ZNF121

Summary

ZNF121 (zinc finger protein 121, HGNC:12904) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 121 (P58317). 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 7675 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 97 total
• MANE Select transcript: NM_001008727

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12904
Approved symbol	ZNF121
Name	zinc finger protein 121
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	ZHC32, ZNF20
Ensembl gene	ENSG00000197961
Ensembl biotype	protein_coding
OMIM	194628
Entrez	7675

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000320451, ENST00000586602, ENST00000591447

RefSeq mRNA: 2 — MANE Select: NM_001008727 NM_001008727, NM_001308269

CCDS: CCDS32902, CCDS77228

Canonical transcript exons

ENST00000320451 — 4 exons

Exon	Start	End
ENSE00001430196	9560329	9567109
ENSE00001486771	9569002	9569082
ENSE00001628419	9584461	9584504
ENSE00003631073	9568095	9568175

Expression profiles

Bgee: expression breadth ubiquitous, 246 present calls, max score 94.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.8173 / max 832.8301, expressed in 1800 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179014	22.1417	1779
179015	11.6757	1716

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of hip	UBERON:0001554	94.61	gold quality
gingiva	UBERON:0001828	94.48	gold quality
gingival epithelium	UBERON:0001949	94.38	gold quality
parietal pleura	UBERON:0002400	93.77	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.53	gold quality
upper leg skin	UBERON:0004262	93.47	gold quality
palpebral conjunctiva	UBERON:0001812	93.31	gold quality
germinal epithelium of ovary	UBERON:0001304	93.13	gold quality
thymus	UBERON:0002370	92.97	gold quality
visceral pleura	UBERON:0002401	92.52	gold quality
mammalian vulva	UBERON:0000997	92.29	gold quality
esophagus squamous epithelium	UBERON:0006920	92.25	gold quality
oral cavity	UBERON:0000167	91.65	gold quality
colonic mucosa	UBERON:0000317	91.63	gold quality
epithelium of nasopharynx	UBERON:0001951	91.07	gold quality
mammary duct	UBERON:0001765	90.96	gold quality
trabecular bone tissue	UBERON:0002483	90.93	gold quality
corpus epididymis	UBERON:0004359	90.69	gold quality
seminal vesicle	UBERON:0000998	90.65	gold quality
cartilage tissue	UBERON:0002418	90.62	gold quality
cauda epididymis	UBERON:0004360	90.59	gold quality
caput epididymis	UBERON:0004358	90.39	gold quality
amniotic fluid	UBERON:0000173	90.30	gold quality
mucosa of paranasal sinus	UBERON:0005030	89.88	gold quality
bronchial epithelial cell	CL:0002328	89.82	gold quality
bronchus	UBERON:0002185	89.52	gold quality
oocyte	CL:0000023	89.51	gold quality
pigmented layer of retina	UBERON:0001782	89.51	gold quality
penis	UBERON:0000989	89.24	gold quality
tibia	UBERON:0000979	89.08	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-9801	yes	6.53
E-ENAD-17	no	907.16
E-GEOD-110499	no	648.55
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2582.1	ZNF121	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:37971293

miRNA regulators (miRDB)

26 targeting ZNF121, 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-4262	100.00	73.26	3931
HSA-MIR-4282	99.99	75.36	6408
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-3692-3P	99.98	70.27	2139
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-4452	99.50	68.45	1493
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-642A-3P	99.23	67.67	1258
HSA-MIR-642B-3P	99.23	67.67	1258
HSA-MIR-4536-5P	98.47	64.39	657
HSA-MIR-4450	98.26	68.35	725
HSA-MIR-6783-5P	97.67	67.21	1528
HSA-MIR-6824-5P	97.41	68.43	583
HSA-MIR-10398-5P	97.12	64.94	1051
HSA-MIR-5579-5P	96.32	68.54	730
HSA-MIR-584-5P	95.82	68.05	848

Literature-anchored findings (GeneRIF, showing 2)

• ZNF121 as a MYC-interacting protein with functional effects on MYC and cell proliferation (PMID:27988300)
• Circular RNA hsa_circRNA_103809 promotes lung cancer progression via facilitating ZNF121-dependent MYC expression by sequestering miR-4302. (PMID:29698681)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp560	ENSMUSG00000045519
rattus_norvegicus	Zfp560	ENSRNOG00000048394

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 121 — P58317 (reviewed: P58317)

Alternative names: Zinc finger protein 20

All UniProt accessions (2): P58317, K7EQI1

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.

