ZNF624

Summary

ZNF624 (zinc finger protein 624, HGNC:29254) is a protein-coding gene on chromosome 17p11.2, encoding Zinc finger protein 624 (Q9P2J8). 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 57547 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 84 total
• MANE Select transcript: NM_020787

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29254
Approved symbol	ZNF624
Name	zinc finger protein 624
Location	17p11.2
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1349
Ensembl gene	ENSG00000197566
Ensembl biotype	protein_coding
Entrez	57547

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000311331, ENST00000423860, ENST00000579528, ENST00000579983, ENST00000583766, ENST00000895853

RefSeq mRNA: 1 — MANE Select: NM_020787 NM_020787

CCDS: CCDS11180

Canonical transcript exons

ENST00000311331 — 6 exons

Exon	Start	End
ENSE00001189339	16620734	16624509
ENSE00001290258	16634630	16634756
ENSE00001400317	16653764	16653850
ENSE00001424346	16647329	16647394
ENSE00001429439	16649658	16649746
ENSE00003785665	16633862	16633957

Expression profiles

Bgee: expression breadth ubiquitous, 203 present calls, max score 85.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.0229 / max 89.0648, expressed in 1527 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164740	4.0229	1527

Top tissues by expression

241 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	85.07	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.47	gold quality
ventricular zone	UBERON:0003053	77.72	gold quality
calcaneal tendon	UBERON:0003701	76.37	gold quality
cortical plate	UBERON:0005343	76.21	gold quality
ganglionic eminence	UBERON:0004023	75.60	gold quality
colonic epithelium	UBERON:0000397	74.53	gold quality
adrenal tissue	UBERON:0018303	73.59	gold quality
islet of Langerhans	UBERON:0000006	72.74	gold quality
stromal cell of endometrium	CL:0002255	72.73	gold quality
leukocyte	CL:0000738	70.59	gold quality
secondary oocyte	CL:0000655	70.46	gold quality
smooth muscle tissue	UBERON:0001135	70.35	gold quality
monocyte	CL:0000576	70.33	gold quality
tendon	UBERON:0000043	69.68	gold quality
sural nerve	UBERON:0015488	69.29	gold quality
bone marrow cell	CL:0002092	69.13	silver quality
amniotic fluid	UBERON:0000173	68.53	gold quality
testis	UBERON:0000473	68.18	gold quality
rectum	UBERON:0001052	68.18	gold quality
right testis	UBERON:0004534	67.34	gold quality
corpus callosum	UBERON:0002336	66.82	gold quality
vermiform appendix	UBERON:0001154	66.43	gold quality
lymph node	UBERON:0000029	66.33	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	66.30	gold quality
left testis	UBERON:0004533	66.16	gold quality
pigmented layer of retina	UBERON:0001782	66.10	gold quality
tibial nerve	UBERON:0001323	66.03	gold quality
granulocyte	CL:0000094	65.99	gold quality
palpebral conjunctiva	UBERON:0001812	65.79	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ENAD-17	no	283.20
E-ANND-3	no	4.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

98 targeting ZNF624, 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-7110-3P	100.00	73.18	2486
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502

Cross-species orthologs

0 orthologs

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 624 — Q9P2J8 (reviewed: Q9P2J8)

All UniProt accessions (3): C9J5H1, Q9P2J8, J3QKY7

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?
Q9P2J8-1	1	yes
Q9P2J8-2	2

RefSeq proteins (1): NP_065838* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF00096, PF01352

UniProt features (28 total): zinc finger region 21, sequence variant 2, sequence conflict 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P2J8-F1	71.10	0.06

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 41 (showing top): ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ZFP28_TARGET_GENES, ZNF22_TARGET_GENES, ZSCAN21_TARGET_GENES, MIR7110_3P, MIR582_5P, MIR548L, MIR5590_3P, MIR142_5P, MIR3059_5P, MIR513A_5P, MIR1252_3P, MIR889_3P

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

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 (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
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	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

