ZNF623

Summary

ZNF623 (zinc finger protein 623, HGNC:29084) is a protein-coding gene on chromosome 8q24.3, encoding Zinc finger protein 623 (O75123). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-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.

Source: NCBI Gene 9831 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 60 total
• MANE Select transcript: NM_001261843

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29084
Approved symbol	ZNF623
Name	zinc finger protein 623
Location	8q24.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0628
Ensembl gene	ENSG00000183309
Ensembl biotype	protein_coding
Entrez	9831

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 16 protein_coding

ENST00000458270, ENST00000501748, ENST00000526926, ENST00000857826, ENST00000857827, ENST00000857828, ENST00000857829, ENST00000857830, ENST00000857831, ENST00000929455, ENST00000929456, ENST00000929457, ENST00000929458, ENST00000929459, ENST00000950233, ENST00000950234

RefSeq mRNA: 3 — MANE Select: NM_001261843 NM_001082480, NM_001261843, NM_014789

CCDS: CCDS34957, CCDS47931

Canonical transcript exons

ENST00000526926 — 2 exons

Exon	Start	End
ENSE00002144416	143636019	143636145
ENSE00003899615	143649898	143653730

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 86.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.2839 / max 87.0869, expressed in 1773 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
91415	11.2839	1773

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	86.31	gold quality
ganglionic eminence	UBERON:0004023	85.61	gold quality
ventricular zone	UBERON:0003053	83.34	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.10	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.52	gold quality
islet of Langerhans	UBERON:0000006	82.32	gold quality
stromal cell of endometrium	CL:0002255	81.89	gold quality
endometrium	UBERON:0001295	80.96	gold quality
calcaneal tendon	UBERON:0003701	80.30	gold quality
smooth muscle tissue	UBERON:0001135	80.23	gold quality
skeletal muscle tissue	UBERON:0001134	79.72	gold quality
corpus callosum	UBERON:0002336	79.66	gold quality
colonic epithelium	UBERON:0000397	79.52	gold quality
muscle tissue	UBERON:0002385	79.13	gold quality
superior frontal gyrus	UBERON:0002661	79.09	gold quality
tonsil	UBERON:0002372	79.04	gold quality
urinary bladder	UBERON:0001255	78.74	gold quality
adrenal tissue	UBERON:0018303	78.63	gold quality
muscle of leg	UBERON:0001383	78.08	gold quality
leukocyte	CL:0000738	78.07	gold quality
gastrocnemius	UBERON:0001388	77.99	gold quality
monocyte	CL:0000576	77.81	gold quality
ovary	UBERON:0000992	77.59	gold quality
granulocyte	CL:0000094	77.58	gold quality
rectum	UBERON:0001052	77.46	gold quality
pancreas	UBERON:0001264	77.42	gold quality
lymph node	UBERON:0000029	77.32	gold quality
popliteal artery	UBERON:0002250	77.29	gold quality
prefrontal cortex	UBERON:0000451	77.27	gold quality
tibial artery	UBERON:0007610	77.26	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.04

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2497.1	ZNF623	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605368

miRNA regulators (miRDB)

65 targeting ZNF623, 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-5193	100.00	67.26	1744
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-7161-5P	99.68	68.92	1592
HSA-MIR-3934-5P	99.67	64.04	846
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-4804-3P	99.65	67.78	866
HSA-MIR-548U	99.65	67.78	1463
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-183-3P	99.41	69.41	1598
HSA-MIR-5697	99.39	67.74	1249

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp623	ENSMUSG00000050846
rattus_norvegicus	Zfp623	ENSRNOG00000009302

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 623 — O75123 (reviewed: O75123)

All UniProt accessions (1): O75123

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

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

Isoforms (2)

UniProt ID	Names	Canonical?
O75123-1	1	yes
O75123-2	2

RefSeq proteins (3): NP_001075949, NP_001248772, NP_055604 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (21 total): zinc finger region 13, region of interest 2, compositionally biased region 2, chain 1, cross-link 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75123-F1	71.83	0.37

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 (1): 445

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 114 (showing top): BROWNE_HCMV_INFECTION_6HR_DN, GENTILE_RESPONSE_CLUSTER_D3, ONKEN_UVEAL_MELANOMA_UP, GENTILE_UV_HIGH_DOSE_DN, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DAZARD_RESPONSE_TO_UV_NHEK_UP, TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C, JOHNSTONE_PARVB_TARGETS_2_DN, chr8q24, SMIRNOV_RESPONSE_TO_IR_6HR_UP, OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP, STK33_NOMO_DN

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), 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 (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	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
cellular anatomical structure	1

Protein interactions and networks

STRING

240 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF623	C19orf25	Q9UFG5	520
ZNF623	ZHX1-C8orf76	Q96EF9	479
ZNF623	POP1	Q99575	479
ZNF623	C8orf76	Q96K31	474
ZNF623	TIGD5	Q53EQ6	449
ZNF623	ARHGAP39	Q9C0H5	447
ZNF623	COMMD5	Q9GZQ3	447
ZNF623	C14orf180	Q8N912	439
ZNF623	C8orf33	Q9H7E9	435
ZNF623	SACK1H	Q6ZRV2	394
ZNF623	PUSL1	Q8N0Z8	377
ZNF623	YDJC	A8MPS7	376
ZNF623	ELMOD3	Q96FG2	374
ZNF623	LRRC14	Q15048	373
ZNF623	NUDCD1	Q96RS6	366

