ZNF124

Summary

ZNF124 (zinc finger protein 124, HGNC:12907) is a protein-coding gene on chromosome 1q44, encoding Zinc finger protein 124 (Q15973). May be involved in transcriptional regulation.

This gene encodes a protein with an amino-terminal KRAB-A box and multiple repeated Kruppel-type (C2H2) zinc finger motifs at its carboxy terminus. The encoded protein may function as a transcription factor. Expression of this gene is increased after vascular endothelial growth factor (VEGF) stimulation in human leukemia cell lines and results in inhibition of apoptotic cell death induced by irradiation or exposure to etoposide. Alternative splicing results in multiple transcript variants encoding distinct proteins.

Source: NCBI Gene 7678 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 56 total — 1 pathogenic
• MANE Select transcript: NM_001297568

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12907
Approved symbol	ZNF124
Name	zinc finger protein 124
Location	1q44
Locus type	gene with protein product
Status	Approved
Aliases	HZF16, HZF-16
Ensembl gene	ENSG00000196418
Ensembl biotype	protein_coding
OMIM	194631
Entrez	7678

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000340684, ENST00000472531, ENST00000476312, ENST00000491356, ENST00000491848, ENST00000543802, ENST00000915841

RefSeq mRNA: 5 — MANE Select: NM_001297568 NM_001243740, NM_001297567, NM_001297568, NM_001297569, NM_003431

CCDS: CCDS31089, CCDS58067, CCDS73057, CCDS76278

Canonical transcript exons

ENST00000543802 — 4 exons

Exon	Start	End
ENSE00002230988	247154989	247157403
ENSE00002714766	247171848	247172020
ENSE00003545914	247159687	247159813
ENSE00003609686	247159006	247159066

Expression profiles

Bgee: expression breadth ubiquitous, 234 present calls, max score 94.68.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0272 / max 18.4945, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
18501	0.0272	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	94.68	gold quality
secondary oocyte	CL:0000655	89.62	gold quality
calcaneal tendon	UBERON:0003701	89.41	gold quality
right testis	UBERON:0004534	87.99	gold quality
left testis	UBERON:0004533	87.87	gold quality
superficial temporal artery	UBERON:0001614	85.74	gold quality
cortical plate	UBERON:0005343	85.32	gold quality
testis	UBERON:0000473	84.16	gold quality
jejunal mucosa	UBERON:0000399	84.10	gold quality
mucosa of sigmoid colon	UBERON:0004993	83.84	gold quality
cauda epididymis	UBERON:0004360	83.12	gold quality
colonic mucosa	UBERON:0000317	82.96	gold quality
adrenal tissue	UBERON:0018303	82.92	gold quality
tendon	UBERON:0000043	81.81	gold quality
caput epididymis	UBERON:0004358	81.78	gold quality
corpus epididymis	UBERON:0004359	81.77	gold quality
monocyte	CL:0000576	81.43	gold quality
mononuclear cell	CL:0000842	80.95	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.79	gold quality
leukocyte	CL:0000738	80.63	gold quality
mucosa of transverse colon	UBERON:0004991	80.36	gold quality
ganglionic eminence	UBERON:0004023	80.27	gold quality
bone marrow cell	CL:0002092	80.01	gold quality
corpus callosum	UBERON:0002336	79.43	gold quality
rectum	UBERON:0001052	79.29	gold quality
endometrium	UBERON:0001295	79.29	gold quality
tonsil	UBERON:0002372	79.16	gold quality
oocyte	CL:0000023	78.58	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.28	gold quality
mammary duct	UBERON:0001765	76.99	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.28

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

113 targeting ZNF124, 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-3613-3P	100.00	76.36	7965
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-651-3P	99.94	73.48	5177
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

Literature-anchored findings (GeneRIF, showing 1)

• RNA-Seq evidence for lung tissue-specific monoallelic expression of ZNF124, located 363 kb upstream of the GCSAML somatic (secondary), imprinted differentially methylated region (iDMR). The ZNF124 locus has no overlapping hemimethylated CGIs in normal tissues, including lung tissue The GCSAML iDMR might regulate the lung tissue-specific, monoallelic expression of ZNF124. In the placenta, ZNF124 is biallelically expressed. (PMID:29545821)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp78	ENSMUSG00000055150
rattus_norvegicus		ENSRNOG00000083797
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 124 — Q15973 (reviewed: Q15973)

Alternative names: Zinc finger protein HZF-16

All UniProt accessions (2): Q15973, J3QKQ6

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 (5)

UniProt ID	Names	Canonical?
Q15973-3	1	yes
Q15973-4	2
Q15973-1	3, HZF-16.2
Q15973-2	4, HZF-16.1
Q15973-5	5