RefSeq proteins (2): NP_001008727, NP_001295198 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF13465

UniProt features (14 total): zinc finger region 11, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P58317-F1	67.95	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 77 (showing top): BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, ATTCTTT_MIR186, DODD_NASOPHARYNGEAL_CARCINOMA_UP, TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_UP, BROWNE_HCMV_INFECTION_14HR_UP, ZHENG_BOUND_BY_FOXP3, CHEN_HOXA5_TARGETS_9HR_UP, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP

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 (1): nucleus (GO:0005634)

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

Protein interactions and networks

STRING

444 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF121	SCRN3	Q0VDG4	287
ZNF121	CCDC82	Q8N4S0	284
ZNF121	ZNF518A	Q6AHZ1	279
ZNF121	LSG1	Q9H089	273
ZNF121	TMEM263	Q8WUH6	270
ZNF121	NDUFV3	P56181	261
ZNF121	KIAA1549L	Q6ZVL6	252
ZNF121	MITD1	Q8WV92	249
ZNF121	TNRC18	O15417	249
ZNF121	FAM76B	Q5HYJ3	245
ZNF121	TM7SF3	Q9NS93	239
ZNF121	C9JR48	C9JR48	238
ZNF121	HSDL1	Q3SXM5	234
ZNF121	MYC	P01106	231
ZNF121	HIPK3	Q9H422	230
ZNF121	SLC66A1	Q6ZP29	230

IntAct

69 interactions, top by confidence:

A	B	Type	Score
CCAR2	MYC	psi-mi:“MI:0915”(physical association)	0.750
NOP53	RRP8	psi-mi:“MI:0914”(association)	0.640
ZNF837	ZNF121	psi-mi:“MI:0915”(physical association)	0.560
ZNF121	ZNF835	psi-mi:“MI:0915”(physical association)	0.560
ZNF121	TRIM41	psi-mi:“MI:0915”(physical association)	0.560
ZNF121	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.560
ZNF121	RBAK	psi-mi:“MI:0915”(physical association)	0.560
ZNF121	CARD9	psi-mi:“MI:0915”(physical association)	0.560
ZNF121	ZNF837	psi-mi:“MI:0915”(physical association)	0.560
ZNF121	KEAP1	psi-mi:“MI:0915”(physical association)	0.560
ZNF169	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF324B	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF512	ZNF724	psi-mi:“MI:0914”(association)	0.530
ZNF2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
ZBTB48	ZBTB24	psi-mi:“MI:0914”(association)	0.530
RPSA	DKC1	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
ZNF286A	HERC2	psi-mi:“MI:0914”(association)	0.530
RPSA	RPS17	psi-mi:“MI:0914”(association)	0.530
ZNF121	MYC	psi-mi:“MI:0915”(physical association)	0.480
MPHOSPH8	HCFC1	psi-mi:“MI:0914”(association)	0.350
MYC	ILVBL	psi-mi:“MI:0914”(association)	0.350
CDX1	ZNF724	psi-mi:“MI:0914”(association)	0.350

BioGRID (62): ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Affinity Capture-MS), ZNF121 (Two-hybrid), ZNF121 (Two-hybrid)

ESM2 similar proteins: A6NP11, B4DXR9, O43361, O95780, P0CJ79, P0DKX0, P17021, P17024, P17035, P51508, P52740, P52741, P58317, Q02386, Q0VGE8, Q13106, Q13360, Q13398, Q5JVG2, Q5RBQ3, Q5RES8, Q5TYW1, Q68DI1, Q68EA5, Q6NX49, Q6P9A1, Q6P9A3, Q6PDB4, Q6ZN06, Q76KX8, Q7L945, Q7Z340, Q86T29, Q8BZW4, Q8IW36, Q8N823, Q8N8Z8, Q8NEP9, Q8TA94, Q8TC21

Diamond homologs: A0JPL0, A1L1L7, A2A761, A2VDP4, A3KN36, A6QLU5, A6QPT6, A7MBI1, A8MT65, B2RXC5, E9PYI1, E9Q8G5, O75290, O94892, O95780, P10076, P17014, P17023, P17025, P17030, P17032, P17098, P51523, P51814, P52736, P52742, P58317, Q02975, Q06730, Q06732, Q08DG8, Q0VCB0, Q13360, Q14584, Q14587, Q14590, Q147U1, Q16587, Q29RZ4, Q2M218

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 71 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
rRNA processing in the nucleus and cytosol	5	16.8×	7e-04
rRNA processing	5	15.2×	7e-04
Peptide chain elongation	5	13.2×	8e-04
Viral mRNA Translation	5	13.2×	8e-04
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	5	13.1×	8e-04
Selenocysteine synthesis	5	12.5×	8e-04
Eukaryotic Translation Termination	5	12.5×	8e-04
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	5	12.3×	8e-04

GO biological processes:

GO term	Partners	Fold	FDR
RNA processing	5	16.1×	2e-03
cytoplasmic translation	5	13.6×	4e-03
rRNA processing	6	12.5×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	90
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1659 predictions. Top by Δscore:

Variant	Effect	Δscore
19:12133986:C:CC	acceptor_gain	1.0000
19:12133990:A:T	acceptor_gain	1.0000
19:12133991:G:GC	acceptor_gain	1.0000
19:12135575:C:CT	acceptor_gain	1.0000
19:12135575:C:T	acceptor_gain	1.0000
19:12135763:TCTTA:T	donor_loss	1.0000
19:12135764:CTTAC:C	donor_loss	1.0000
19:12135765:TTAC:T	donor_loss	1.0000
19:12135766:TA:T	donor_loss	1.0000
19:12135767:A:AC	donor_gain	1.0000
19:12135767:A:T	donor_loss	1.0000
19:12135768:C:CA	donor_loss	1.0000
19:12135768:C:CC	donor_gain	1.0000
19:12135768:CCTA:C	donor_gain	1.0000
19:12135907:C:CT	acceptor_gain	1.0000
19:12135909:C:CT	acceptor_gain	1.0000
19:12135910:A:C	acceptor_gain	1.0000
19:12135912:A:C	acceptor_gain	1.0000
19:12140175:CTCA:C	donor_loss	1.0000
19:12140178:A:AC	donor_gain	1.0000
19:12140178:AC:A	donor_gain	1.0000
19:12140179:C:CT	donor_gain	1.0000
19:12140179:CC:C	donor_gain	1.0000
19:12140179:CCA:C	donor_gain	1.0000
19:9568176:C:CC	acceptor_gain	1.0000
19:9568187:C:CT	acceptor_gain	1.0000
19:9568188:A:T	acceptor_gain	1.0000
19:9568998:TCACC:T	donor_loss	1.0000
19:9568999:CA:C	donor_loss	1.0000
19:9569000:A:AC	donor_gain	1.0000

AlphaMissense

2594 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:9566133:A:G	L327P	0.996
19:9566150:A:C	F321L	0.996
19:9566150:A:T	F321L	0.996
19:9566152:A:G	F321L	0.996
19:9566066:G:C	F349L	0.995
19:9566066:G:T	F349L	0.995
19:9566068:A:G	F349L	0.995
19:9566234:G:C	F293L	0.995
19:9566234:G:T	F293L	0.995
19:9566236:A:G	F293L	0.995
19:9566486:G:C	F209L	0.995
19:9566486:G:T	F209L	0.995
19:9566488:A:G	F209L	0.995
19:9566570:G:C	F181L	0.995
19:9566570:G:T	F181L	0.995
19:9566572:A:G	F181L	0.995
19:9566049:A:G	L355P	0.994
19:9566123:A:C	H330Q	0.994
19:9566123:A:T	H330Q	0.994
19:9566301:A:G	L271P	0.993
19:9566454:C:G	R220P	0.993
19:9566622:C:G	R164P	0.993
19:9566207:A:C	H302Q	0.992
19:9566207:A:T	H302Q	0.992
19:9566291:G:C	H274Q	0.992
19:9566291:G:T	H274Q	0.992
19:9566318:G:C	F265L	0.992
19:9566318:G:T	F265L	0.992
19:9566320:A:G	F265L	0.992
19:9566459:A:C	H218Q	0.992

dbSNP variants (sampled 300 via entrez): RS1000014409 (19:9584516 G>T), RS1000069908 (19:9569263 T>C), RS1000093531 (19:9582964 C>T), RS1000157393 (19:9560955 T>C), RS1000166167 (19:9574682 A>C), RS1000375271 (19:9579683 T>A,C), RS1000379335 (19:9585597 C>T), RS1000462802 (19:9562036 T>C), RS1000493983 (19:9562391 C>T), RS1000574318 (19:9575596 A>G), RS1000672639 (19:9568197 GAAAAA>G,GAAAA,GAAAAAA,GAAAAAAA), RS1000911584 (19:9575880 G>A), RS1001024836 (19:9570298 C>T), RS1001142697 (19:9564077 T>C), RS1001289753 (19:9571777 C>A)

Disease associations

OMIM: gene MIM:194628 | 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

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

Chemical	Actions (top 5)	PubMed papers
Estradiol	increases expression	2
Tobacco Smoke Pollution	increases expression	2
Aflatoxin B1	increases methylation, increases expression	2
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
trichostatin A	affects expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
zinc chromate	increases abundance, increases expression	1
coumarin	decreases phosphorylation	1
cupric oxide	increases expression	1
chromium hexavalent ion	increases abundance, increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
abrine	increases expression	1
jinfukang	decreases expression	1
Resveratrol	increases expression, affects cotreatment	1
Temozolomide	increases expression	1
Leflunomide	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Amiodarone	increases expression	1
Vehicle Emissions	decreases methylation	1
Benzo(a)pyrene	affects methylation	1
Caffeine	increases phosphorylation	1
Dimethyl Sulfoxide	increases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Urethane	increases expression	1
Cadmium Chloride	increases expression	1
Copper Sulfate	increases expression	1

Cellosaurus cell lines

4 cell lines: 3 embryonic stem cell, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_A8F0	SEES3-1V human ZNF121, clone1	Embryonic stem cell	Male
CVCL_A8F1	SEES3-1V human ZNF121, clone2	Embryonic stem cell	Male
CVCL_A8F2	SEES3-1V human ZNF121, clone3	Embryonic stem cell	Male
CVCL_XW04	HEK293 eGFP-ZNF121	Transformed cell line	Female

Clinical trials (associated diseases)

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