Protein interactions and networks

STRING

426 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF624	TXNRD3	Q86VQ6	718
ZNF624	CFAP144	A6NL82	514
ZNF624	PRDM7	Q9NQW5	360
ZNF624	NRIP3	Q9NQ35	348
ZNF624	RBM11	P57052	329
ZNF624	ATXN1L	P0C7T5	323
ZNF624	SLC25A23	Q9BV35	317
ZNF624	POLR3E	Q9NVU0	312
ZNF624	NSMCE3	Q96MG7	310
ZNF624	BTF3	P20290	306
ZNF624	NLRP9	Q7RTR0	296
ZNF624	HELZ2	Q9BYK8	295
ZNF624	TIMM13	P62206	293
ZNF624	SYBU	Q9NX95	292
ZNF624	NGLY1	Q96IV0	264
ZNF624	NIPA2	Q8N8Q9	264

IntAct

60 interactions, top by confidence:

A	B	Type	Score
ZNF624	MTUS2	psi-mi:“MI:0915”(physical association)	0.720
MTUS2	ZNF624	psi-mi:“MI:0915”(physical association)	0.720
MTUS2	ZNF624	psi-mi:“MI:0915”(physical association)	0.560
ZNF624	MTUS2	psi-mi:“MI:0915”(physical association)	0.560
PICK1	ZNF624	psi-mi:“MI:0915”(physical association)	0.560
KRTAP12-2	ZNF624	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	ZNF624	psi-mi:“MI:0915”(physical association)	0.560
BICD2	ZNF624	psi-mi:“MI:0915”(physical association)	0.560
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF324B	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF624	PALM	psi-mi:“MI:0915”(physical association)	0.400
ZNF624	ECE1	psi-mi:“MI:0915”(physical association)	0.370
Msn	ELOC	psi-mi:“MI:0914”(association)	0.350
Cep55	UMAD1	psi-mi:“MI:0914”(association)	0.350
PB2		psi-mi:“MI:0914”(association)	0.350
ZNF467	ZNF320	psi-mi:“MI:0914”(association)	0.350
NOP2	ZNF320	psi-mi:“MI:0914”(association)	0.350
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
LTBP2	ZNF320	psi-mi:“MI:0914”(association)	0.350
RPL36	GTPBP10	psi-mi:“MI:0914”(association)	0.350
RPL28	GTPBP10	psi-mi:“MI:0914”(association)	0.350
ADARB1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
OASL	ZNF316	psi-mi:“MI:0914”(association)	0.350

BioGRID (52): ZNF624 (Two-hybrid), ZNF624 (Two-hybrid), ZNF624 (Affinity Capture-MS), ZNF624 (Affinity Capture-MS), ZNF624 (Affinity Capture-MS), ZNF624 (Affinity Capture-MS), MTUS2 (Two-hybrid), ZNF624 (Affinity Capture-MS), ZNF624 (Affinity Capture-MS), ZNF624 (Affinity Capture-MS), ZNF624 (Affinity Capture-MS), ZNF624 (Affinity Capture-MS), ZNF624 (Affinity Capture-MS), ZNF624 (Two-hybrid), ZNF624 (Two-hybrid)

ESM2 similar proteins: A1YEP8, A1YFW2, A2RRD8, A2T6E3, A2T6V8, A2T7D2, A2T7F4, A2T812, A6NHJ4, O14709, O43309, O60765, P17036, P17097, P51814, P52738, Q02975, Q08ER8, Q0VGE8, Q12901, Q2M218, Q2M3X9, Q3KNS6, Q4V8A8, Q5RBX0, Q5RCD9, Q5VIY5, Q61751, Q6GQR8, Q6ZMS4, Q7TSH9, Q86Y25, Q8BQC8, Q8IYX0, Q8IZ26, Q8N9F8, Q8NF99, Q8TF39, Q8TF47, Q96N58

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 53 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Peptide chain elongation	5	18.7×	2e-04
Viral mRNA Translation	5	18.7×	2e-04
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	5	18.5×	2e-04
Selenocysteine synthesis	5	17.7×	2e-04
Eukaryotic Translation Termination	5	17.7×	2e-04
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	5	17.3×	2e-04
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	5	17.3×	2e-04
Formation of a pool of free 40S subunits	5	16.5×	2e-04

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	5	21.0×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	71
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

872 predictions. Top by Δscore:

