ZFP69B

Summary

ZFP69B (ZFP69 zinc finger protein B, HGNC:28053) is a protein-coding gene on chromosome 1p34.2, encoding Zinc finger protein 69 homolog B (Q9UJL9). May be involved in transcriptional regulation.

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 Golgi organization. Located in nucleolus.

Source: NCBI Gene 65243 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 70 total
• MANE Select transcript: NM_023070

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28053
Approved symbol	ZFP69B
Name	ZFP69 zinc finger protein B
Location	1p34.2
Locus type	gene with protein product
Status	Approved
Aliases	ZKSCAN23B, FLJ34293, ZSCAN54B
Ensembl gene	ENSG00000187801
Ensembl biotype	protein_coding
Entrez	65243

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 retained_intron

ENST00000361584, ENST00000411995, ENST00000469416, ENST00000484445, ENST00000863980, ENST00000863981, ENST00000961485, ENST00000961486

RefSeq mRNA: 2 — MANE Select: NM_023070 NM_001369565, NM_023070

CCDS: CCDS452

Canonical transcript exons

ENST00000361584 — 5 exons

Exon	Start	End
ENSE00003600713	40454203	40454288
ENSE00003642773	40462421	40463715
ENSE00003847313	40450476	40451088
ENSE00003888829	40457344	40457439
ENSE00003895681	40456945	40457071

Expression profiles

Bgee: expression breadth ubiquitous, 170 present calls, max score 88.26.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.2832 / max 58.5584, expressed in 1206 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2386	3.0307	1159
201485	0.1680	58
2387	0.0736	28
2388	0.0109	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.26	gold quality
cortical plate	UBERON:0005343	82.57	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.55	gold quality
ganglionic eminence	UBERON:0004023	78.37	gold quality
stromal cell of endometrium	CL:0002255	74.00	gold quality
ventricular zone	UBERON:0003053	72.28	gold quality
islet of Langerhans	UBERON:0000006	70.70	gold quality
secondary oocyte	CL:0000655	69.93	gold quality
prefrontal cortex	UBERON:0000451	68.63	gold quality
embryo	UBERON:0000922	66.73	gold quality
oocyte	CL:0000023	64.29	gold quality
vermiform appendix	UBERON:0001154	63.78	gold quality
cingulate cortex	UBERON:0003027	63.38	gold quality
right frontal lobe	UBERON:0002810	63.36	gold quality
pancreas	UBERON:0001264	63.16	gold quality
anterior cingulate cortex	UBERON:0009835	63.07	gold quality
smooth muscle tissue	UBERON:0001135	62.99	gold quality
Brodmann (1909) area 9	UBERON:0013540	62.97	gold quality
nucleus accumbens	UBERON:0001882	62.68	gold quality
rectum	UBERON:0001052	62.54	gold quality
neocortex	UBERON:0001950	62.54	gold quality
gall bladder	UBERON:0002110	62.48	gold quality
frontal cortex	UBERON:0001870	62.05	gold quality
bone marrow cell	CL:0002092	61.06	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	60.94	gold quality
lymph node	UBERON:0000029	60.64	gold quality
caudate nucleus	UBERON:0001873	60.33	gold quality
body of pancreas	UBERON:0001150	60.16	gold quality
caecum	UBERON:0001153	60.15	gold quality
leukocyte	CL:0000738	60.07	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-6142	no	36.53
E-ANND-3	no	1.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting ZFP69B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-181A-2-3P	98.91	67.60	1168
HSA-MIR-1246	98.54	66.21	959
HSA-MIR-376A-5P	97.70	65.61	863
HSA-MIR-376C-3P	97.63	68.88	1263
HSA-MIR-12128	96.67	66.98	1471
HSA-MIR-6834-5P	96.25	64.88	823

Literature-anchored findings (GeneRIF, showing 1)

• ZNF643/ZFP69B Exerts Oncogenic Properties and Associates with Cell Adhesion and Immune Processes. (PMID:38003570)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	CG2712	FBGN0024975
drosophila_melanogaster	Phs	FBGN0036522
drosophila_melanogaster	CG3281	FBGN0260741

Paralogs (62): ZNF582 (ENSG00000018869), ZNF264 (ENSG00000083844), ZNF343 (ENSG00000088876), ZNF684 (ENSG00000117010), ZNF133 (ENSG00000125846), ZNF557 (ENSG00000130544), ZNF337 (ENSG00000130684), ZNF20 (ENSG00000132010), ZFP37 (ENSG00000136866), ZNF614 (ENSG00000142556), KRBOX4 (ENSG00000147121), ZNF599 (ENSG00000153896), ZNF19 (ENSG00000157429), ZNF589 (ENSG00000164048), PRDM9 (ENSG00000164256), ZNF180 (ENSG00000167384), ZNF558 (ENSG00000167785), ZNF35 (ENSG00000169981), ZNF778 (ENSG00000170100), ZNF439 (ENSG00000171291), ZNF440 (ENSG00000171295), ZNF556 (ENSG00000172000), ZNF554 (ENSG00000172006), ZNF596 (ENSG00000172748), ZNF80 (ENSG00000174255), ZNF266 (ENSG00000174652), ZNF25 (ENSG00000175395), ZNF77 (ENSG00000175691), ZNF169 (ENSG00000175787), ZNF404 (ENSG00000176222), ZNF491 (ENSG00000177599), ZNF620 (ENSG00000177842), ZNF619 (ENSG00000177873), ZNF875 (ENSG00000181666), ZNF329 (ENSG00000181894), ZFP90 (ENSG00000184939), ZNF566 (ENSG00000186017), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300)