IntAct

9 interactions, top by confidence:

A	B	Type	Score
ZNF623	ZNF76	psi-mi:“MI:0915”(physical association)	0.560
ZNF623		psi-mi:“MI:0915”(physical association)	0.370
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF623	GAPDHS	psi-mi:“MI:0914”(association)	0.350
PRKAR1B	ZNF749	psi-mi:“MI:0914”(association)	0.350
SLC7A9	CDC7	psi-mi:“MI:0914”(association)	0.350
ZNF76	ZNF623	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (12): ZNF623 (Affinity Capture-RNA), ZNF623 (Affinity Capture-RNA), ZNF623 (Two-hybrid), ZNF623 (Affinity Capture-RNA), ZNF623 (Two-hybrid), GAPDHS (Affinity Capture-MS), ZNF623 (Affinity Capture-MS), ARIH1 (Affinity Capture-MS), ZNF623 (Affinity Capture-MS), ZNF623 (Affinity Capture-MS), ZNF623 (Affinity Capture-RNA), ZNF623 (Affinity Capture-RNA)

ESM2 similar proteins: A0JNB1, A1YF12, A1YG88, A2T759, A6QLU5, B2RUI1, D3ZVT0, O14709, O43296, O75123, P10072, P15621, P17020, P17097, P51814, P85977, Q08ER8, Q0VGE8, Q14590, Q32KN0, Q3KQV3, Q4V8A8, Q5CZA5, Q5RBX0, Q5RCD9, Q5VIY5, Q61116, Q61967, Q6GQR8, Q6P9A3, Q6ZMS4, Q7TSH9, Q7TSI0, Q7Z3I7, Q86UD4, Q86WZ6, Q8BFS8, Q8IZ26, Q8N9F8, Q8TAF7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	48
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

287 predictions. Top by Δscore:

Variant	Effect	Δscore
8:143649734:GCT:G	donor_gain	0.9800
8:143651340:AGTC:A	donor_gain	0.9800
8:143651345:G:GG	donor_gain	0.9800
8:143649751:GAGCT:G	donor_gain	0.9700
8:143651338:GTA:G	donor_gain	0.9700
8:143651344:A:AG	donor_gain	0.9700
8:143651339:T:TA	donor_gain	0.9600
8:143651419:G:GG	donor_gain	0.9600
8:143649712:G:GT	donor_gain	0.9400
8:143649753:GCT:G	donor_gain	0.9400
8:143649761:T:TA	donor_gain	0.9000
8:143649762:A:AA	donor_gain	0.9000
8:143651341:G:GG	donor_gain	0.8900
8:143651343:C:A	donor_gain	0.8900
8:143649780:G:GT	donor_gain	0.8800
8:143651418:A:AG	donor_gain	0.8800
8:143649746:G:GT	donor_gain	0.8600
8:143649857:T:G	donor_gain	0.8600
8:143649861:G:GG	donor_gain	0.8600
8:143651268:A:T	donor_gain	0.8500
8:143649794:G:GT	donor_gain	0.8300
8:143650020:G:GT	donor_gain	0.8300
8:143649795:A:T	donor_gain	0.8200
8:143651341:GTCA:G	donor_gain	0.8200
8:143649693:TTAA:T	donor_gain	0.8100
8:143651340:A:AG	donor_gain	0.8000
8:143651184:A:T	donor_gain	0.7800
8:143651252:GTGC:G	donor_gain	0.7800
8:143649777:C:A	donor_gain	0.7700
8:143649993:A:AG	donor_gain	0.7700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000014832 (8:143642877 C>A), RS1000054712 (8:143637465 C>G), RS1000097853 (8:143647366 G>A), RS1000107844 (8:143650807 T>G), RS1000387442 (8:143642666 T>C), RS1000451187 (8:143636390 G>C), RS1000476473 (8:143647884 C>T), RS1000703437 (8:143646112 G>A), RS1000714527 (8:143652186 G>A), RS1000762592 (8:143652629 A>T), RS1000772782 (8:143653387 T>G), RS1000989012 (8:143646274 C>T), RS1001056431 (8:143635384 G>C), RS1001084788 (8:143651980 G>A), RS1001164489 (8:143636336 C>G,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

1 associations (top):

Study	Trait	p-value
GCST004750_21	Squamous cell lung carcinoma	5.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases expression, increases abundance, increases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
urushiol	increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
ferrous chloride	decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Caffeine	increases phosphorylation	1
Coumestrol	decreases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
T-2 Toxin	increases expression	1
Tretinoin	decreases expression	1
Valproic Acid	decreases expression	1
Vanadates	increases expression	1
Aflatoxin B1	increases methylation	1
Copper Sulfate	decreases 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_HD34	HEK293 eGFP-ZNF623	Transformed cell line	Female

Clinical trials (associated diseases)

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