Variant	Effect	Δscore
17:16634624:CCTTA:C	donor_loss	1.0000
17:16634626:TTA:T	donor_loss	1.0000
17:16634627:TACCC:T	donor_loss	1.0000
17:16634628:A:AC	donor_gain	1.0000
17:16634628:A:AT	donor_loss	1.0000
17:16634628:AC:A	donor_gain	1.0000
17:16634629:C:CA	donor_loss	1.0000
17:16634629:C:CC	donor_gain	1.0000
17:16634629:CC:C	donor_gain	1.0000
17:16634645:T:TA	donor_gain	1.0000
17:16634668:T:TA	donor_gain	1.0000
17:16634754:TTC:T	acceptor_gain	1.0000
17:16634758:T:G	acceptor_loss	1.0000
17:16633956:CC:C	acceptor_gain	0.9900
17:16633957:CC:C	acceptor_gain	0.9900
17:16634628:ACC:A	donor_gain	0.9900
17:16634629:CCC:C	donor_gain	0.9900
17:16634755:TC:T	acceptor_gain	0.9900
17:16634756:CC:C	acceptor_gain	0.9900
17:16634757:C:CC	acceptor_gain	0.9900
17:16645452:A:AC	donor_gain	0.9900
17:16645453:G:C	donor_gain	0.9900
17:16647393:CT:C	acceptor_gain	0.9900
17:16647395:C:CC	acceptor_gain	0.9900
17:16649651:AACTT:A	donor_loss	0.9900
17:16649652:ACTT:A	donor_loss	0.9900
17:16649653:CTTA:C	donor_loss	0.9900
17:16649654:TTACC:T	donor_loss	0.9900
17:16649655:TACC:T	donor_loss	0.9900
17:16649656:A:AC	donor_gain	0.9900

AlphaMissense

5782 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:16622603:G:C	F761L	0.999
17:16622603:G:T	F761L	0.999
17:16622605:A:G	F761L	0.999
17:16622687:A:C	F733L	0.999
17:16622687:A:T	F733L	0.999
17:16622689:A:G	F733L	0.999
17:16622823:C:G	R688P	0.999
17:16622855:G:C	F677L	0.999
17:16622855:G:T	F677L	0.999
17:16622857:A:G	F677L	0.999
17:16623023:G:C	F621L	0.999
17:16623023:G:T	F621L	0.999
17:16623025:A:G	F621L	0.999
17:16623082:G:C	H602D	0.999
17:16623107:G:C	F593L	0.999
17:16623107:G:T	F593L	0.999
17:16623109:A:G	F593L	0.999
17:16623159:C:G	R576P	0.999
17:16623275:G:C	F537L	0.999
17:16623275:G:T	F537L	0.999
17:16623277:A:G	F537L	0.999
17:16623327:C:G	R520P	0.999
17:16622435:G:C	F817L	0.998
17:16622435:G:T	F817L	0.998
17:16622437:A:G	F817L	0.998
17:16622744:A:C	H714Q	0.998
17:16622744:A:T	H714Q	0.998
17:16622746:G:C	H714D	0.998
17:16622771:G:C	F705L	0.998
17:16622771:G:T	F705L	0.998

dbSNP variants (sampled 300 via entrez): RS1000055732 (17:16642781 T>C), RS1000078097 (17:16639932 A>G), RS1000232499 (17:16635719 C>T), RS1000321074 (17:16643927 G>A,T), RS1000403693 (17:16642375 A>G), RS1000448978 (17:16637308 T>C), RS1000479044 (17:16638627 C>G,T), RS1000505360 (17:16620827 T>C), RS1000534519 (17:16643102 T>C), RS1000547907 (17:16651141 T>A), RS1000683805 (17:16638260 T>C), RS1000748285 (17:16636830 C>A,T), RS1000923585 (17:16631872 G>A), RS1001014055 (17:16625278 T>G), RS1001099264 (17:16617693 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, affects expression, decreases expression	4
Air Pollutants	decreases expression, affects cotreatment, increases abundance, increases oxidation	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
pirinixic acid	increases activity, increases expression, affects binding	1
bisphenol A	affects cotreatment, increases expression	1
titanium dioxide	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	increases expression	1
manganese chloride	increases abundance, increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
methacrylaldehyde	increases oxidation, increases abundance, affects cotreatment	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
bisphenol S	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1
Glyphosate	decreases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Amiodarone	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Carbamazepine	affects expression	1
Coal	decreases expression, increases abundance	1
Dexamethasone	affects cotreatment, 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_XW68	HEK293 eGFP-ZNF624	Transformed cell line	Female

Clinical trials (associated diseases)

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