
7:89327346:A:T	R84S	0.999
7:89327348:T:C	L85P	0.999
7:89327357:T:C	L88S	0.999
7:89327361:G:C	K89N	0.999
7:89327361:G:T	K89N	0.999

dbSNP variants (sampled 300 via entrez): RS1000008246 (7:89079761 G>A,T), RS1000011944 (7:89239785 A>C), RS1000013832 (7:89243533 A>T), RS1000017357 (7:89166194 A>G), RS1000025734 (7:89296024 TA>T,TAA), RS1000028767 (7:88916100 T>C), RS1000031785 (7:88836533 T>A), RS1000034520 (7:89319300 G>A), RS1000037093 (7:89314555 T>C), RS1000037623 (7:89205783 G>A), RS1000067518 (7:89085988 A>G), RS1000073222 (7:88759417 T>C), RS1000080461 (7:88995179 A>G), RS1000082632 (7:88833334 A>T), RS1000083160 (7:89328796 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

17 associations (top):

Study	Trait	p-value
GCST000840_5	Body mass index	9.000000e-06
GCST000873_6	Anorexia nervosa	2.000000e-06
GCST001474_17	Hypothyroidism	7.000000e-06
GCST001786_18	Dental caries	7.000000e-06
GCST002405_4	Cervical cancer	9.000000e-06
GCST002579_29	Heschl’s gyrus morphology	4.000000e-06
GCST002931_2	Aluminium levels	7.000000e-06
GCST005042_10	Restless legs syndrome	2.000000e-34
GCST005586_10	Breast milk fatty acid composition (maternal genotype effect)	5.000000e-08
GCST005586_6	Breast milk fatty acid composition (maternal genotype effect)	5.000000e-09
GCST005587_5	Breast milk fatty acid composition (infant genotype effect)	5.000000e-06
GCST006999_1	Logical memory (immediate recall) in mild cognitive impairment	5.000000e-06
GCST007000_3	Logical memory (delayed recall) in mild cognitive impairment	3.000000e-09
GCST007239_15	Ovarian cancer	9.000000e-06
GCST009207_8	Lateral ventricle volume	3.000000e-07
GCST011155_5	Nontraumatic osteonecrosis of the femoral head	1.000000e-07
GCST011426_24	Systemic lupus erythematosus	1.000000e-06

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0005939	parental genotype effect measurement
EFO:0007959	fetal genotype effect measurement
EFO:0004874	memory performance
EFO:0008487	lateral ventricle volume measurement
EFO:1001930	idiopathic osteonecrosis of the femoral head

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	increases phosphorylation	1
bisphenol A	affects cotreatment, affects methylation, decreases methylation	1
2,3,4,5-tetrachlorophenate	affects response to substance	1
Fulvestrant	affects cotreatment, affects methylation	1
Benzo(a)pyrene	increases methylation	1
Phthalic Acids	decreases methylation	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.