Protein

Protein identifiers

Zinc finger protein 69 homolog B — Q9UJL9 (reviewed: Q9UJL9)

Alternative names: Zinc finger protein 643

All UniProt accessions (2): E9PS66, Q9UJL9

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation. Essential for Golgi structural integrity.

Subcellular location. Nucleus.

Induction. Up-regulated by Golgi stress-inducing agent nigericin.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UJL9-1	1	yes
Q9UJL9-2	2

RefSeq proteins (2): NP_001356494, NP_075558* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR003309	SCAN_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF01352, PF13465

UniProt features (18 total): zinc finger region 9, cross-link 4, sequence variant 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UJL9-F1	63.17	0.13

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 37, 40, 178, 235

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 59 (showing top): YAGI_AML_WITH_INV_16_TRANSLOCATION, chr1p34, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, HUANG_FOXA2_TARGETS_UP, GOBP_GOLGI_ORGANIZATION, GOCC_NUCLEOLUS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, HATADA_METHYLATED_IN_LUNG_CANCER_UP, VERHAAK_GLIOBLASTOMA_PRONEURAL, PEDRIOLI_MIR31_TARGETS_UP, PHONG_TNF_RESPONSE_VIA_P38_COMPLETE, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ZNF528_TARGET_GENES, ZNF610_TARGET_GENES, ZSCAN30_TARGET_GENES

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), Golgi organization (GO:0007030), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (6): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), nucleolus (GO:0005730), nuclear lumen (GO:0031981)

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
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
organelle organization	1
endomembrane system organization	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular membraneless organelle	1
nucleus	1
intracellular organelle lumen	1

Protein interactions and networks

STRING

340 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZFP69B	C3orf70	A6NLC5	507
ZFP69B	SMAP2	Q8WU79	507
ZFP69B	C16orf96	A6NNT2	433
ZFP69B	ELFN2	Q5R3F8	391
ZFP69B	POC1A	Q8NBT0	365
ZFP69B	DCAF10	Q5QP82	352
ZFP69B	CYTH4	Q9UIA0	349
ZFP69B	ZDHHC23	Q8IYP9	327
ZFP69B	LYSMD3	Q7Z3D4	324
ZFP69B	SORCS1	Q8WY21	320
ZFP69B	NXPE3	Q969Y0	311
ZFP69B	CILP2	Q8IUL8	311
ZFP69B	SNED1	Q8TER0	305
ZFP69B	FAM174B	Q3ZCQ3	305
ZFP69B	KLHL6	Q8WZ60	301

IntAct

10 interactions, top by confidence:

A	B	Type	Score
KRT40	ZFP69B	psi-mi:“MI:0915”(physical association)	0.560
PRPF31	ZFP69B	psi-mi:“MI:0915”(physical association)	0.560
ZFP69B	HNRNPA2B1	psi-mi:“MI:0915”(physical association)	0.400
ZFP69B	HNRNPDL	psi-mi:“MI:0915”(physical association)	0.400
ZFP69B	CNP	psi-mi:“MI:0914”(association)	0.350
PRPF31	ZFP69B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): KRT40 (Two-hybrid), ZFP69B (Affinity Capture-MS), ZFP69B (Two-hybrid), ZFP69B (Proximity Label-MS), ZFP69B (Proximity Label-MS), DBNL (Affinity Capture-MS), ACOT1 (Affinity Capture-MS), UGT1A10 (Affinity Capture-MS), SMAD3 (Affinity Capture-MS), CNP (Affinity Capture-MS), KCTD16 (Affinity Capture-MS), CORO1A (Affinity Capture-MS), ZFP69B (Affinity Capture-MS)

ESM2 similar proteins: A0JPL0, A3KN36, A7MBI1, A8MT65, B2RXC5, D3ZVT0, P08042, P21506, P51508, P52738, Q02525, Q06730, Q12901, Q2KI58, Q2M218, Q2M3W8, Q2M3X9, Q2VY69, Q49AA0, Q4R6J4, Q4V8A8, Q5FWF6, Q5HY98, Q5RB33, Q5RC79, Q5REF1, Q5T5D7, Q5VIY5, Q61967, Q6P2D0, Q6ZN11, Q86XU0, Q86Y25, Q8N782, Q8N859, Q8NB42, Q8TF39, Q8TF47, Q8WXB4, Q95K49