RefSeq proteins (5): NP_001230669, NP_001284496, NP_001284497, NP_001284498, NP_003422 (=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 (14 total): zinc finger region 8, splice variant 4, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15973-F1	76.71	0.41

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 161 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_DN, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP, MODULE_123, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN, MODULE_98, chr1q44, TGGAAA_NFAT_Q4_01, SANSOM_APC_TARGETS, MODULE_198, DIAZ_CHRONIC_MYELOGENOUS_LEUKEMIA_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, LEE_BMP2_TARGETS_UP, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D

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 transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA binding (GO:0003677), zinc ion binding (GO:0008270), 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
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
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
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

394 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF124	TMEM128	Q5BJH2	400
ZNF124	TBC1D3G	Q6DHY5	325
ZNF124	TMEM179	Q6ZVK1	323
ZNF124	OR2A7	Q96R45	322
ZNF124	FAM81A	Q8TBF8	310
ZNF124	GCSAML	Q5JQS6	297
ZNF124	PLCXD2	Q0VAA5	293
ZNF124	YES1	P07947	277
ZNF124	SPATA3	Q8NHX4	273
ZNF124	SCML4	Q8N228	272
ZNF124	TXNL4A	P83876	270
ZNF124	GABPB2	Q8TAK5	270
ZNF124	NRIP2	Q9BQI9	264
ZNF124	CDYL2	Q8N8U2	261
ZNF124	DCUN1D4	Q92564	253

IntAct

205 interactions, top by confidence:

A	B	Type	Score
ZNF124	KRTAP5-9	psi-mi:“MI:0915”(physical association)	0.720
ZNF124	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-9	ZNF124	psi-mi:“MI:0915”(physical association)	0.720
ZNF124	TRAF1	psi-mi:“MI:0915”(physical association)	0.720
MDFI	ZNF124	psi-mi:“MI:0915”(physical association)	0.720
KRTAP5-9	ZNF124	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-8	ZNF124	psi-mi:“MI:0915”(physical association)	0.720
TRAF1	ZNF124	psi-mi:“MI:0915”(physical association)	0.720
ZNF124	MDFI	psi-mi:“MI:0915”(physical association)	0.720
FSD2	ZNF124	psi-mi:“MI:0915”(physical association)	0.560
MEOX2	ZNF124	psi-mi:“MI:0915”(physical association)	0.560
ZNF124	CCNDBP1	psi-mi:“MI:0915”(physical association)	0.560
TCF4	ZNF124	psi-mi:“MI:0915”(physical association)	0.560
ZNF124	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.560
GOLGA2	ZNF124	psi-mi:“MI:0915”(physical association)	0.560
KRT31	ZNF124	psi-mi:“MI:0915”(physical association)	0.560
KRT40	ZNF124	psi-mi:“MI:0915”(physical association)	0.560
ZNF124	SYCE1	psi-mi:“MI:0915”(physical association)	0.560
ZNF124	KRTAP4-2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (71): ZNF124 (Two-hybrid), ZNF124 (Two-hybrid), ZNF124 (Two-hybrid), ZNF124 (Two-hybrid), ZNF124 (Two-hybrid), ZNF124 (Two-hybrid), ZNF124 (Two-hybrid), CCNDBP1 (Two-hybrid), TSGA10 (Two-hybrid), KRTAP4-2 (Two-hybrid), SYCE1 (Two-hybrid), SSX2IP (Two-hybrid), FSD2 (Two-hybrid), KRT40 (Two-hybrid), KRTAP10-7 (Two-hybrid)

ESM2 similar proteins: A0A1W2PQL4, A0JPL0, A2RRD8, A6NHJ4, A6NP11, B4DX44, O75346, O95780, P0CB33, P21506, P51508, P52738, Q0D2J5, Q0VGE8, Q12901, Q13360, Q14593, Q15973, Q2M218, Q2M3X9, Q2VY69, Q3SXZ3, Q5HY98, Q5RCJ2, Q5VIY5, Q6J6I6, Q7L2R6, Q86XU0, Q86Y25, Q8IW36, Q8IYN0, Q8IYX0, Q8N782, Q8N883, Q8N9Z0, Q8NDP4, Q95K49, Q969W8, Q96H40, Q96N58

Diamond homologs: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 58 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
Keratinization	11	17.5×	2e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	49
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
3391873	GRCh37/hg19 1q43-44(chr1:243204376-249224684)x1	Pathogenic

SpliceAI

772 predictions. Top by Δscore:

Variant	Effect	Δscore
1:247171843:CTCA:C	donor_loss	1.0000
1:247171844:TCA:T	donor_loss	1.0000
1:247171845:CACC:C	donor_loss	1.0000
1:247171846:A:AC	donor_gain	1.0000
1:247171846:AC:A	donor_gain	1.0000
1:247171847:C:CC	donor_gain	1.0000
1:247171847:CC:C	donor_gain	1.0000
1:247159682:CTTA:C	donor_loss	0.9900
1:247159683:TTA:T	donor_loss	0.9900
1:247159685:A:C	donor_loss	0.9900
1:247159686:C:CA	donor_loss	0.9900
1:247171847:CCA:C	donor_gain	0.9900
1:247157122:C:CC	acceptor_gain	0.9800
1:247159001:ATTAC:A	donor_loss	0.9800
1:247159002:TTA:T	donor_loss	0.9800
1:247159003:TACCT:T	donor_loss	0.9800
1:247159005:CC:C	donor_loss	0.9800
1:247159081:C:T	acceptor_gain	0.9800
1:247171847:CCAT:C	donor_gain	0.9800
1:247158999:AAATT:A	donor_loss	0.9700
1:247159000:AATTA:A	donor_loss	0.9700
1:247159797:T:TG	acceptor_gain	0.9700
1:247171860:T:TA	donor_gain	0.9700
1:247159006:C:A	donor_loss	0.9600
1:247159067:C:CC	acceptor_gain	0.9600
1:247159685:A:AC	donor_gain	0.9600
1:247159686:C:CC	donor_gain	0.9600
1:247171847:CCATT:C	donor_gain	0.9600
1:247159064:TTCCT:T	acceptor_loss	0.9500
1:247159065:TCCT:T	acceptor_loss	0.9500

AlphaMissense

2361 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:247157061:G:C	F187L	0.994
1:247157061:G:T	F187L	0.994
1:247157063:A:G	F187L	0.994
1:247156641:A:C	F327L	0.993
1:247156641:A:T	F327L	0.993
1:247156643:A:G	F327L	0.993
1:247156977:G:C	F215L	0.993
1:247156977:G:T	F215L	0.993
1:247156979:A:G	F215L	0.993
1:247156893:G:C	F243L	0.992
1:247156893:G:T	F243L	0.992
1:247156895:A:G	F243L	0.992
1:247156725:G:C	F299L	0.990
1:247156725:G:T	F299L	0.990
1:247156727:A:G	F299L	0.990
1:247156809:G:C	F271L	0.987
1:247156809:G:T	F271L	0.987
1:247156811:A:G	F271L	0.987
1:247157044:A:G	L193P	0.987
1:247157022:A:C	H200Q	0.984
1:247157022:A:T	H200Q	0.984
1:247156938:G:C	H228Q	0.979
1:247156938:G:T	H228Q	0.979
1:247157034:A:C	H196Q	0.977
1:247157034:A:T	H196Q	0.977
1:247156686:A:C	H312Q	0.976
1:247156686:A:T	H312Q	0.976
1:247159734:A:G	L37P	0.976
1:247156698:A:C	H308Q	0.975
1:247156698:A:T	H308Q	0.975

dbSNP variants (sampled 300 via entrez): RS1000084169 (1:247163587 C>G,T), RS1000114198 (1:247124895 C>G,T), RS1000163293 (1:247121485 T>C), RS1000274956 (1:247139908 T>C,G), RS1000330848 (1:247128291 G>A), RS1000435083 (1:247157966 A>T), RS1000615109 (1:247141547 C>T), RS1000668148 (1:247126158 C>A,T), RS1000720164 (1:247126016 C>A,T), RS1000779025 (1:247167598 A>G), RS1000819173 (1:247167287 A>G), RS1000857461 (1:247145987 C>A), RS1000864253 (1:247151275 C>G,T), RS1000870837 (1:247163321 A>AG), RS1000885191 (1:247168727 G>A)

Disease associations

OMIM: gene MIM:194631 | 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
GCST000977_3	Alcohol dependence	4.000000e-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
trichostatin A	affects cotreatment, increases expression	2
Cyclosporine	decreases expression	2
bisphenol F	affects cotreatment, increases expression	1
TAK-243	increases sumoylation	1
bisphenol A	increases expression	1
sodium arsenite	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	decreases expression	1
PCI 5002	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, increases expression	1
Coumestrol	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diazinon	increases methylation	1
Formaldehyde	increases expression	1
Gold	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Tretinoin	increases expression	1
Tunicamycin	decreases expression	1
Valproic Acid	decreases expression	1
Zinc	affects cotreatment, increases expression	1
1-Methyl-3-isobutylxanthine	increases expression, affects cotreatment	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1

Clinical trials (associated diseases)

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