Diamond homologs: A0A087WUV0, Q96K75, Q99676, Q9HBT8, Q9UJL9, Q9UJN7, A0A1W2PQL4, A0JNB1, A0JPL0, A6NK53, A6QLU5, A6QPT6, A7MBI1, A8MT65, A8MUV8, A8MWA4, B2RXC5, B4DU55, B4DX44, E9PYI1, O14628, O75346, P0CH99, P0CI00, P17014, P17030, P17032, P17098, P51786, P85977, Q02386, Q06730, Q06732, Q0VAW7, Q12901, Q13360, Q14586, Q14588, Q14590, Q16587

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	59
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

744 predictions. Top by Δscore:

Variant	Effect	Δscore
1:40451085:GAAG:G	donor_gain	1.0000
1:40454201:A:AG	acceptor_gain	1.0000
1:40454202:G:GG	acceptor_gain	1.0000
1:40456939:TTCTA:T	acceptor_loss	1.0000
1:40456940:TCTA:T	acceptor_loss	1.0000
1:40456941:CTA:C	acceptor_loss	1.0000
1:40456942:TA:T	acceptor_loss	1.0000
1:40457067:AGTGG:A	donor_loss	1.0000
1:40457068:GTGG:G	donor_gain	1.0000
1:40457070:GG:G	donor_gain	1.0000
1:40457071:GG:G	donor_gain	1.0000
1:40451087:AGG:A	donor_loss	0.9900
1:40451089:G:C	donor_loss	0.9900
1:40451089:G:GG	donor_gain	0.9900
1:40454284:CCCAG:C	donor_loss	0.9900
1:40454285:CCAGG:C	donor_loss	0.9900
1:40454286:CAGGT:C	donor_loss	0.9900
1:40454287:AG:A	donor_loss	0.9900
1:40454288:GG:G	donor_loss	0.9900
1:40454290:T:A	donor_loss	0.9900
1:40456938:GTTCT:G	acceptor_loss	0.9900
1:40456943:A:AG	acceptor_gain	0.9900
1:40456944:G:GG	acceptor_gain	0.9900
1:40457032:G:GT	donor_gain	0.9900
1:40457032:G:T	donor_gain	0.9900
1:40457038:A:AG	donor_gain	0.9900
1:40457072:G:GG	donor_gain	0.9900
1:40457073:T:TC	donor_loss	0.9900
1:40457077:G:GT	donor_gain	0.9900
1:40457339:A:G	acceptor_gain	0.9900

AlphaMissense

3550 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:40462930:T:C	F316L	0.999
1:40462932:T:A	F316L	0.999
1:40462932:T:G	F316L	0.999
1:40463350:T:C	F456L	0.999
1:40463352:T:A	F456L	0.999
1:40463352:T:G	F456L	0.999
1:40463014:T:C	F344L	0.998
1:40463016:C:A	F344L	0.998
1:40463016:C:G	F344L	0.998
1:40463098:T:C	F372L	0.998
1:40463100:C:A	F372L	0.998
1:40463100:C:G	F372L	0.998
1:40463266:T:C	F428L	0.998
1:40463268:C:A	F428L	0.998
1:40463268:C:G	F428L	0.998
1:40463434:T:C	F484L	0.998
1:40463436:T:A	F484L	0.998
1:40463436:T:G	F484L	0.998
1:40463293:C:G	H437D	0.997
1:40463369:T:C	L462P	0.997
1:40463377:C:G	H465D	0.997
1:40463518:T:C	F512L	0.997
1:40463520:C:A	F512L	0.997
1:40463520:C:G	F512L	0.997
1:40462971:T:A	H329Q	0.996
1:40462971:T:G	H329Q	0.996
1:40463033:T:C	L350P	0.996
1:40463043:T:A	H353Q	0.996
1:40463043:T:G	H353Q	0.996
1:40463117:T:C	L378P	0.996

dbSNP variants (sampled 300 via entrez): RS1000057720 (1:40452814 C>T), RS1000088450 (1:40452495 C>T), RS1000354739 (1:40459277 T>G), RS1000694220 (1:40464072 C>G,T), RS1000707415 (1:40450283 T>A,G), RS1000759356 (1:40450528 G>A), RS1001432361 (1:40458464 G>A), RS1002275040 (1:40452352 A>G), RS1002306116 (1:40451988 G>A), RS1002639741 (1:40450476 G>A), RS1002824216 (1:40463809 A>G), RS1002878150 (1:40463462 A>C,G), RS1003132407 (1:40457211 T>C), RS1003184198 (1:40458419 C>T), RS1003212345 (1:40448934 G>A)

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

1 associations (top):

Study	Trait	p-value
GCST006658_11	Longevity	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases expression	4
Valproic Acid	affects cotreatment, decreases expression, affects expression	4
Cyclosporine	affects expression, increases expression	4
trichostatin A	affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
Aflatoxin B1	decreases expression, affects expression	2
TAK-243	increases sumoylation	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
terbufos	decreases methylation	1
resorcinol	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Fonofos	decreases methylation	1
Estradiol	affects cotreatment, increases expression	1
N-Nitrosopyrrolidine	increases expression	1
Parathion	decreases methylation	1
Quercetin	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	increases expression	1
Oxyquinoline	decreases expression	1
Okadaic Acid	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_XV97	HEK293 eGFP-ZFP69B	Transformed cell line	Female

Clinical trials (associated diseases)

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